Starting phenix.real_space_refine on Fri Sep 11 04:24:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xjh_22210/09_2026/6xjh_22210_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xjh_22210/09_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_22210/09_2026/6xjh_22210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xjh_22210/09_2026/6xjh_22210.map" model { file = "/net/cci-nas-00/data/ceres_data/6xjh_22210/09_2026/6xjh_22210_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xjh_22210/09_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-2.2.1-6174/lib/python3.11/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: 2.15, 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: 0.46 Conformation dependent library (CDL) restraints added in 277.5 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: 0.17 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: 0.98 Time building geometry restraints manager: 0.58 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 - 1.90: 8447 1.90 - 3.80: 1690 3.80 - 5.70: 275 5.70 - 7.60: 62 7.60 - 9.50: 8 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 - 16.52: 4426 16.52 - 33.04: 132 33.04 - 49.56: 48 49.56 - 66.08: 30 66.08 - 82.60: 20 Dihedral angle restraints: 4656 sinusoidal: 1916 harmonic: 2740 Sorted by residual: 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 dihedral pdb=" C ILE A 188 " pdb=" N ILE A 188 " pdb=" CA ILE A 188 " pdb=" CB ILE A 188 " ideal model delta harmonic sigma weight residual -122.00 -130.45 8.45 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" N ARG D 189 " pdb=" C ARG D 189 " pdb=" CA ARG D 189 " pdb=" CB ARG D 189 " ideal model delta harmonic sigma weight residual 122.80 130.40 -7.60 0 2.50e+00 1.60e-01 9.24e+00 ... (remaining 4653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 673 0.067 - 0.134: 382 0.134 - 0.201: 124 0.201 - 0.268: 36 0.268 - 0.335: 11 Chirality restraints: 1226 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 1223 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: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.330 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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= 1.078 Angle : 1.620 9.500 10482 Z= 1.122 Chirality : 0.095 0.335 1226 Planarity : 0.008 0.036 1264 Dihedral : 12.611 82.598 2888 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/Z covalent geometry : bond 0.01947 / 1.08 ( 7754) covalent geometry : angle 1.61975 / 1.12 (10482) hydrogen bonds : bond 0.15736 / 10.53 ( 483) hydrogen bonds : angle 6.87876 / 5.13 ( 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 : 0.255 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: 0.0780 time to fit residues: 43.8416 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 : 0.259 ------------------------------------------------------------------------------- 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... ** 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.091901 restraints weight = 13717.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.095375 restraints weight = 6894.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.097762 restraints weight = 4433.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.099365 restraints weight = 3305.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100516 restraints weight = 2716.726| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7754 Z= 0.220 Angle : 0.733 7.847 10482 Z= 0.397 Chirality : 0.048 0.191 1226 Planarity : 0.004 0.032 1264 Dihedral : 10.819 73.621 1076 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.99 % Allowed : 12.00 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.91 (0.27), residues: 928 helix: 2.27 (0.20), residues: 556 sheet: 0.51 (0.67), residues: 58 loop : -0.42 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 189 TYR 0.025 0.002 TYR B 206 PHE 0.020 0.002 PHE C 23 TRP 0.025 0.002 TRP A 223 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 ( 7754) covalent geometry : angle 0.73341 / 0.40 (10482) hydrogen bonds : bond 0.06150 / 4.16 ( 483) hydrogen bonds : angle 5.05626 / 3.75 ( 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: 42 poor density : 278 time to evaluate : 0.241 Fit side-chains REVERT: A 21 TYR cc_start: 0.7452 (m-80) cc_final: 0.7222 (m-80) REVERT: A 34 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7353 (mm-40) REVERT: A 141 TRP cc_start: 0.7844 (m100) cc_final: 0.7541 (m100) REVERT: A 166 MET cc_start: 0.6556 (mmp) cc_final: 0.5534 (ttm) REVERT: A 188 ILE cc_start: 0.6121 (OUTLIER) cc_final: 0.5825 (mm) REVERT: A 204 PHE cc_start: 0.7462 (m-80) cc_final: 0.6314 (m-80) REVERT: A 220 ASN cc_start: 0.8136 (m-40) cc_final: 0.7908 (m110) REVERT: A 221 TRP cc_start: 0.8165 (m100) cc_final: 0.7942 (m100) REVERT: A 233 PHE cc_start: 0.8256 (m-80) cc_final: 0.7967 (m-80) REVERT: A 243 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7791 (mmtt) REVERT: B -2 ARG cc_start: 0.6410 (mtm-85) cc_final: 0.6076 (mmm160) REVERT: B 87 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7366 (mmm) REVERT: B 115 HIS cc_start: 0.7803 (t-90) cc_final: 0.7530 (t-170) REVERT: B 143 PHE cc_start: 0.8759 (m-80) cc_final: 0.8524 (m-80) REVERT: B 152 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8644 (mm) REVERT: B 243 LYS cc_start: 0.8431 (mmtt) cc_final: 0.7888 (mmtt) REVERT: C 4 GLU cc_start: 0.6919 (mp0) cc_final: 0.6506 (mp0) REVERT: C 43 MET cc_start: 0.8016 (mtm) cc_final: 0.7773 (mtt) REVERT: C 49 ASN cc_start: 0.8153 (m110) cc_final: 0.7937 (m-40) REVERT: C 58 ASP cc_start: 0.6800 (t0) cc_final: 0.6477 (t70) REVERT: C 70 GLU cc_start: 0.7684 (tp30) cc_final: 0.7336 (tp30) REVERT: C 71 HIS cc_start: 0.7068 (m-70) cc_final: 0.6696 (m90) REVERT: C 99 TYR cc_start: 0.8062 (t80) cc_final: 0.7572 (t80) REVERT: C 172 ARG cc_start: 0.7254 (mmt-90) cc_final: 0.6963 (mmm160) REVERT: C 181 GLU cc_start: 0.8343 (mp0) cc_final: 0.7952 (pm20) REVERT: D 43 MET cc_start: 0.8235 (mtm) cc_final: 0.7698 (mtt) REVERT: D 64 ASN cc_start: 0.7613 (m-40) cc_final: 0.7323 (m110) REVERT: D 99 TYR cc_start: 0.8380 (t80) cc_final: 0.8161 (t80) REVERT: D 165 LEU cc_start: 0.8734 (mt) cc_final: 0.8527 (mt) REVERT: D 181 GLU cc_start: 0.8470 (mp0) cc_final: 0.7750 (pm20) REVERT: D 185 LEU cc_start: 0.8596 (tp) cc_final: 0.8314 (tt) REVERT: D 194 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.7528 (ttp80) outliers start: 42 outliers final: 30 residues processed: 306 average time/residue: 0.0669 time to fit residues: 28.7268 Evaluate side-chains 255 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 35 SER 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 19 ILE 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 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 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: 3.9990 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN B 220 ASN C 200 GLN C 285 ASN D 35 ASN D 71 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.090767 restraints weight = 13951.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.094156 restraints weight = 6929.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.096489 restraints weight = 4482.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097787 restraints weight = 3361.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.098977 restraints weight = 2819.450| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7754 Z= 0.191 Angle : 0.677 8.042 10482 Z= 0.361 Chirality : 0.046 0.185 1226 Planarity : 0.004 0.034 1264 Dihedral : 9.306 73.152 1076 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 6.06 % Allowed : 15.91 % Favored : 78.03 % 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: 1.52 (0.27), residues: 928 helix: 2.03 (0.21), residues: 556 sheet: 0.14 (0.68), residues: 58 loop : -0.68 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 194 TYR 0.046 0.002 TYR A 206 PHE 0.030 0.002 PHE A 111 TRP 0.018 0.002 TRP A 223 HIS 0.002 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 7754) covalent geometry : angle 0.67691 / 0.36 (10482) hydrogen bonds : bond 0.05474 / 3.74 ( 483) hydrogen bonds : angle 4.94875 / 3.70 ( 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 293 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 242 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 141 TRP cc_start: 0.7769 (m100) cc_final: 0.7405 (m100) REVERT: A 166 MET cc_start: 0.6390 (mmp) cc_final: 0.5584 (ttm) REVERT: A 220 ASN cc_start: 0.8123 (m-40) cc_final: 0.7903 (m110) REVERT: A 221 TRP cc_start: 0.7959 (m100) cc_final: 0.7707 (m100) REVERT: A 233 PHE cc_start: 0.8328 (m-80) cc_final: 0.8075 (m-80) REVERT: B 11 LEU cc_start: 0.8283 (mt) cc_final: 0.7964 (tt) REVERT: B 84 GLN cc_start: 0.8432 (tt0) cc_final: 0.8104 (tt0) REVERT: B 87 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7260 (mmm) REVERT: B 115 HIS cc_start: 0.7734 (t-90) cc_final: 0.7506 (t-170) REVERT: B 152 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8687 (mm) REVERT: B 200 ASP cc_start: 0.8336 (m-30) cc_final: 0.7932 (t0) REVERT: B 243 LYS cc_start: 0.8445 (mmtt) cc_final: 0.7935 (mmtt) REVERT: C 4 GLU cc_start: 0.6831 (mp0) cc_final: 0.6439 (mp0) REVERT: C 43 MET cc_start: 0.8039 (mtm) cc_final: 0.7496 (mtt) REVERT: C 49 ASN cc_start: 0.8284 (m110) cc_final: 0.8070 (m-40) REVERT: C 71 HIS cc_start: 0.7074 (m-70) cc_final: 0.6665 (m90) REVERT: C 99 TYR cc_start: 0.8121 (t80) cc_final: 0.7737 (t80) REVERT: C 181 GLU cc_start: 0.8333 (mp0) cc_final: 0.8049 (pm20) REVERT: C 200 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7436 (mt0) REVERT: D 43 MET cc_start: 0.8191 (mtm) cc_final: 0.7933 (mtm) REVERT: D 56 LYS cc_start: 0.7303 (tmtt) cc_final: 0.6970 (tppt) REVERT: D 71 HIS cc_start: 0.7489 (m170) cc_final: 0.7120 (m-70) REVERT: D 99 TYR cc_start: 0.8520 (t80) cc_final: 0.8168 (t80) REVERT: D 102 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7741 (mttm) REVERT: D 165 LEU cc_start: 0.8715 (mt) cc_final: 0.8483 (mt) REVERT: D 181 GLU cc_start: 0.8334 (mp0) cc_final: 0.7677 (pm20) REVERT: D 194 ARG cc_start: 0.7914 (ttp-170) cc_final: 0.7461 (ttp80) outliers start: 51 outliers final: 41 residues processed: 273 average time/residue: 0.0657 time to fit residues: 25.3370 Evaluate side-chains 265 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 110 LEU 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 152 LEU 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 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 101 THR 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 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 100 THR Chi-restraints excluded: chain C residue 133 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 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 105 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 276 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 82 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 200 GLN D 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.092151 restraints weight = 14049.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095508 restraints weight = 6982.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097831 restraints weight = 4474.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.099358 restraints weight = 3326.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100137 restraints weight = 2736.505| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4809 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= 0.142 Angle : 0.614 7.482 10482 Z= 0.326 Chirality : 0.044 0.182 1226 Planarity : 0.004 0.035 1264 Dihedral : 7.998 71.390 1076 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.11 % Allowed : 17.70 % Favored : 77.20 % 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: 1.25 (0.27), residues: 928 helix: 1.89 (0.20), residues: 562 sheet: 0.05 (0.67), residues: 58 loop : -1.01 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 172 TYR 0.043 0.002 TYR A 206 PHE 0.030 0.002 PHE B 143 TRP 0.020 0.002 TRP A 60 HIS 0.003 0.001 HIS D 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7754) covalent geometry : angle 0.61370 / 0.33 (10482) hydrogen bonds : bond 0.04935 / 3.38 ( 483) hydrogen bonds : angle 4.76532 / 3.56 ( 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 278 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8737 (mt0) cc_final: 0.8077 (tp40) REVERT: A 141 TRP cc_start: 0.7770 (m100) cc_final: 0.7389 (m100) REVERT: A 166 MET cc_start: 0.6052 (mmp) cc_final: 0.5330 (ttm) REVERT: A 204 PHE cc_start: 0.7187 (m-80) cc_final: 0.5996 (m-80) REVERT: A 220 ASN cc_start: 0.8079 (m-40) cc_final: 0.7845 (m110) REVERT: A 221 TRP cc_start: 0.7892 (m100) cc_final: 0.7599 (m100) REVERT: A 243 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7763 (mmtt) REVERT: B 11 LEU cc_start: 0.8127 (mt) cc_final: 0.7864 (tt) REVERT: B 84 GLN cc_start: 0.8396 (tt0) cc_final: 0.8022 (tp40) REVERT: B 87 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7314 (mmm) REVERT: B 115 HIS cc_start: 0.7642 (t-90) cc_final: 0.7366 (t-170) REVERT: B 152 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8643 (mm) REVERT: B 200 ASP cc_start: 0.8329 (m-30) cc_final: 0.7958 (t0) REVERT: B 243 LYS cc_start: 0.8372 (mmtt) cc_final: 0.7950 (mmtt) REVERT: C 2 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7305 (mtpp) REVERT: C 70 GLU cc_start: 0.7736 (tp30) cc_final: 0.7366 (tp30) REVERT: C 71 HIS cc_start: 0.6962 (m-70) cc_final: 0.6571 (m90) REVERT: C 99 TYR cc_start: 0.8076 (t80) cc_final: 0.7706 (t80) REVERT: C 181 GLU cc_start: 0.8388 (mp0) cc_final: 0.8033 (pm20) REVERT: C 187 CYS cc_start: 0.5870 (t) cc_final: 0.5484 (p) REVERT: C 200 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7551 (mt0) REVERT: D 56 LYS cc_start: 0.7053 (tmtt) cc_final: 0.6758 (tppt) REVERT: D 165 LEU cc_start: 0.8571 (mt) cc_final: 0.8362 (mt) REVERT: D 181 GLU cc_start: 0.8233 (mp0) cc_final: 0.7652 (pm20) REVERT: D 183 ILE cc_start: 0.7896 (mp) cc_final: 0.7625 (mp) REVERT: D 194 ARG cc_start: 0.7942 (ttp-170) cc_final: 0.7464 (ttp80) outliers start: 43 outliers final: 31 residues processed: 258 average time/residue: 0.0650 time to fit residues: 24.0303 Evaluate side-chains 258 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 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 63 LEU Chi-restraints excluded: chain A residue 64 ILE 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 152 LEU 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 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 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 164 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 200 GLN 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 38 optimal weight: 6.9990 chunk 29 optimal weight: 0.0170 chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN C 89 GLN C 200 GLN D 35 ASN D 71 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.112321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.091911 restraints weight = 14023.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095263 restraints weight = 7039.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097572 restraints weight = 4503.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099086 restraints weight = 3352.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.100002 restraints weight = 2758.567| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7754 Z= 0.144 Angle : 0.610 6.947 10482 Z= 0.324 Chirality : 0.046 0.389 1226 Planarity : 0.004 0.034 1264 Dihedral : 7.473 70.463 1076 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 6.18 % Allowed : 17.34 % 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: 1.04 (0.27), residues: 928 helix: 1.71 (0.21), residues: 568 sheet: -0.19 (0.70), residues: 50 loop : -1.09 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 278 TYR 0.043 0.002 TYR A 206 PHE 0.018 0.001 PHE A 111 TRP 0.022 0.002 TRP A 60 HIS 0.003 0.000 HIS D 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7754) covalent geometry : angle 0.61030 / 0.32 (10482) hydrogen bonds : bond 0.04744 / 3.26 ( 483) hydrogen bonds : angle 4.72610 / 3.53 ( 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 288 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 236 time to evaluate : 0.304 Fit side-chains REVERT: A 141 TRP cc_start: 0.7784 (m100) cc_final: 0.7390 (m100) REVERT: A 166 MET cc_start: 0.5896 (mmp) cc_final: 0.5280 (ttm) REVERT: A 204 PHE cc_start: 0.7196 (m-80) cc_final: 0.5960 (m-80) REVERT: A 220 ASN cc_start: 0.8141 (m-40) cc_final: 0.7911 (m110) REVERT: A 221 TRP cc_start: 0.7866 (m100) cc_final: 0.7624 (m100) REVERT: A 233 PHE cc_start: 0.8267 (m-80) cc_final: 0.7897 (m-80) REVERT: B 11 LEU cc_start: 0.8047 (mt) cc_final: 0.7799 (tt) REVERT: B 84 GLN cc_start: 0.8409 (tt0) cc_final: 0.8037 (tp40) REVERT: B 87 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7243 (mmm) REVERT: B 115 HIS cc_start: 0.7692 (t70) cc_final: 0.7413 (t-170) REVERT: B 152 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8635 (mm) REVERT: B 166 MET cc_start: 0.5416 (mmt) cc_final: 0.4660 (ttm) REVERT: B 188 ILE cc_start: 0.5973 (mm) cc_final: 0.5653 (mt) REVERT: B 200 ASP cc_start: 0.8323 (m-30) cc_final: 0.7845 (p0) REVERT: B 243 LYS cc_start: 0.8353 (mmtt) cc_final: 0.7949 (mmtt) REVERT: C 2 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7226 (mtpp) REVERT: C 4 GLU cc_start: 0.7099 (mp0) cc_final: 0.6586 (mp0) REVERT: C 49 ASN cc_start: 0.8247 (m110) cc_final: 0.8013 (m-40) REVERT: C 70 GLU cc_start: 0.7709 (tp30) cc_final: 0.7329 (tp30) REVERT: C 71 HIS cc_start: 0.6945 (m-70) cc_final: 0.6526 (m90) REVERT: C 99 TYR cc_start: 0.8158 (t80) cc_final: 0.7762 (t80) REVERT: C 181 GLU cc_start: 0.8536 (mp0) cc_final: 0.8138 (pm20) REVERT: C 202 VAL cc_start: 0.7723 (t) cc_final: 0.7378 (m) REVERT: C 204 MET cc_start: 0.6305 (pmm) cc_final: 0.6038 (pmm) REVERT: D 43 MET cc_start: 0.8234 (mtm) cc_final: 0.7866 (mtt) REVERT: D 124 MET cc_start: 0.8344 (mtm) cc_final: 0.7936 (ttm) REVERT: D 165 LEU cc_start: 0.8596 (mt) cc_final: 0.8340 (mt) REVERT: D 176 SER cc_start: 0.7990 (OUTLIER) cc_final: 0.7202 (p) REVERT: D 181 GLU cc_start: 0.8225 (mp0) cc_final: 0.7661 (pm20) REVERT: D 194 ARG cc_start: 0.7692 (ttp-170) cc_final: 0.7230 (ttp80) outliers start: 52 outliers final: 37 residues processed: 265 average time/residue: 0.0640 time to fit residues: 24.1906 Evaluate side-chains 256 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 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 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 14 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 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 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 180 LEU Chi-restraints excluded: chain C residue 200 GLN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 81 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN C 200 GLN D 35 ASN D 49 ASN D 71 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.112467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.092003 restraints weight = 14101.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095258 restraints weight = 6952.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.097561 restraints weight = 4469.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.099002 restraints weight = 3334.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100150 restraints weight = 2760.768| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7754 Z= 0.138 Angle : 0.589 7.699 10482 Z= 0.315 Chirality : 0.045 0.434 1226 Planarity : 0.003 0.034 1264 Dihedral : 7.142 68.707 1076 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.06 % Allowed : 18.65 % 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: 1.05 (0.27), residues: 928 helix: 1.74 (0.21), residues: 570 sheet: -0.20 (0.69), residues: 50 loop : -1.14 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 172 TYR 0.044 0.002 TYR A 206 PHE 0.017 0.001 PHE A 111 TRP 0.017 0.002 TRP A 60 HIS 0.002 0.001 HIS D 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 7754) covalent geometry : angle 0.58908 / 0.32 (10482) hydrogen bonds : bond 0.04509 / 3.10 ( 483) hydrogen bonds : angle 4.67465 / 3.48 ( 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 278 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8859 (mp) REVERT: A 141 TRP cc_start: 0.7787 (m100) cc_final: 0.7420 (m100) REVERT: A 166 MET cc_start: 0.5810 (mmp) cc_final: 0.5123 (ttm) REVERT: A 174 LEU cc_start: 0.8401 (mm) cc_final: 0.8110 (mt) REVERT: A 204 PHE cc_start: 0.7172 (m-80) cc_final: 0.6094 (m-80) REVERT: A 221 TRP cc_start: 0.7855 (m100) cc_final: 0.7620 (m100) REVERT: A 233 PHE cc_start: 0.8203 (m-80) cc_final: 0.7898 (m-80) REVERT: B 11 LEU cc_start: 0.8046 (mt) cc_final: 0.7420 (tt) REVERT: B 15 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7158 (m-10) REVERT: B 84 GLN cc_start: 0.8402 (tt0) cc_final: 0.8000 (tp40) REVERT: B 87 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7298 (mmm) REVERT: B 115 HIS cc_start: 0.7699 (t70) cc_final: 0.7451 (t-170) REVERT: B 152 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8550 (mm) REVERT: B 166 MET cc_start: 0.5393 (mmt) cc_final: 0.4615 (ttm) REVERT: B 188 ILE cc_start: 0.5828 (mm) cc_final: 0.5528 (mt) REVERT: B 200 ASP cc_start: 0.8251 (m-30) cc_final: 0.7858 (p0) REVERT: B 243 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7962 (mmtt) REVERT: C 1 MET cc_start: 0.6649 (tpp) cc_final: 0.6386 (tpt) REVERT: C 2 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7169 (mtpp) REVERT: C 4 GLU cc_start: 0.7096 (mp0) cc_final: 0.6550 (mp0) REVERT: C 70 GLU cc_start: 0.7653 (tp30) cc_final: 0.7349 (tp30) REVERT: C 71 HIS cc_start: 0.6983 (m-70) cc_final: 0.6745 (m170) REVERT: C 99 TYR cc_start: 0.8114 (t80) cc_final: 0.7872 (t80) REVERT: C 181 GLU cc_start: 0.8553 (mp0) cc_final: 0.8139 (pm20) REVERT: C 187 CYS cc_start: 0.6661 (t) cc_final: 0.5436 (p) REVERT: C 200 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7427 (mt0) REVERT: C 202 VAL cc_start: 0.7626 (t) cc_final: 0.7265 (m) REVERT: C 204 MET cc_start: 0.6325 (pmm) cc_final: 0.6080 (pmm) REVERT: D 124 MET cc_start: 0.8239 (mtm) cc_final: 0.7909 (ttm) REVERT: D 165 LEU cc_start: 0.8460 (mt) cc_final: 0.8167 (mt) REVERT: D 181 GLU cc_start: 0.8121 (mp0) cc_final: 0.7610 (pm20) REVERT: D 194 ARG cc_start: 0.7682 (ttp-170) cc_final: 0.7221 (ttp80) outliers start: 51 outliers final: 32 residues processed: 253 average time/residue: 0.0652 time to fit residues: 23.7476 Evaluate side-chains 262 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 196 LEU 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 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 145 GLU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain D residue 19 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 276 SER 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: 0.8980 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 GLN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN B 123 GLN B 220 ASN D 35 ASN D 71 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.089845 restraints weight = 14200.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.092995 restraints weight = 7207.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095260 restraints weight = 4684.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.096623 restraints weight = 3513.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097749 restraints weight = 2922.161| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7754 Z= 0.175 Angle : 0.629 8.562 10482 Z= 0.331 Chirality : 0.045 0.356 1226 Planarity : 0.004 0.035 1264 Dihedral : 7.087 69.976 1076 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 6.41 % Allowed : 19.71 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.04 (0.27), residues: 928 helix: 1.70 (0.21), residues: 570 sheet: -0.03 (0.62), residues: 58 loop : -1.16 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 189 TYR 0.044 0.002 TYR A 206 PHE 0.018 0.001 PHE A 111 TRP 0.016 0.002 TRP A 60 HIS 0.005 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 7754) covalent geometry : angle 0.62900 / 0.33 (10482) hydrogen bonds : bond 0.04597 / 3.16 ( 483) hydrogen bonds : angle 4.70224 / 3.52 ( 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 273 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 219 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8826 (mp) REVERT: A 141 TRP cc_start: 0.7807 (m100) cc_final: 0.7413 (m100) REVERT: A 166 MET cc_start: 0.5699 (mmp) cc_final: 0.5077 (ttm) REVERT: A 221 TRP cc_start: 0.7841 (m100) cc_final: 0.7604 (m100) REVERT: B 15 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7188 (m-10) REVERT: B 84 GLN cc_start: 0.8443 (tt0) cc_final: 0.8100 (tp40) REVERT: B 87 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7426 (mmm) REVERT: B 152 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8665 (mm) REVERT: B 166 MET cc_start: 0.5644 (mmt) cc_final: 0.4712 (ttm) REVERT: B 188 ILE cc_start: 0.5997 (mm) cc_final: 0.5715 (mt) REVERT: C 1 MET cc_start: 0.6621 (tpp) cc_final: 0.6259 (tpt) REVERT: C 4 GLU cc_start: 0.7182 (mp0) cc_final: 0.6695 (mp0) REVERT: C 70 GLU cc_start: 0.7666 (tp30) cc_final: 0.7423 (tp30) REVERT: C 71 HIS cc_start: 0.7118 (m-70) cc_final: 0.6887 (m170) REVERT: C 99 TYR cc_start: 0.8122 (t80) cc_final: 0.7856 (t80) REVERT: C 181 GLU cc_start: 0.8548 (mp0) cc_final: 0.8167 (pm20) REVERT: C 191 VAL cc_start: 0.8967 (p) cc_final: 0.8749 (m) REVERT: D 4 GLU cc_start: 0.7768 (mp0) cc_final: 0.7271 (mp0) REVERT: D 124 MET cc_start: 0.8263 (mtm) cc_final: 0.7924 (ttm) REVERT: D 165 LEU cc_start: 0.8573 (mt) cc_final: 0.8291 (mt) REVERT: D 181 GLU cc_start: 0.8125 (mp0) cc_final: 0.7545 (pm20) REVERT: D 194 ARG cc_start: 0.7835 (ttp-170) cc_final: 0.7277 (ttp80) outliers start: 54 outliers final: 42 residues processed: 249 average time/residue: 0.0675 time to fit residues: 24.0123 Evaluate side-chains 257 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 113 LEU 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 226 SER Chi-restraints excluded: chain A residue 236 LEU 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 64 ILE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 114 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 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 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 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 180 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 279 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 35 ASN D 71 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.111173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.090620 restraints weight = 14207.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.093781 restraints weight = 7146.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096111 restraints weight = 4666.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097509 restraints weight = 3491.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098605 restraints weight = 2898.770| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7754 Z= 0.154 Angle : 0.619 9.090 10482 Z= 0.326 Chirality : 0.045 0.365 1226 Planarity : 0.003 0.036 1264 Dihedral : 7.015 69.847 1076 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 6.41 % Allowed : 19.12 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.27), residues: 928 helix: 1.69 (0.21), residues: 570 sheet: -0.05 (0.68), residues: 50 loop : -1.22 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 189 TYR 0.045 0.002 TYR A 206 PHE 0.019 0.001 PHE A 111 TRP 0.027 0.002 TRP A 60 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7754) covalent geometry : angle 0.61878 / 0.33 (10482) hydrogen bonds : bond 0.04426 / 3.05 ( 483) hydrogen bonds : angle 4.66713 / 3.50 ( 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 273 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 219 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8800 (mp) REVERT: A 141 TRP cc_start: 0.7781 (m100) cc_final: 0.7449 (m100) REVERT: A 166 MET cc_start: 0.6014 (mmp) cc_final: 0.5171 (ttm) REVERT: A 221 TRP cc_start: 0.7878 (m100) cc_final: 0.7590 (m100) REVERT: B 12 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: B 15 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7142 (m-10) REVERT: B 51 TYR cc_start: 0.7000 (m-80) cc_final: 0.6694 (m-80) REVERT: B 84 GLN cc_start: 0.8437 (tt0) cc_final: 0.8107 (tp40) REVERT: B 87 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7381 (mmm) REVERT: B 152 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8654 (mm) REVERT: B 166 MET cc_start: 0.5545 (mmt) cc_final: 0.4608 (ttm) REVERT: B 188 ILE cc_start: 0.5989 (mm) cc_final: 0.5700 (mt) REVERT: C 1 MET cc_start: 0.6624 (tpp) cc_final: 0.6251 (tpt) REVERT: C 2 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7295 (mtpp) REVERT: C 4 GLU cc_start: 0.7159 (mp0) cc_final: 0.6676 (mp0) REVERT: C 70 GLU cc_start: 0.7663 (tp30) cc_final: 0.7395 (tp30) REVERT: C 71 HIS cc_start: 0.7116 (m-70) cc_final: 0.6860 (m170) REVERT: C 181 GLU cc_start: 0.8434 (mp0) cc_final: 0.8149 (pm20) REVERT: C 183 ILE cc_start: 0.8366 (tp) cc_final: 0.8115 (tt) REVERT: C 187 CYS cc_start: 0.6415 (t) cc_final: 0.5473 (p) REVERT: C 200 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7324 (mt0) REVERT: D 4 GLU cc_start: 0.7764 (mp0) cc_final: 0.7262 (mp0) REVERT: D 124 MET cc_start: 0.8284 (mtm) cc_final: 0.7940 (ttm) REVERT: D 165 LEU cc_start: 0.8574 (mt) cc_final: 0.8290 (mt) REVERT: D 181 GLU cc_start: 0.8100 (mp0) cc_final: 0.7626 (pm20) REVERT: D 194 ARG cc_start: 0.7844 (ttp-170) cc_final: 0.7268 (ttp80) outliers start: 54 outliers final: 40 residues processed: 249 average time/residue: 0.0678 time to fit residues: 24.2877 Evaluate side-chains 262 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain A residue 113 LEU 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 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 12 TYR 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 64 ILE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 114 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 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 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 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 276 SER Chi-restraints excluded: chain D residue 279 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN D 35 ASN D 71 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.089556 restraints weight = 14206.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.092730 restraints weight = 7328.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095005 restraints weight = 4837.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.096383 restraints weight = 3655.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097519 restraints weight = 3053.256| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7754 Z= 0.172 Angle : 0.656 9.325 10482 Z= 0.342 Chirality : 0.046 0.347 1226 Planarity : 0.004 0.037 1264 Dihedral : 7.017 70.824 1076 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.58 % Allowed : 19.71 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.89 (0.27), residues: 928 helix: 1.63 (0.21), residues: 570 sheet: -0.20 (0.70), residues: 50 loop : -1.28 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 189 TYR 0.044 0.002 TYR A 206 PHE 0.020 0.002 PHE A 111 TRP 0.043 0.003 TRP B 60 HIS 0.003 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 7754) covalent geometry : angle 0.65629 / 0.34 (10482) hydrogen bonds : bond 0.04438 / 3.06 ( 483) hydrogen bonds : angle 4.68569 / 3.51 ( 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 269 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8820 (mp) REVERT: A 141 TRP cc_start: 0.7803 (m100) cc_final: 0.7455 (m100) REVERT: A 166 MET cc_start: 0.5870 (mmp) cc_final: 0.5143 (ttm) REVERT: A 221 TRP cc_start: 0.7895 (m100) cc_final: 0.7617 (m100) REVERT: B 12 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: B 15 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7198 (m-10) REVERT: B 84 GLN cc_start: 0.8453 (tt0) cc_final: 0.8105 (tp40) REVERT: B 87 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7354 (mmm) REVERT: B 115 HIS cc_start: 0.7761 (t-90) cc_final: 0.7370 (t-170) REVERT: B 152 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8714 (mm) REVERT: B 166 MET cc_start: 0.5475 (mmt) cc_final: 0.4546 (ttm) REVERT: B 188 ILE cc_start: 0.6024 (mm) cc_final: 0.5734 (mt) REVERT: C 3 LEU cc_start: 0.8532 (mt) cc_final: 0.8268 (mt) REVERT: C 4 GLU cc_start: 0.7183 (mp0) cc_final: 0.6705 (mp0) REVERT: C 70 GLU cc_start: 0.7635 (tp30) cc_final: 0.7418 (tp30) REVERT: C 71 HIS cc_start: 0.7084 (m-70) cc_final: 0.6834 (m170) REVERT: C 181 GLU cc_start: 0.8339 (mp0) cc_final: 0.8060 (pm20) REVERT: C 183 ILE cc_start: 0.8377 (tp) cc_final: 0.8120 (tt) REVERT: C 187 CYS cc_start: 0.6619 (t) cc_final: 0.5470 (p) REVERT: D 124 MET cc_start: 0.8307 (mtm) cc_final: 0.7944 (ttm) REVERT: D 181 GLU cc_start: 0.8068 (mp0) cc_final: 0.7598 (pm20) REVERT: D 194 ARG cc_start: 0.7874 (ttp-170) cc_final: 0.7289 (ttp80) outliers start: 47 outliers final: 38 residues processed: 248 average time/residue: 0.0605 time to fit residues: 21.9905 Evaluate side-chains 258 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 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 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 113 LEU 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 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 12 TYR 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 64 ILE Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 114 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 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 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 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 180 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 279 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 75 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 35 ASN D 71 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.090592 restraints weight = 14050.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.093742 restraints weight = 7229.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096089 restraints weight = 4767.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097586 restraints weight = 3588.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098488 restraints weight = 2971.760| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7754 Z= 0.145 Angle : 0.657 9.983 10482 Z= 0.340 Chirality : 0.047 0.322 1226 Planarity : 0.003 0.035 1264 Dihedral : 6.909 70.029 1076 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.34 % Allowed : 20.43 % Favored : 74.23 % 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: 0.93 (0.27), residues: 928 helix: 1.69 (0.21), residues: 568 sheet: -0.28 (0.70), residues: 50 loop : -1.27 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 172 TYR 0.046 0.002 TYR A 206 PHE 0.035 0.002 PHE B 218 TRP 0.043 0.003 TRP B 60 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 7754) covalent geometry : angle 0.65670 / 0.34 (10482) hydrogen bonds : bond 0.04305 / 2.96 ( 483) hydrogen bonds : angle 4.66410 / 3.50 ( 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 270 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8794 (mp) REVERT: A 34 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7732 (mp10) REVERT: A 141 TRP cc_start: 0.7757 (m100) cc_final: 0.7430 (m100) REVERT: A 166 MET cc_start: 0.6139 (mmp) cc_final: 0.5268 (ttm) REVERT: A 221 TRP cc_start: 0.7934 (m100) cc_final: 0.7707 (m100) REVERT: B 12 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6802 (m-80) REVERT: B 15 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7201 (m-10) REVERT: B 84 GLN cc_start: 0.8428 (tt0) cc_final: 0.8103 (tp40) REVERT: B 87 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7425 (mmm) REVERT: B 115 HIS cc_start: 0.7721 (t-90) cc_final: 0.7328 (t-170) REVERT: B 152 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8574 (mm) REVERT: B 161 SER cc_start: 0.7678 (m) cc_final: 0.7432 (p) REVERT: B 166 MET cc_start: 0.5439 (mmt) cc_final: 0.4500 (ttm) REVERT: C 3 LEU cc_start: 0.8514 (mt) cc_final: 0.8257 (mt) REVERT: C 4 GLU cc_start: 0.7170 (mp0) cc_final: 0.6682 (mp0) REVERT: C 43 MET cc_start: 0.7742 (mtm) cc_final: 0.6898 (mtt) REVERT: C 181 GLU cc_start: 0.8416 (mp0) cc_final: 0.8091 (pm20) REVERT: C 183 ILE cc_start: 0.8329 (tp) cc_final: 0.7955 (tt) REVERT: C 187 CYS cc_start: 0.6894 (t) cc_final: 0.5752 (p) REVERT: C 200 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7467 (mt0) REVERT: C 285 ASN cc_start: 0.7603 (t0) cc_final: 0.7006 (t0) REVERT: D 124 MET cc_start: 0.8321 (mtm) cc_final: 0.7999 (ttm) REVERT: D 181 GLU cc_start: 0.8044 (mp0) cc_final: 0.7604 (pm20) REVERT: D 194 ARG cc_start: 0.7896 (ttp-170) cc_final: 0.7310 (ttp80) outliers start: 45 outliers final: 35 residues processed: 249 average time/residue: 0.0622 time to fit residues: 22.7030 Evaluate side-chains 259 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 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 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 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 12 TYR 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 87 MET Chi-restraints excluded: chain B residue 114 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 223 TRP Chi-restraints excluded: chain B residue 226 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 193 LEU Chi-restraints excluded: chain C residue 200 GLN 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 276 SER Chi-restraints excluded: chain D residue 279 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 71 HIS 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 = 0.112140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.090983 restraints weight = 14010.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.094237 restraints weight = 7294.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.096537 restraints weight = 4778.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097742 restraints weight = 3602.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.098971 restraints weight = 3042.963| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7754 Z= 0.146 Angle : 0.664 9.921 10482 Z= 0.344 Chirality : 0.046 0.301 1226 Planarity : 0.003 0.035 1264 Dihedral : 6.804 69.470 1076 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.99 % Allowed : 21.50 % Favored : 73.52 % 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: 0.89 (0.27), residues: 928 helix: 1.67 (0.21), residues: 570 sheet: -0.27 (0.70), residues: 50 loop : -1.34 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 172 TYR 0.045 0.002 TYR A 206 PHE 0.033 0.002 PHE B 218 TRP 0.047 0.003 TRP B 60 HIS 0.002 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 7754) covalent geometry : angle 0.66352 / 0.34 (10482) hydrogen bonds : bond 0.04280 / 2.94 ( 483) hydrogen bonds : angle 4.65316 / 3.50 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1233.77 seconds wall clock time: 22 minutes 6.29 seconds (1326.29 seconds total)