Starting phenix.real_space_refine on Thu Jul 2 19:23:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nms_49554/07_2026/9nms_49554.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nms_49554/07_2026/9nms_49554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nms_49554/07_2026/9nms_49554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nms_49554/07_2026/9nms_49554.map" model { file = "/net/cci-nas-00/data/ceres_data/9nms_49554/07_2026/9nms_49554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nms_49554/07_2026/9nms_49554.cif" } resolution = 3.5 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= 0.052 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: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 72 5.16 5 C 6300 2.51 5 N 1616 2.21 5 O 1764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9755 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2438 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 15, 'TRANS': 290} Chain breaks: 1 Chain: "B" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2438 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 15, 'TRANS': 290} Chain breaks: 1 Chain: "C" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2438 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 15, 'TRANS': 290} Chain breaks: 1 Chain: "D" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2438 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 15, 'TRANS': 290} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' K': 3} Chain breaks: 3 Time building chain proxies: 2.58, per 1000 atoms: 0.26 Number of scatterers: 9755 At special positions: 0 Unit cell: (96.6, 96.6, 115.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 72 16.00 O 1764 8.00 N 1616 7.00 C 6300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 131 " distance=2.04 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 131 " distance=2.04 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 131 " distance=2.04 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 131 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 355.9 milliseconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 37.1% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 43 through 51 Processing helix chain 'A' and resid 52 through 83 removed outlier: 3.557A pdb=" N LEU A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 131 through 161 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 252 through 259 removed outlier: 4.070A pdb=" N LEU A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 315 through 318 Processing helix chain 'B' and resid 39 through 42 Processing helix chain 'B' and resid 43 through 51 removed outlier: 3.547A pdb=" N ILE B 47 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 83 removed outlier: 3.558A pdb=" N LEU B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE B 64 " --> pdb=" O PHE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 131 through 161 Processing helix chain 'B' and resid 162 through 168 removed outlier: 3.511A pdb=" N PHE B 168 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 removed outlier: 3.958A pdb=" N LEU B 256 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'C' and resid 38 through 42 removed outlier: 3.630A pdb=" N ARG C 42 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 51 Processing helix chain 'C' and resid 52 through 83 removed outlier: 3.558A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 118 Processing helix chain 'C' and resid 131 through 161 Processing helix chain 'C' and resid 162 through 168 removed outlier: 3.559A pdb=" N ASN C 165 " --> pdb=" O GLN C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 removed outlier: 3.891A pdb=" N LEU C 256 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 315 through 318 Processing helix chain 'D' and resid 43 through 51 removed outlier: 3.517A pdb=" N ILE D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 83 removed outlier: 3.552A pdb=" N LEU D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE D 64 " --> pdb=" O PHE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 Processing helix chain 'D' and resid 131 through 161 Processing helix chain 'D' and resid 162 through 168 Processing helix chain 'D' and resid 252 through 259 removed outlier: 4.016A pdb=" N LEU D 256 " --> pdb=" O PRO D 252 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS D 259 " --> pdb=" O THR D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 315 through 318 Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 removed outlier: 3.745A pdb=" N PHE A 189 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 243 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 222 removed outlier: 3.526A pdb=" N TYR A 218 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 220 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 206 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N SER A 201 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET A 274 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 Processing sheet with id=AA5, first strand: chain 'A' and resid 303 through 305 Processing sheet with id=AA6, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AA7, first strand: chain 'B' and resid 170 through 172 removed outlier: 3.716A pdb=" N PHE B 189 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 217 through 222 removed outlier: 3.515A pdb=" N THR B 220 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 206 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N SER B 201 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N MET B 274 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 267 " --> pdb=" O TYR B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 297 through 298 Processing sheet with id=AB1, first strand: chain 'B' and resid 303 through 304 removed outlier: 3.554A pdb=" N GLN B 312 " --> pdb=" O THR B 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AB3, first strand: chain 'C' and resid 170 through 172 removed outlier: 3.818A pdb=" N PHE C 189 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR C 243 " --> pdb=" O PHE C 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 217 through 222 removed outlier: 3.608A pdb=" N THR C 220 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 206 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER C 201 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET C 274 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 297 through 298 Processing sheet with id=AB6, first strand: chain 'C' and resid 303 through 304 removed outlier: 3.578A pdb=" N GLN C 312 " --> pdb=" O THR C 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 170 through 171 Processing sheet with id=AB8, first strand: chain 'D' and resid 170 through 171 removed outlier: 3.794A pdb=" N PHE D 189 " --> pdb=" O TYR D 243 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 243 " --> pdb=" O PHE D 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 217 through 222 removed outlier: 3.538A pdb=" N THR D 220 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 206 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER D 201 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET D 274 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 297 through 298 Processing sheet with id=AC2, first strand: chain 'D' and resid 303 through 305 457 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3088 1.34 - 1.46: 2514 1.46 - 1.58: 4290 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 10016 Sorted by residual: bond pdb=" CB GLN A 210 " pdb=" CG GLN A 210 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.96e-01 bond pdb=" CA ILE A 98 " pdb=" CB ILE A 98 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.05e-02 9.07e+03 9.01e-01 bond pdb=" CB GLN D 210 " pdb=" CG GLN D 210 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.65e-01 bond pdb=" CA GLN D 210 " pdb=" CB GLN D 210 " ideal model delta sigma weight residual 1.532 1.545 -0.013 1.58e-02 4.01e+03 6.36e-01 bond pdb=" CG ARG A 203 " pdb=" CD ARG A 203 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 4.75e-01 ... (remaining 10011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 13404 1.44 - 2.87: 136 2.87 - 4.31: 48 4.31 - 5.74: 8 5.74 - 7.18: 4 Bond angle restraints: 13600 Sorted by residual: angle pdb=" N ILE A 238 " pdb=" CA ILE A 238 " pdb=" C ILE A 238 " ideal model delta sigma weight residual 112.12 109.51 2.61 8.40e-01 1.42e+00 9.66e+00 angle pdb=" CA GLN A 210 " pdb=" CB GLN A 210 " pdb=" CG GLN A 210 " ideal model delta sigma weight residual 114.10 119.41 -5.31 2.00e+00 2.50e-01 7.06e+00 angle pdb=" CA GLN D 210 " pdb=" CB GLN D 210 " pdb=" CG GLN D 210 " ideal model delta sigma weight residual 114.10 119.35 -5.25 2.00e+00 2.50e-01 6.88e+00 angle pdb=" C VAL D 70 " pdb=" N PHE D 71 " pdb=" CA PHE D 71 " ideal model delta sigma weight residual 121.14 116.94 4.20 1.75e+00 3.27e-01 5.75e+00 angle pdb=" CB MET C 142 " pdb=" CG MET C 142 " pdb=" SD MET C 142 " ideal model delta sigma weight residual 112.70 119.88 -7.18 3.00e+00 1.11e-01 5.73e+00 ... (remaining 13595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.58: 4982 14.58 - 29.15: 635 29.15 - 43.73: 217 43.73 - 58.31: 61 58.31 - 72.88: 17 Dihedral angle restraints: 5912 sinusoidal: 2332 harmonic: 3580 Sorted by residual: dihedral pdb=" CA ASN C 193 " pdb=" CB ASN C 193 " pdb=" CG ASN C 193 " pdb=" OD1 ASN C 193 " ideal model delta sinusoidal sigma weight residual 120.00 -167.12 -72.88 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASN D 193 " pdb=" CB ASN D 193 " pdb=" CG ASN D 193 " pdb=" OD1 ASN D 193 " ideal model delta sinusoidal sigma weight residual -90.00 -159.98 69.98 2 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CB ARG B 195 " pdb=" CG ARG B 195 " pdb=" CD ARG B 195 " pdb=" NE ARG B 195 " ideal model delta sinusoidal sigma weight residual -60.00 -117.94 57.94 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 941 0.027 - 0.054: 372 0.054 - 0.081: 84 0.081 - 0.109: 90 0.109 - 0.136: 29 Chirality restraints: 1516 Sorted by residual: chirality pdb=" CA PHE B 71 " pdb=" N PHE B 71 " pdb=" C PHE B 71 " pdb=" CB PHE B 71 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA PHE C 71 " pdb=" N PHE C 71 " pdb=" C PHE C 71 " pdb=" CB PHE C 71 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA PHE D 71 " pdb=" N PHE D 71 " pdb=" C PHE D 71 " pdb=" CB PHE D 71 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1513 not shown) Planarity restraints: 1720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 289 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO D 290 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 290 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 290 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 289 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO C 290 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 290 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 290 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 289 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.73e+00 pdb=" N PRO A 290 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " 0.018 5.00e-02 4.00e+02 ... (remaining 1717 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.07: 5888 3.07 - 3.59: 10925 3.59 - 4.10: 15200 4.10 - 4.62: 23179 4.62 - 5.14: 31477 Nonbonded interactions: 86669 Sorted by model distance: nonbonded pdb=" O THR C 194 " pdb=" OG1 THR C 194 " model vdw 2.550 3.040 nonbonded pdb=" O LEU D 118 " pdb=" OG1 THR D 119 " model vdw 2.612 3.040 nonbonded pdb=" O LEU C 118 " pdb=" OG1 THR C 119 " model vdw 2.613 3.040 nonbonded pdb=" O LEU A 118 " pdb=" OG1 THR A 119 " model vdw 2.613 3.040 nonbonded pdb=" O LEU B 118 " pdb=" OG1 THR B 119 " model vdw 2.615 3.040 ... (remaining 86664 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 325) selection = chain 'B' selection = 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: 1.220 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.400 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.002 0.030 10020 Z= 0.091 Angle : 0.467 7.179 13608 Z= 0.245 Chirality : 0.039 0.136 1516 Planarity : 0.003 0.034 1720 Dihedral : 15.623 72.883 3580 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.40 % Favored : 97.27 % Rotamer: Outliers : 3.65 % Allowed : 20.32 % Favored : 76.03 % 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: 1.61 (0.24), residues: 1208 helix: 2.29 (0.26), residues: 372 sheet: 0.85 (0.30), residues: 252 loop : 0.47 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 203 TYR 0.004 0.000 TYR C 243 PHE 0.012 0.001 PHE A 156 TRP 0.006 0.001 TRP B 53 HIS 0.006 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00174 / 0.09 (10016) covalent geometry : angle 0.46693 / 0.24 (13600) SS BOND : bond 0.00504 / 0.25 ( 4) SS BOND : angle 0.64836 / 0.34 ( 8) hydrogen bonds : bond 0.21599 / 14.96 ( 449) hydrogen bonds : angle 6.30943 / 4.64 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.5816 (OUTLIER) cc_final: 0.4248 (mtt-85) REVERT: A 181 MET cc_start: 0.6695 (pmm) cc_final: 0.6148 (mpp) REVERT: A 297 HIS cc_start: 0.4331 (OUTLIER) cc_final: 0.3760 (m90) REVERT: B 297 HIS cc_start: 0.4237 (OUTLIER) cc_final: 0.3385 (m90) REVERT: C 19 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.5047 (mtm-85) REVERT: C 297 HIS cc_start: 0.4218 (OUTLIER) cc_final: 0.3734 (m90) REVERT: D 297 HIS cc_start: 0.4254 (OUTLIER) cc_final: 0.3471 (m90) outliers start: 39 outliers final: 16 residues processed: 237 average time/residue: 0.1000 time to fit residues: 33.2759 Evaluate side-chains 181 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 297 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.0070 chunk 117 optimal weight: 6.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN B 162 GLN B 180 HIS C 180 HIS D 180 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.221921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.173548 restraints weight = 13197.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.173319 restraints weight = 9981.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.175006 restraints weight = 8610.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175475 restraints weight = 7249.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.176928 restraints weight = 6933.051| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10020 Z= 0.125 Angle : 0.547 6.664 13608 Z= 0.279 Chirality : 0.043 0.190 1516 Planarity : 0.004 0.034 1720 Dihedral : 6.355 59.262 1357 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.48 % Favored : 97.19 % Rotamer: Outliers : 4.49 % Allowed : 19.76 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.24), residues: 1208 helix: 2.37 (0.27), residues: 376 sheet: 1.26 (0.29), residues: 252 loop : 0.56 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 203 TYR 0.011 0.001 TYR D 244 PHE 0.014 0.001 PHE B 71 TRP 0.006 0.001 TRP B 53 HIS 0.003 0.001 HIS C 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (10016) covalent geometry : angle 0.54653 / 0.28 (13600) SS BOND : bond 0.00515 / 0.26 ( 4) SS BOND : angle 0.82618 / 0.45 ( 8) hydrogen bonds : bond 0.04792 / 3.09 ( 449) hydrogen bonds : angle 5.00010 / 3.72 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8330 (pttt) cc_final: 0.8060 (tppt) REVERT: A 181 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6611 (mpp) REVERT: A 297 HIS cc_start: 0.4816 (OUTLIER) cc_final: 0.4042 (m90) REVERT: B 297 HIS cc_start: 0.4650 (OUTLIER) cc_final: 0.3821 (m90) REVERT: B 323 PRO cc_start: 0.6238 (Cg_endo) cc_final: 0.5524 (Cg_exo) REVERT: C 210 GLN cc_start: 0.6371 (tm-30) cc_final: 0.6075 (tm-30) REVERT: C 297 HIS cc_start: 0.4755 (OUTLIER) cc_final: 0.4006 (m90) REVERT: D 19 ARG cc_start: 0.5558 (OUTLIER) cc_final: 0.4729 (mtt-85) REVERT: D 210 GLN cc_start: 0.6406 (tm-30) cc_final: 0.6114 (tm-30) REVERT: D 297 HIS cc_start: 0.4642 (OUTLIER) cc_final: 0.3866 (m90) REVERT: D 323 PRO cc_start: 0.6202 (Cg_endo) cc_final: 0.5507 (Cg_exo) outliers start: 48 outliers final: 26 residues processed: 219 average time/residue: 0.0897 time to fit residues: 28.4258 Evaluate side-chains 187 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 297 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN B 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.224934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.177984 restraints weight = 12754.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.179344 restraints weight = 7524.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.179871 restraints weight = 6227.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.181024 restraints weight = 5855.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.181020 restraints weight = 5163.786| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10020 Z= 0.100 Angle : 0.485 6.266 13608 Z= 0.246 Chirality : 0.042 0.188 1516 Planarity : 0.003 0.036 1720 Dihedral : 5.705 52.557 1343 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.73 % Favored : 96.94 % Rotamer: Outliers : 4.12 % Allowed : 21.54 % Favored : 74.34 % 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: 1.94 (0.24), residues: 1208 helix: 2.63 (0.27), residues: 368 sheet: 1.45 (0.29), residues: 252 loop : 0.40 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 19 TYR 0.011 0.001 TYR D 288 PHE 0.012 0.001 PHE C 71 TRP 0.007 0.001 TRP C 53 HIS 0.004 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (10016) covalent geometry : angle 0.48510 / 0.25 (13600) SS BOND : bond 0.00432 / 0.22 ( 4) SS BOND : angle 0.72143 / 0.40 ( 8) hydrogen bonds : bond 0.04246 / 2.70 ( 449) hydrogen bonds : angle 4.56254 / 3.40 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8291 (pttt) cc_final: 0.8026 (tppt) REVERT: A 181 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6817 (mpp) REVERT: A 297 HIS cc_start: 0.4884 (OUTLIER) cc_final: 0.4052 (m90) REVERT: B 19 ARG cc_start: 0.5566 (OUTLIER) cc_final: 0.5276 (mtm180) REVERT: B 164 LYS cc_start: 0.8402 (tttt) cc_final: 0.7957 (tppt) REVERT: B 297 HIS cc_start: 0.4501 (OUTLIER) cc_final: 0.3793 (m90) REVERT: B 323 PRO cc_start: 0.6111 (Cg_endo) cc_final: 0.5517 (Cg_exo) REVERT: C 210 GLN cc_start: 0.6351 (tm-30) cc_final: 0.5994 (tm-30) REVERT: C 297 HIS cc_start: 0.4824 (OUTLIER) cc_final: 0.4048 (m90) REVERT: D 184 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8339 (mmmt) REVERT: D 210 GLN cc_start: 0.6393 (tm-30) cc_final: 0.6061 (tm-30) REVERT: D 297 HIS cc_start: 0.4678 (OUTLIER) cc_final: 0.3995 (m90) REVERT: D 323 PRO cc_start: 0.6183 (Cg_endo) cc_final: 0.5462 (Cg_exo) outliers start: 44 outliers final: 19 residues processed: 205 average time/residue: 0.0944 time to fit residues: 27.5779 Evaluate side-chains 176 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 297 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 46 optimal weight: 9.9990 chunk 3 optimal weight: 0.0170 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 0.0470 chunk 93 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 HIS A 190 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.216835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.176920 restraints weight = 12804.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.179630 restraints weight = 9004.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.179479 restraints weight = 9451.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.180791 restraints weight = 5972.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.181526 restraints weight = 5210.234| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10020 Z= 0.092 Angle : 0.472 6.887 13608 Z= 0.239 Chirality : 0.041 0.173 1516 Planarity : 0.003 0.037 1720 Dihedral : 5.264 46.944 1339 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.15 % Favored : 97.52 % Rotamer: Outliers : 3.65 % Allowed : 22.66 % Favored : 73.69 % 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: 2.05 (0.24), residues: 1208 helix: 2.72 (0.27), residues: 368 sheet: 1.22 (0.30), residues: 256 loop : 0.63 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 203 TYR 0.014 0.001 TYR A 244 PHE 0.011 0.001 PHE B 71 TRP 0.006 0.001 TRP C 53 HIS 0.002 0.000 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (10016) covalent geometry : angle 0.47189 / 0.24 (13600) SS BOND : bond 0.00274 / 0.14 ( 4) SS BOND : angle 0.49626 / 0.28 ( 8) hydrogen bonds : bond 0.03881 / 2.46 ( 449) hydrogen bonds : angle 4.23462 / 3.10 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6603 (mpp) REVERT: A 297 HIS cc_start: 0.4681 (OUTLIER) cc_final: 0.4049 (m90) REVERT: B 164 LYS cc_start: 0.8389 (tttt) cc_final: 0.8100 (tppt) REVERT: B 297 HIS cc_start: 0.4321 (OUTLIER) cc_final: 0.3755 (m90) REVERT: B 323 PRO cc_start: 0.6171 (Cg_endo) cc_final: 0.5651 (Cg_exo) REVERT: C 210 GLN cc_start: 0.6380 (tm-30) cc_final: 0.6024 (tm-30) REVERT: C 297 HIS cc_start: 0.4610 (OUTLIER) cc_final: 0.4000 (m90) REVERT: D 297 HIS cc_start: 0.4342 (OUTLIER) cc_final: 0.3832 (m90) REVERT: D 323 PRO cc_start: 0.6138 (Cg_endo) cc_final: 0.5508 (Cg_exo) outliers start: 39 outliers final: 25 residues processed: 193 average time/residue: 0.0939 time to fit residues: 25.7981 Evaluate side-chains 183 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 297 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS C 190 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.215534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.174169 restraints weight = 12922.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.176193 restraints weight = 9609.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.177261 restraints weight = 8689.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.177775 restraints weight = 5770.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.178566 restraints weight = 5352.418| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10020 Z= 0.159 Angle : 0.549 8.336 13608 Z= 0.277 Chirality : 0.043 0.177 1516 Planarity : 0.004 0.038 1720 Dihedral : 5.510 48.866 1334 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.64 % Favored : 96.03 % Rotamer: Outliers : 4.21 % Allowed : 22.19 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.24), residues: 1208 helix: 2.39 (0.26), residues: 368 sheet: 1.33 (0.30), residues: 244 loop : 0.76 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 203 TYR 0.014 0.001 TYR A 311 PHE 0.022 0.002 PHE D 71 TRP 0.009 0.001 TRP B 75 HIS 0.006 0.001 HIS D 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (10016) covalent geometry : angle 0.54865 / 0.28 (13600) SS BOND : bond 0.00568 / 0.29 ( 4) SS BOND : angle 0.59101 / 0.32 ( 8) hydrogen bonds : bond 0.04872 / 3.08 ( 449) hydrogen bonds : angle 4.31496 / 3.15 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6701 (mpp) REVERT: A 297 HIS cc_start: 0.4986 (OUTLIER) cc_final: 0.4006 (m90) REVERT: B 164 LYS cc_start: 0.8419 (tttt) cc_final: 0.8108 (tppt) REVERT: B 297 HIS cc_start: 0.4494 (OUTLIER) cc_final: 0.3367 (m-70) REVERT: B 323 PRO cc_start: 0.6512 (Cg_endo) cc_final: 0.6209 (Cg_exo) REVERT: C 297 HIS cc_start: 0.4850 (OUTLIER) cc_final: 0.4162 (m90) REVERT: D 19 ARG cc_start: 0.5535 (OUTLIER) cc_final: 0.4303 (ptt-90) REVERT: D 297 HIS cc_start: 0.4651 (OUTLIER) cc_final: 0.3565 (m-70) REVERT: D 323 PRO cc_start: 0.6398 (Cg_endo) cc_final: 0.6132 (Cg_exo) outliers start: 45 outliers final: 31 residues processed: 188 average time/residue: 0.1053 time to fit residues: 27.2766 Evaluate side-chains 187 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 297 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 57 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 0.0040 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 7 optimal weight: 0.0040 chunk 64 optimal weight: 0.5980 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN C 26 HIS D 312 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.216197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.177237 restraints weight = 12859.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.182623 restraints weight = 9452.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.182104 restraints weight = 7395.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.182791 restraints weight = 5195.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.183191 restraints weight = 4712.425| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10020 Z= 0.094 Angle : 0.494 7.893 13608 Z= 0.248 Chirality : 0.041 0.157 1516 Planarity : 0.003 0.038 1720 Dihedral : 5.004 46.706 1330 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.07 % Favored : 97.60 % Rotamer: Outliers : 2.43 % Allowed : 23.97 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.25), residues: 1208 helix: 2.72 (0.27), residues: 368 sheet: 1.39 (0.30), residues: 244 loop : 0.67 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 203 TYR 0.010 0.001 TYR B 288 PHE 0.009 0.001 PHE B 156 TRP 0.007 0.001 TRP C 53 HIS 0.002 0.000 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (10016) covalent geometry : angle 0.49367 / 0.25 (13600) SS BOND : bond 0.00226 / 0.11 ( 4) SS BOND : angle 0.32956 / 0.19 ( 8) hydrogen bonds : bond 0.03890 / 2.46 ( 449) hydrogen bonds : angle 4.06940 / 2.94 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 HIS cc_start: 0.4620 (OUTLIER) cc_final: 0.4158 (m90) REVERT: B 164 LYS cc_start: 0.8425 (tttt) cc_final: 0.8133 (tppt) REVERT: B 297 HIS cc_start: 0.4276 (OUTLIER) cc_final: 0.3669 (m90) REVERT: B 323 PRO cc_start: 0.6280 (Cg_endo) cc_final: 0.5614 (Cg_exo) REVERT: C 210 GLN cc_start: 0.6320 (tm-30) cc_final: 0.6073 (tm-30) REVERT: C 297 HIS cc_start: 0.4567 (OUTLIER) cc_final: 0.4143 (m-70) REVERT: D 19 ARG cc_start: 0.5479 (OUTLIER) cc_final: 0.5229 (mtm180) REVERT: D 210 GLN cc_start: 0.6277 (tm-30) cc_final: 0.5985 (tm-30) REVERT: D 297 HIS cc_start: 0.4274 (OUTLIER) cc_final: 0.3389 (m-70) REVERT: D 323 PRO cc_start: 0.6235 (Cg_endo) cc_final: 0.5810 (Cg_exo) outliers start: 26 outliers final: 17 residues processed: 181 average time/residue: 0.0814 time to fit residues: 21.2521 Evaluate side-chains 174 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 297 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN D 312 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.214955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.173441 restraints weight = 12764.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.175142 restraints weight = 9505.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.176211 restraints weight = 8565.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.176984 restraints weight = 5966.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.177878 restraints weight = 5427.750| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10020 Z= 0.160 Angle : 0.551 9.222 13608 Z= 0.276 Chirality : 0.042 0.150 1516 Planarity : 0.004 0.038 1720 Dihedral : 5.311 48.474 1330 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.64 % Favored : 96.03 % Rotamer: Outliers : 3.46 % Allowed : 23.13 % Favored : 73.41 % 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: 2.03 (0.25), residues: 1208 helix: 2.42 (0.26), residues: 368 sheet: 1.45 (0.30), residues: 236 loop : 0.74 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 203 TYR 0.007 0.001 TYR B 288 PHE 0.022 0.001 PHE D 71 TRP 0.009 0.001 TRP D 75 HIS 0.005 0.001 HIS D 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (10016) covalent geometry : angle 0.55082 / 0.28 (13600) SS BOND : bond 0.00508 / 0.26 ( 4) SS BOND : angle 0.48402 / 0.26 ( 8) hydrogen bonds : bond 0.04769 / 3.01 ( 449) hydrogen bonds : angle 4.18473 / 3.03 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 297 HIS cc_start: 0.4950 (OUTLIER) cc_final: 0.4145 (m90) REVERT: B 164 LYS cc_start: 0.8425 (tttt) cc_final: 0.8104 (tppt) REVERT: B 297 HIS cc_start: 0.4529 (OUTLIER) cc_final: 0.3513 (m-70) REVERT: B 323 PRO cc_start: 0.6614 (Cg_endo) cc_final: 0.6312 (Cg_exo) REVERT: C 184 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8435 (tptp) REVERT: C 210 GLN cc_start: 0.6283 (tm-30) cc_final: 0.6004 (tm-30) REVERT: C 297 HIS cc_start: 0.4829 (OUTLIER) cc_final: 0.4184 (m90) REVERT: D 19 ARG cc_start: 0.5537 (OUTLIER) cc_final: 0.4239 (ptt-90) REVERT: D 297 HIS cc_start: 0.4554 (OUTLIER) cc_final: 0.3562 (m-70) outliers start: 37 outliers final: 21 residues processed: 180 average time/residue: 0.0956 time to fit residues: 23.8100 Evaluate side-chains 176 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 297 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 7 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.213470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.174121 restraints weight = 12736.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.177987 restraints weight = 9536.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.178524 restraints weight = 7738.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.179015 restraints weight = 5387.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.179685 restraints weight = 5000.933| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10020 Z= 0.113 Angle : 0.528 9.424 13608 Z= 0.260 Chirality : 0.041 0.140 1516 Planarity : 0.004 0.050 1720 Dihedral : 5.186 47.500 1330 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.24 % Favored : 97.43 % Rotamer: Outliers : 2.72 % Allowed : 24.25 % Favored : 73.03 % 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: 1.98 (0.25), residues: 1208 helix: 2.55 (0.27), residues: 368 sheet: 1.09 (0.30), residues: 244 loop : 0.73 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 203 TYR 0.015 0.001 TYR A 311 PHE 0.013 0.001 PHE B 71 TRP 0.007 0.001 TRP C 53 HIS 0.003 0.001 HIS C 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (10016) covalent geometry : angle 0.52840 / 0.26 (13600) SS BOND : bond 0.00379 / 0.19 ( 4) SS BOND : angle 0.31504 / 0.17 ( 8) hydrogen bonds : bond 0.04275 / 2.70 ( 449) hydrogen bonds : angle 4.05314 / 2.92 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.281 Fit side-chains REVERT: A 181 MET cc_start: 0.6987 (mpp) cc_final: 0.6703 (mpp) REVERT: A 297 HIS cc_start: 0.4765 (OUTLIER) cc_final: 0.4314 (m90) REVERT: B 164 LYS cc_start: 0.8447 (tttt) cc_final: 0.8158 (tppt) REVERT: B 297 HIS cc_start: 0.4509 (OUTLIER) cc_final: 0.4129 (m-70) REVERT: C 184 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8491 (tptp) REVERT: C 297 HIS cc_start: 0.4704 (OUTLIER) cc_final: 0.4320 (m90) REVERT: D 19 ARG cc_start: 0.5516 (OUTLIER) cc_final: 0.4147 (ptt-90) REVERT: D 210 GLN cc_start: 0.6329 (tm-30) cc_final: 0.6029 (tm-30) REVERT: D 297 HIS cc_start: 0.4436 (OUTLIER) cc_final: 0.3468 (m-70) outliers start: 29 outliers final: 21 residues processed: 178 average time/residue: 0.0841 time to fit residues: 21.2988 Evaluate side-chains 172 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 297 HIS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 297 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 22 optimal weight: 5.9990 chunk 114 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 105 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 0.0980 chunk 100 optimal weight: 0.0980 overall best weight: 0.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.226024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.184074 restraints weight = 12755.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.187039 restraints weight = 8616.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.187100 restraints weight = 8211.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.188145 restraints weight = 5527.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.190055 restraints weight = 4914.446| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10020 Z= 0.089 Angle : 0.511 9.620 13608 Z= 0.250 Chirality : 0.040 0.127 1516 Planarity : 0.003 0.039 1720 Dihedral : 4.834 45.548 1330 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.32 % Favored : 97.35 % Rotamer: Outliers : 1.50 % Allowed : 25.37 % Favored : 73.13 % 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: 2.12 (0.25), residues: 1208 helix: 2.83 (0.27), residues: 368 sheet: 1.23 (0.30), residues: 244 loop : 0.66 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 203 TYR 0.008 0.001 TYR B 288 PHE 0.011 0.001 PHE B 156 TRP 0.007 0.001 TRP C 53 HIS 0.002 0.000 HIS C 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (10016) covalent geometry : angle 0.51117 / 0.25 (13600) SS BOND : bond 0.00171 / 0.09 ( 4) SS BOND : angle 0.20060 / 0.11 ( 8) hydrogen bonds : bond 0.03581 / 2.26 ( 449) hydrogen bonds : angle 3.89151 / 2.79 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.383 Fit side-chains REVERT: A 181 MET cc_start: 0.6965 (mpp) cc_final: 0.6715 (mpp) REVERT: B 164 LYS cc_start: 0.8473 (tttt) cc_final: 0.8156 (tppt) REVERT: C 184 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8474 (tptp) REVERT: D 184 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8390 (mmmt) REVERT: D 210 GLN cc_start: 0.6273 (tm-30) cc_final: 0.5966 (tm-30) REVERT: D 297 HIS cc_start: 0.4487 (OUTLIER) cc_final: 0.4145 (m90) outliers start: 16 outliers final: 10 residues processed: 171 average time/residue: 0.0789 time to fit residues: 19.7253 Evaluate side-chains 162 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 297 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 23 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS B 312 GLN C 296 HIS D 312 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.214311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.168510 restraints weight = 12804.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.171677 restraints weight = 9561.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.172725 restraints weight = 7464.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.173098 restraints weight = 5657.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.173734 restraints weight = 5656.986| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10020 Z= 0.183 Angle : 0.604 10.593 13608 Z= 0.298 Chirality : 0.043 0.154 1516 Planarity : 0.004 0.052 1720 Dihedral : 4.724 42.948 1322 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.56 % Favored : 96.11 % Rotamer: Outliers : 1.59 % Allowed : 25.47 % Favored : 72.94 % 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: 1.96 (0.25), residues: 1208 helix: 2.34 (0.26), residues: 368 sheet: 1.35 (0.30), residues: 236 loop : 0.74 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 203 TYR 0.010 0.001 TYR A 244 PHE 0.024 0.002 PHE C 71 TRP 0.011 0.002 TRP D 75 HIS 0.008 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (10016) covalent geometry : angle 0.60368 / 0.30 (13600) SS BOND : bond 0.00581 / 0.29 ( 4) SS BOND : angle 0.47856 / 0.26 ( 8) hydrogen bonds : bond 0.04850 / 3.06 ( 449) hydrogen bonds : angle 4.16161 / 3.01 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.369 Fit side-chains REVERT: A 181 MET cc_start: 0.6888 (mpp) cc_final: 0.6688 (mpp) REVERT: B 297 HIS cc_start: 0.4655 (OUTLIER) cc_final: 0.4034 (m90) REVERT: C 184 LYS cc_start: 0.8702 (mmmt) cc_final: 0.8348 (tptp) REVERT: D 164 LYS cc_start: 0.7882 (tppt) cc_final: 0.7550 (tttt) REVERT: D 210 GLN cc_start: 0.6270 (tm-30) cc_final: 0.5975 (tm-30) REVERT: D 297 HIS cc_start: 0.4641 (OUTLIER) cc_final: 0.3587 (m-70) outliers start: 17 outliers final: 14 residues processed: 159 average time/residue: 0.0893 time to fit residues: 20.2786 Evaluate side-chains 158 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 297 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 53 optimal weight: 0.0870 chunk 111 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 113 optimal weight: 0.0370 chunk 16 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN D 312 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.216517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.177269 restraints weight = 13015.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.181406 restraints weight = 10102.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.181641 restraints weight = 7903.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.182151 restraints weight = 5621.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.182647 restraints weight = 5161.355| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10020 Z= 0.097 Angle : 0.537 10.753 13608 Z= 0.261 Chirality : 0.041 0.133 1516 Planarity : 0.004 0.039 1720 Dihedral : 4.374 40.148 1322 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.32 % Favored : 97.35 % Rotamer: Outliers : 1.69 % Allowed : 25.66 % Favored : 72.66 % 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: 2.07 (0.25), residues: 1208 helix: 2.71 (0.27), residues: 368 sheet: 1.17 (0.30), residues: 244 loop : 0.71 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 203 TYR 0.012 0.001 TYR A 311 PHE 0.010 0.001 PHE B 156 TRP 0.009 0.001 TRP C 53 HIS 0.004 0.000 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (10016) covalent geometry : angle 0.53732 / 0.26 (13600) SS BOND : bond 0.00251 / 0.13 ( 4) SS BOND : angle 0.27516 / 0.16 ( 8) hydrogen bonds : bond 0.03823 / 2.41 ( 449) hydrogen bonds : angle 3.95515 / 2.83 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1536.44 seconds wall clock time: 27 minutes 16.33 seconds (1636.33 seconds total)