Starting phenix.real_space_refine on Wed Feb 4 09:13:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nms_49554/02_2026/9nms_49554.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nms_49554/02_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_49554/02_2026/9nms_49554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nms_49554/02_2026/9nms_49554.map" model { file = "/net/cci-nas-00/data/ceres_data/9nms_49554/02_2026/9nms_49554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nms_49554/02_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.07, per 1000 atoms: 0.21 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: 0.61 Conformation dependent library (CDL) restraints added in 439.6 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: 0.22 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: 1.36 Time building geometry restraints manager: 0.89 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.200 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 covalent geometry : bond 0.00174 (10016) covalent geometry : angle 0.46693 (13600) SS BOND : bond 0.00504 ( 4) SS BOND : angle 0.64836 ( 8) hydrogen bonds : bond 0.21599 ( 449) hydrogen bonds : angle 6.30943 ( 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 : 0.386 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: 0.0864 time to fit residues: 28.6486 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 : 0.330 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4518 r_free = 0.4518 target = 0.219926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.179515 restraints weight = 12784.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.182896 restraints weight = 9095.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.183149 restraints weight = 8210.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.184239 restraints weight = 5538.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.184618 restraints weight = 4938.738| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10020 Z= 0.122 Angle : 0.540 6.781 13608 Z= 0.275 Chirality : 0.042 0.201 1516 Planarity : 0.004 0.033 1720 Dihedral : 6.356 59.541 1357 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.57 % Favored : 97.10 % Rotamer: Outliers : 4.59 % Allowed : 20.51 % Favored : 74.91 % 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: 1.85 (0.24), residues: 1208 helix: 2.36 (0.27), residues: 376 sheet: 1.20 (0.29), residues: 252 loop : 0.59 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 19 TYR 0.012 0.001 TYR D 244 PHE 0.014 0.001 PHE B 71 TRP 0.007 0.001 TRP B 53 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00274 (10016) covalent geometry : angle 0.53961 (13600) SS BOND : bond 0.00570 ( 4) SS BOND : angle 0.73560 ( 8) hydrogen bonds : bond 0.04940 ( 449) hydrogen bonds : angle 4.94824 ( 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 225 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6589 (mpp) REVERT: A 297 HIS cc_start: 0.4803 (OUTLIER) cc_final: 0.4051 (m90) REVERT: B 297 HIS cc_start: 0.4650 (OUTLIER) cc_final: 0.3810 (m90) REVERT: B 323 PRO cc_start: 0.6223 (Cg_endo) cc_final: 0.5507 (Cg_exo) REVERT: C 297 HIS cc_start: 0.4724 (OUTLIER) cc_final: 0.4010 (m90) REVERT: D 19 ARG cc_start: 0.5565 (OUTLIER) cc_final: 0.4723 (mtt-85) REVERT: D 210 GLN cc_start: 0.6413 (tm-30) cc_final: 0.6128 (tm-30) REVERT: D 297 HIS cc_start: 0.4634 (OUTLIER) cc_final: 0.3862 (m90) REVERT: D 323 PRO cc_start: 0.6173 (Cg_endo) cc_final: 0.5484 (Cg_exo) outliers start: 49 outliers final: 25 residues processed: 218 average time/residue: 0.0820 time to fit residues: 25.7521 Evaluate side-chains 184 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 81 optimal weight: 0.3980 chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 190 GLN B 26 HIS B 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.217711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.172012 restraints weight = 12843.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.174765 restraints weight = 9681.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.176155 restraints weight = 7323.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.176186 restraints weight = 5669.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.176627 restraints weight = 5801.467| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10020 Z= 0.136 Angle : 0.523 6.831 13608 Z= 0.265 Chirality : 0.042 0.190 1516 Planarity : 0.004 0.037 1720 Dihedral : 5.947 53.267 1343 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.98 % Favored : 96.69 % Rotamer: Outliers : 4.87 % Allowed : 21.35 % Favored : 73.78 % 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: 1.95 (0.24), residues: 1208 helix: 2.19 (0.27), residues: 376 sheet: 1.21 (0.30), residues: 244 loop : 0.88 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 19 TYR 0.008 0.001 TYR A 209 PHE 0.017 0.001 PHE B 71 TRP 0.008 0.001 TRP C 53 HIS 0.005 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00313 (10016) covalent geometry : angle 0.52226 (13600) SS BOND : bond 0.00605 ( 4) SS BOND : angle 1.01718 ( 8) hydrogen bonds : bond 0.04810 ( 449) hydrogen bonds : angle 4.62390 ( 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 218 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6757 (mpp) REVERT: A 297 HIS cc_start: 0.4835 (OUTLIER) cc_final: 0.3966 (m-70) REVERT: B 164 LYS cc_start: 0.8365 (tttt) cc_final: 0.8047 (tppt) REVERT: B 297 HIS cc_start: 0.4393 (OUTLIER) cc_final: 0.3240 (m-70) REVERT: B 323 PRO cc_start: 0.6246 (Cg_endo) cc_final: 0.6046 (Cg_exo) REVERT: C 210 GLN cc_start: 0.6415 (tm-30) cc_final: 0.6075 (tm-30) REVERT: C 297 HIS cc_start: 0.4802 (OUTLIER) cc_final: 0.3942 (m90) REVERT: D 210 GLN cc_start: 0.6454 (tm-30) cc_final: 0.6142 (tm-30) REVERT: D 297 HIS cc_start: 0.4424 (OUTLIER) cc_final: 0.3267 (m-70) outliers start: 52 outliers final: 33 residues processed: 201 average time/residue: 0.0837 time to fit residues: 23.7865 Evaluate side-chains 190 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL 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 19 ARG Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 VAL 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 287 SER Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 77 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 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 74 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 46 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 8 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN C 26 HIS C 190 GLN D 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.215048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.168845 restraints weight = 12921.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.170091 restraints weight = 9609.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.171474 restraints weight = 7823.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.172090 restraints weight = 5971.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.172547 restraints weight = 5782.900| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10020 Z= 0.120 Angle : 0.511 7.098 13608 Z= 0.258 Chirality : 0.042 0.199 1516 Planarity : 0.004 0.037 1720 Dihedral : 5.569 47.959 1339 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.06 % Favored : 96.61 % Rotamer: Outliers : 4.21 % Allowed : 23.31 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.24), residues: 1208 helix: 2.27 (0.27), residues: 376 sheet: 1.37 (0.30), residues: 248 loop : 0.73 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 203 TYR 0.009 0.001 TYR A 288 PHE 0.015 0.001 PHE B 71 TRP 0.008 0.001 TRP C 53 HIS 0.003 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00273 (10016) covalent geometry : angle 0.51126 (13600) SS BOND : bond 0.00371 ( 4) SS BOND : angle 0.58914 ( 8) hydrogen bonds : bond 0.04528 ( 449) hydrogen bonds : angle 4.43114 ( 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 204 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6710 (mpp) REVERT: A 297 HIS cc_start: 0.4844 (OUTLIER) cc_final: 0.4045 (m90) REVERT: B 164 LYS cc_start: 0.8406 (tttt) cc_final: 0.8062 (tppt) REVERT: B 297 HIS cc_start: 0.4547 (OUTLIER) cc_final: 0.3850 (m90) REVERT: B 323 PRO cc_start: 0.6395 (Cg_endo) cc_final: 0.5581 (Cg_exo) REVERT: C 297 HIS cc_start: 0.4825 (OUTLIER) cc_final: 0.4104 (m90) REVERT: D 194 THR cc_start: 0.8281 (p) cc_final: 0.8062 (t) REVERT: D 297 HIS cc_start: 0.4757 (OUTLIER) cc_final: 0.3975 (m90) outliers start: 45 outliers final: 28 residues processed: 191 average time/residue: 0.0848 time to fit residues: 22.6656 Evaluate side-chains 186 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 297 HIS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 51 MET 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 21 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 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 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 23 LYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 67 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN C 190 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.212962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.163048 restraints weight = 12996.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171698 restraints weight = 12209.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.171307 restraints weight = 6308.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.170994 restraints weight = 5420.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.171453 restraints weight = 5937.066| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10020 Z= 0.198 Angle : 0.587 8.349 13608 Z= 0.297 Chirality : 0.044 0.176 1516 Planarity : 0.004 0.038 1720 Dihedral : 5.918 48.246 1339 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.81 % Favored : 95.86 % Rotamer: Outliers : 5.06 % Allowed : 21.82 % 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: 1.84 (0.25), residues: 1208 helix: 1.89 (0.26), residues: 376 sheet: 1.45 (0.30), residues: 236 loop : 0.84 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 203 TYR 0.008 0.001 TYR D 122 PHE 0.021 0.002 PHE B 71 TRP 0.009 0.002 TRP A 53 HIS 0.006 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00469 (10016) covalent geometry : angle 0.58658 (13600) SS BOND : bond 0.00634 ( 4) SS BOND : angle 0.66432 ( 8) hydrogen bonds : bond 0.05428 ( 449) hydrogen bonds : angle 4.52607 ( 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 210 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6564 (mpp) REVERT: A 297 HIS cc_start: 0.4853 (OUTLIER) cc_final: 0.4089 (m90) REVERT: B 19 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.5113 (ptt180) REVERT: B 164 LYS cc_start: 0.8395 (tttt) cc_final: 0.8065 (tppt) REVERT: B 297 HIS cc_start: 0.4446 (OUTLIER) cc_final: 0.3377 (m-70) REVERT: B 323 PRO cc_start: 0.6437 (Cg_endo) cc_final: 0.6146 (Cg_exo) REVERT: C 210 GLN cc_start: 0.6331 (tm-30) cc_final: 0.6081 (tm-30) REVERT: C 297 HIS cc_start: 0.4890 (OUTLIER) cc_final: 0.4226 (m90) REVERT: D 19 ARG cc_start: 0.5831 (OUTLIER) cc_final: 0.4969 (ptt180) REVERT: D 210 GLN cc_start: 0.6371 (tm-30) cc_final: 0.6115 (tm-30) REVERT: D 297 HIS cc_start: 0.4715 (OUTLIER) cc_final: 0.3570 (m-70) REVERT: D 316 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7576 (tp30) outliers start: 54 outliers final: 36 residues processed: 188 average time/residue: 0.0859 time to fit residues: 22.4785 Evaluate side-chains 191 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 107 THR 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 19 ARG Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 77 VAL 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 271 LEU Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 107 THR 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 20 MET 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 107 THR 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: 10.0000 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 7 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN D 162 GLN D 312 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.216793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.167440 restraints weight = 13259.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173110 restraints weight = 12119.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174147 restraints weight = 7473.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.173842 restraints weight = 6055.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.174633 restraints weight = 6511.138| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10020 Z= 0.126 Angle : 0.529 8.405 13608 Z= 0.265 Chirality : 0.042 0.151 1516 Planarity : 0.004 0.038 1720 Dihedral : 5.544 43.663 1339 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.98 % Favored : 96.69 % Rotamer: Outliers : 4.40 % Allowed : 22.94 % 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: 1.93 (0.25), residues: 1208 helix: 2.16 (0.27), residues: 376 sheet: 1.44 (0.30), residues: 236 loop : 0.76 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 203 TYR 0.006 0.001 TYR B 243 PHE 0.015 0.001 PHE C 71 TRP 0.009 0.001 TRP C 53 HIS 0.003 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00288 (10016) covalent geometry : angle 0.52900 (13600) SS BOND : bond 0.00410 ( 4) SS BOND : angle 0.37088 ( 8) hydrogen bonds : bond 0.04723 ( 449) hydrogen bonds : angle 4.32109 ( 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 200 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6627 (mpp) REVERT: A 297 HIS cc_start: 0.4847 (OUTLIER) cc_final: 0.4297 (m90) REVERT: B 297 HIS cc_start: 0.4481 (OUTLIER) cc_final: 0.3452 (m-70) REVERT: B 323 PRO cc_start: 0.6479 (Cg_endo) cc_final: 0.5959 (Cg_exo) REVERT: C 210 GLN cc_start: 0.6295 (tm-30) cc_final: 0.6020 (tm-30) REVERT: C 297 HIS cc_start: 0.4744 (OUTLIER) cc_final: 0.4324 (m90) REVERT: D 297 HIS cc_start: 0.4643 (OUTLIER) cc_final: 0.3531 (m-70) outliers start: 47 outliers final: 36 residues processed: 186 average time/residue: 0.0920 time to fit residues: 23.8502 Evaluate side-chains 192 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 107 THR 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 282 CYS Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 23 LYS 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 107 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 246 SER 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 21 VAL Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 77 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4498 r_free = 0.4498 target = 0.217431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.177030 restraints weight = 12778.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.182799 restraints weight = 9217.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.181536 restraints weight = 7632.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.182089 restraints weight = 5370.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.182550 restraints weight = 4923.849| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10020 Z= 0.102 Angle : 0.512 8.948 13608 Z= 0.254 Chirality : 0.041 0.160 1516 Planarity : 0.004 0.042 1720 Dihedral : 5.079 40.985 1331 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.15 % Favored : 96.52 % Rotamer: Outliers : 2.62 % Allowed : 24.91 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.25), residues: 1208 helix: 2.39 (0.27), residues: 376 sheet: 1.27 (0.30), residues: 248 loop : 0.63 (0.28), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 203 TYR 0.010 0.001 TYR A 244 PHE 0.011 0.001 PHE C 71 TRP 0.008 0.001 TRP B 53 HIS 0.002 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00224 (10016) covalent geometry : angle 0.51205 (13600) SS BOND : bond 0.00269 ( 4) SS BOND : angle 0.27620 ( 8) hydrogen bonds : bond 0.04244 ( 449) hydrogen bonds : angle 4.15668 ( 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 188 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 HIS cc_start: 0.4599 (OUTLIER) cc_final: 0.4282 (m90) REVERT: B 184 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8543 (mmmt) REVERT: B 297 HIS cc_start: 0.4509 (OUTLIER) cc_final: 0.3624 (m-70) REVERT: B 323 PRO cc_start: 0.6497 (Cg_endo) cc_final: 0.6015 (Cg_exo) REVERT: C 297 HIS cc_start: 0.4667 (OUTLIER) cc_final: 0.4445 (m90) REVERT: D 210 GLN cc_start: 0.6179 (tm-30) cc_final: 0.5913 (tm-30) REVERT: D 297 HIS cc_start: 0.4612 (OUTLIER) cc_final: 0.3646 (m-70) outliers start: 28 outliers final: 21 residues processed: 183 average time/residue: 0.0812 time to fit residues: 21.0713 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 : 0.364 ------------------------------------------------------------------------------- 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 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 268 VAL Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 74 LEU 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 D residue 21 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 74 LEU 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 282 CYS 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: 7.9990 chunk 71 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 0.0020 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.214384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.175797 restraints weight = 12749.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.178937 restraints weight = 9581.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.179673 restraints weight = 7885.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.180209 restraints weight = 5465.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.180838 restraints weight = 5055.968| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10020 Z= 0.102 Angle : 0.518 9.352 13608 Z= 0.256 Chirality : 0.041 0.136 1516 Planarity : 0.004 0.050 1720 Dihedral : 4.981 40.118 1331 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.65 % Favored : 97.02 % Rotamer: Outliers : 3.00 % Allowed : 24.44 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.25), residues: 1208 helix: 2.45 (0.27), residues: 376 sheet: 1.27 (0.30), residues: 244 loop : 0.86 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 203 TYR 0.007 0.001 TYR B 243 PHE 0.012 0.001 PHE B 71 TRP 0.008 0.001 TRP B 53 HIS 0.002 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00229 (10016) covalent geometry : angle 0.51841 (13600) SS BOND : bond 0.00362 ( 4) SS BOND : angle 0.27590 ( 8) hydrogen bonds : bond 0.04099 ( 449) hydrogen bonds : angle 4.06707 ( 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 188 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6740 (mpp) REVERT: B 297 HIS cc_start: 0.4493 (OUTLIER) cc_final: 0.3560 (m-70) REVERT: D 210 GLN cc_start: 0.6245 (tm-30) cc_final: 0.5970 (tm-30) REVERT: D 297 HIS cc_start: 0.4612 (OUTLIER) cc_final: 0.4264 (m90) outliers start: 32 outliers final: 23 residues processed: 184 average time/residue: 0.0774 time to fit residues: 20.3423 Evaluate side-chains 178 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 181 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 268 VAL 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 282 CYS Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 74 LEU 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 246 SER Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 77 VAL 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: 9.9990 chunk 114 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 312 GLN C 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.215918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.167107 restraints weight = 12693.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.167664 restraints weight = 8014.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.168796 restraints weight = 7369.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.169844 restraints weight = 5893.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.170157 restraints weight = 5633.003| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10020 Z= 0.120 Angle : 0.540 10.424 13608 Z= 0.265 Chirality : 0.042 0.140 1516 Planarity : 0.004 0.052 1720 Dihedral : 4.688 40.205 1326 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.48 % Favored : 96.19 % Rotamer: Outliers : 2.72 % Allowed : 24.63 % 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: 2.04 (0.25), residues: 1208 helix: 2.37 (0.27), residues: 376 sheet: 1.27 (0.30), residues: 244 loop : 0.85 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 203 TYR 0.010 0.001 TYR A 244 PHE 0.015 0.001 PHE C 71 TRP 0.007 0.001 TRP B 53 HIS 0.003 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00277 (10016) covalent geometry : angle 0.53965 (13600) SS BOND : bond 0.00412 ( 4) SS BOND : angle 0.26710 ( 8) hydrogen bonds : bond 0.04296 ( 449) hydrogen bonds : angle 4.08061 ( 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 182 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6846 (mpp) REVERT: B 297 HIS cc_start: 0.4700 (OUTLIER) cc_final: 0.3748 (m-70) REVERT: D 210 GLN cc_start: 0.6145 (tm-30) cc_final: 0.5869 (tm-30) REVERT: D 297 HIS cc_start: 0.4825 (OUTLIER) cc_final: 0.3919 (m-70) outliers start: 29 outliers final: 24 residues processed: 177 average time/residue: 0.0832 time to fit residues: 20.9381 Evaluate side-chains 179 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 181 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 268 VAL 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 282 CYS Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain C residue 74 LEU 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 23 LYS Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 77 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 23 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 0.0570 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.212483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.168845 restraints weight = 13058.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.169757 restraints weight = 9872.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.171039 restraints weight = 9300.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.171687 restraints weight = 6199.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.172591 restraints weight = 5641.627| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10020 Z= 0.209 Angle : 0.636 10.807 13608 Z= 0.317 Chirality : 0.044 0.157 1516 Planarity : 0.005 0.072 1720 Dihedral : 5.301 44.450 1326 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.30 % Favored : 95.36 % Rotamer: Outliers : 3.65 % Allowed : 23.78 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.24), residues: 1208 helix: 1.81 (0.26), residues: 376 sheet: 1.25 (0.30), residues: 236 loop : 0.68 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 203 TYR 0.008 0.001 TYR A 122 PHE 0.024 0.002 PHE C 71 TRP 0.015 0.002 TRP A 55 HIS 0.006 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00499 (10016) covalent geometry : angle 0.63637 (13600) SS BOND : bond 0.00660 ( 4) SS BOND : angle 0.57933 ( 8) hydrogen bonds : bond 0.05505 ( 449) hydrogen bonds : angle 4.40806 ( 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 192 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6934 (mpp) REVERT: B 297 HIS cc_start: 0.4720 (OUTLIER) cc_final: 0.3721 (m-70) REVERT: C 210 GLN cc_start: 0.6026 (tm-30) cc_final: 0.5723 (tm-30) REVERT: D 297 HIS cc_start: 0.4879 (OUTLIER) cc_final: 0.3941 (m-70) outliers start: 39 outliers final: 29 residues processed: 181 average time/residue: 0.0856 time to fit residues: 21.6180 Evaluate side-chains 183 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 107 THR 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 B residue 51 MET Chi-restraints excluded: chain B residue 77 VAL 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 282 CYS Chi-restraints excluded: chain B residue 297 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 23 LYS 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 246 SER Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain D residue 20 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 111 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 56 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4493 r_free = 0.4493 target = 0.216426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.176392 restraints weight = 12807.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.180187 restraints weight = 9082.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.180528 restraints weight = 7698.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.181202 restraints weight = 5234.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.181840 restraints weight = 4758.805| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10020 Z= 0.105 Angle : 0.555 10.952 13608 Z= 0.271 Chirality : 0.041 0.138 1516 Planarity : 0.004 0.042 1720 Dihedral : 4.729 40.563 1326 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.06 % Favored : 96.61 % Rotamer: Outliers : 2.34 % Allowed : 25.37 % Favored : 72.28 % 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: 2.00 (0.25), residues: 1208 helix: 2.38 (0.27), residues: 376 sheet: 1.33 (0.30), residues: 236 loop : 0.76 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 203 TYR 0.007 0.001 TYR C 243 PHE 0.011 0.001 PHE B 156 TRP 0.009 0.001 TRP B 53 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00231 (10016) covalent geometry : angle 0.55472 (13600) SS BOND : bond 0.00301 ( 4) SS BOND : angle 0.30728 ( 8) hydrogen bonds : bond 0.04159 ( 449) hydrogen bonds : angle 4.10631 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1356.68 seconds wall clock time: 24 minutes 5.72 seconds (1445.72 seconds total)