Starting phenix.real_space_refine on Thu Sep 18 17:48:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i2n_0333/09_2025/6i2n_0333.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i2n_0333/09_2025/6i2n_0333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6i2n_0333/09_2025/6i2n_0333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i2n_0333/09_2025/6i2n_0333.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6i2n_0333/09_2025/6i2n_0333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i2n_0333/09_2025/6i2n_0333.map" } resolution = 3.3 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= 0.002 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 P 21 5.49 5 S 119 5.16 5 C 11907 2.51 5 N 3269 2.21 5 O 3654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18970 Number of models: 1 Model: "" Number of chains: 2 Chain: "U" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "D" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2650 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Restraints were copied for chains: A, C, F, H, J, L, B, E, G, I, K, M Time building chain proxies: 2.62, per 1000 atoms: 0.14 Number of scatterers: 18970 At special positions: 0 Unit cell: (106.7, 105.633, 190.993, 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) S 119 16.00 P 21 15.00 O 3654 8.00 N 3269 7.00 C 11907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 882.9 milliseconds Enol-peptide restraints added in 1.7 microseconds 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4424 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 0 sheets defined 50.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'D' and resid 121 through 128 removed outlier: 3.794A pdb=" N SER D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 142 Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 207 through 213 Processing helix chain 'D' and resid 218 through 221 No H-bonds generated for 'chain 'D' and resid 218 through 221' Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 232 through 240 removed outlier: 3.741A pdb=" N GLU D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 279 through 291 removed outlier: 3.518A pdb=" N ALA D 290 " --> pdb=" O GLN D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 308 No H-bonds generated for 'chain 'D' and resid 305 through 308' Processing helix chain 'D' and resid 326 through 346 Processing helix chain 'D' and resid 351 through 357 Processing helix chain 'D' and resid 361 through 372 removed outlier: 4.046A pdb=" N MET D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 404 through 421 Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.795A pdb=" N SER B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 218 through 221 No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 232 through 240 removed outlier: 3.741A pdb=" N GLU B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 279 through 291 removed outlier: 3.518A pdb=" N ALA B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 308 No H-bonds generated for 'chain 'B' and resid 305 through 308' Processing helix chain 'B' and resid 326 through 346 Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 361 through 372 removed outlier: 4.047A pdb=" N MET B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 388 Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 404 through 421 Processing helix chain 'E' and resid 121 through 128 removed outlier: 3.793A pdb=" N SER E 128 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 142 Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 207 through 213 Processing helix chain 'E' and resid 218 through 221 No H-bonds generated for 'chain 'E' and resid 218 through 221' Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'E' and resid 232 through 240 removed outlier: 3.741A pdb=" N GLU E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 275 Processing helix chain 'E' and resid 279 through 291 removed outlier: 3.518A pdb=" N ALA E 290 " --> pdb=" O GLN E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 308 No H-bonds generated for 'chain 'E' and resid 305 through 308' Processing helix chain 'E' and resid 326 through 346 Processing helix chain 'E' and resid 351 through 357 Processing helix chain 'E' and resid 361 through 372 removed outlier: 4.047A pdb=" N MET E 372 " --> pdb=" O ARG E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 388 Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 404 through 421 Processing helix chain 'G' and resid 121 through 128 removed outlier: 3.794A pdb=" N SER G 128 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 142 Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'G' and resid 195 through 205 Processing helix chain 'G' and resid 207 through 213 Processing helix chain 'G' and resid 218 through 221 No H-bonds generated for 'chain 'G' and resid 218 through 221' Processing helix chain 'G' and resid 225 through 230 Processing helix chain 'G' and resid 232 through 240 removed outlier: 3.741A pdb=" N GLU G 237 " --> pdb=" O SER G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 275 Processing helix chain 'G' and resid 279 through 291 removed outlier: 3.519A pdb=" N ALA G 290 " --> pdb=" O GLN G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 308 No H-bonds generated for 'chain 'G' and resid 305 through 308' Processing helix chain 'G' and resid 326 through 346 Processing helix chain 'G' and resid 351 through 357 Processing helix chain 'G' and resid 361 through 372 removed outlier: 4.047A pdb=" N MET G 372 " --> pdb=" O ARG G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 388 Processing helix chain 'G' and resid 390 through 395 Processing helix chain 'G' and resid 404 through 421 Processing helix chain 'I' and resid 121 through 128 removed outlier: 3.794A pdb=" N SER I 128 " --> pdb=" O VAL I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 142 Processing helix chain 'I' and resid 145 through 151 Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 207 through 213 Processing helix chain 'I' and resid 218 through 221 No H-bonds generated for 'chain 'I' and resid 218 through 221' Processing helix chain 'I' and resid 225 through 230 Processing helix chain 'I' and resid 232 through 240 removed outlier: 3.742A pdb=" N GLU I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 275 Processing helix chain 'I' and resid 279 through 291 removed outlier: 3.518A pdb=" N ALA I 290 " --> pdb=" O GLN I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 305 through 308 No H-bonds generated for 'chain 'I' and resid 305 through 308' Processing helix chain 'I' and resid 326 through 346 Processing helix chain 'I' and resid 351 through 357 Processing helix chain 'I' and resid 361 through 372 removed outlier: 4.046A pdb=" N MET I 372 " --> pdb=" O ARG I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 378 through 388 Processing helix chain 'I' and resid 390 through 395 Processing helix chain 'I' and resid 404 through 421 Processing helix chain 'K' and resid 121 through 128 removed outlier: 3.795A pdb=" N SER K 128 " --> pdb=" O VAL K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 142 Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'K' and resid 195 through 205 Processing helix chain 'K' and resid 207 through 213 Processing helix chain 'K' and resid 218 through 221 No H-bonds generated for 'chain 'K' and resid 218 through 221' Processing helix chain 'K' and resid 225 through 230 Processing helix chain 'K' and resid 232 through 240 removed outlier: 3.741A pdb=" N GLU K 237 " --> pdb=" O SER K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 275 Processing helix chain 'K' and resid 279 through 291 removed outlier: 3.519A pdb=" N ALA K 290 " --> pdb=" O GLN K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 305 through 308 No H-bonds generated for 'chain 'K' and resid 305 through 308' Processing helix chain 'K' and resid 326 through 346 Processing helix chain 'K' and resid 351 through 357 Processing helix chain 'K' and resid 361 through 372 removed outlier: 4.045A pdb=" N MET K 372 " --> pdb=" O ARG K 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 388 Processing helix chain 'K' and resid 390 through 395 Processing helix chain 'K' and resid 404 through 421 Processing helix chain 'M' and resid 121 through 128 removed outlier: 3.794A pdb=" N SER M 128 " --> pdb=" O VAL M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 142 Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'M' and resid 195 through 205 Processing helix chain 'M' and resid 207 through 213 Processing helix chain 'M' and resid 218 through 221 No H-bonds generated for 'chain 'M' and resid 218 through 221' Processing helix chain 'M' and resid 225 through 230 Processing helix chain 'M' and resid 232 through 240 removed outlier: 3.741A pdb=" N GLU M 237 " --> pdb=" O SER M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 262 through 275 Processing helix chain 'M' and resid 279 through 291 removed outlier: 3.518A pdb=" N ALA M 290 " --> pdb=" O GLN M 286 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 308 No H-bonds generated for 'chain 'M' and resid 305 through 308' Processing helix chain 'M' and resid 326 through 346 Processing helix chain 'M' and resid 351 through 357 Processing helix chain 'M' and resid 361 through 372 removed outlier: 4.047A pdb=" N MET M 372 " --> pdb=" O ARG M 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 378 through 388 Processing helix chain 'M' and resid 390 through 395 Processing helix chain 'M' and resid 404 through 421 686 hydrogen bonds defined for protein. 2058 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: 2.71 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5038 1.33 - 1.45: 3200 1.45 - 1.57: 10872 1.57 - 1.69: 35 1.69 - 1.80: 203 Bond restraints: 19348 Sorted by residual: bond pdb=" C PHE G 129 " pdb=" N VAL G 130 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.42e-02 4.96e+03 2.37e+00 bond pdb=" C PHE E 129 " pdb=" N VAL E 130 " ideal model delta sigma weight residual 1.330 1.309 0.022 1.42e-02 4.96e+03 2.34e+00 bond pdb=" C PHE K 129 " pdb=" N VAL K 130 " ideal model delta sigma weight residual 1.330 1.309 0.022 1.42e-02 4.96e+03 2.30e+00 bond pdb=" C PHE I 129 " pdb=" N VAL I 130 " ideal model delta sigma weight residual 1.330 1.309 0.021 1.42e-02 4.96e+03 2.28e+00 bond pdb=" C PHE D 129 " pdb=" N VAL D 130 " ideal model delta sigma weight residual 1.330 1.309 0.021 1.42e-02 4.96e+03 2.24e+00 ... (remaining 19343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 25153 2.10 - 4.20: 886 4.20 - 6.30: 92 6.30 - 8.40: 56 8.40 - 10.50: 14 Bond angle restraints: 26201 Sorted by residual: angle pdb=" N VAL G 131 " pdb=" CA VAL G 131 " pdb=" C VAL G 131 " ideal model delta sigma weight residual 108.88 119.38 -10.50 2.16e+00 2.14e-01 2.36e+01 angle pdb=" N VAL E 131 " pdb=" CA VAL E 131 " pdb=" C VAL E 131 " ideal model delta sigma weight residual 108.88 119.37 -10.49 2.16e+00 2.14e-01 2.36e+01 angle pdb=" N VAL D 131 " pdb=" CA VAL D 131 " pdb=" C VAL D 131 " ideal model delta sigma weight residual 108.88 119.36 -10.48 2.16e+00 2.14e-01 2.36e+01 angle pdb=" N VAL K 131 " pdb=" CA VAL K 131 " pdb=" C VAL K 131 " ideal model delta sigma weight residual 108.88 119.35 -10.47 2.16e+00 2.14e-01 2.35e+01 angle pdb=" N VAL I 131 " pdb=" CA VAL I 131 " pdb=" C VAL I 131 " ideal model delta sigma weight residual 108.88 119.34 -10.46 2.16e+00 2.14e-01 2.35e+01 ... (remaining 26196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 11049 14.80 - 29.59: 634 29.59 - 44.39: 169 44.39 - 59.18: 48 59.18 - 73.98: 35 Dihedral angle restraints: 11935 sinusoidal: 5110 harmonic: 6825 Sorted by residual: dihedral pdb=" CA PHE I 165 " pdb=" C PHE I 165 " pdb=" N GLU I 166 " pdb=" CA GLU I 166 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE E 165 " pdb=" C PHE E 165 " pdb=" N GLU E 166 " pdb=" CA GLU E 166 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE G 165 " pdb=" C PHE G 165 " pdb=" N GLU G 166 " pdb=" CA GLU G 166 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 11932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1739 0.039 - 0.078: 875 0.078 - 0.117: 238 0.117 - 0.157: 81 0.157 - 0.196: 42 Chirality restraints: 2975 Sorted by residual: chirality pdb=" CG LEU G 413 " pdb=" CB LEU G 413 " pdb=" CD1 LEU G 413 " pdb=" CD2 LEU G 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CG LEU E 413 " pdb=" CB LEU E 413 " pdb=" CD1 LEU E 413 " pdb=" CD2 LEU E 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CG LEU M 413 " pdb=" CB LEU M 413 " pdb=" CD1 LEU M 413 " pdb=" CD2 LEU M 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 2972 not shown) Planarity restraints: 3297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 131 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO G 132 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO G 132 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 132 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 131 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO M 132 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO M 132 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO M 132 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 131 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO E 132 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 132 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 132 " -0.029 5.00e-02 4.00e+02 ... (remaining 3294 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6062 2.84 - 3.35: 18066 3.35 - 3.87: 30532 3.87 - 4.38: 35559 4.38 - 4.90: 60406 Nonbonded interactions: 150625 Sorted by model distance: nonbonded pdb=" OD1 ASP E 88 " pdb=" OH TYR E 98 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASP B 88 " pdb=" OH TYR B 98 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASP D 88 " pdb=" OH TYR D 98 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASP M 88 " pdb=" OH TYR M 98 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASP K 88 " pdb=" OH TYR K 98 " model vdw 2.323 3.040 ... (remaining 150620 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: 0.11 Found NCS groups: ncs_group { reference = chain 'U' selection = chain 'A' selection = chain 'C' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' } 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 individual isotropic 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: 5.660 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.100 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.007 0.060 19348 Z= 0.284 Angle : 0.970 10.499 26201 Z= 0.508 Chirality : 0.053 0.196 2975 Planarity : 0.007 0.051 3297 Dihedral : 11.929 73.978 7511 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.13), residues: 2324 helix: -2.47 (0.10), residues: 1316 sheet: -0.73 (0.43), residues: 112 loop : -2.64 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 197 TYR 0.028 0.003 TYR B 178 PHE 0.023 0.004 PHE M 384 TRP 0.018 0.004 TRP E 119 HIS 0.018 0.003 HIS K 89 Details of bonding type rmsd covalent geometry : bond 0.00689 (19348) covalent geometry : angle 0.97011 (26201) hydrogen bonds : bond 0.06763 ( 686) hydrogen bonds : angle 4.60283 ( 2058) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 348 VAL cc_start: 0.8873 (p) cc_final: 0.8526 (t) REVERT: B 109 ILE cc_start: 0.7388 (mt) cc_final: 0.7039 (mt) REVERT: B 406 LEU cc_start: 0.9048 (tm) cc_final: 0.8843 (tp) REVERT: E 88 ASP cc_start: 0.7881 (t70) cc_final: 0.6468 (t0) REVERT: E 136 LYS cc_start: 0.8294 (mttt) cc_final: 0.8007 (mttm) REVERT: G 88 ASP cc_start: 0.7383 (t70) cc_final: 0.6589 (t0) REVERT: G 183 ASN cc_start: 0.7801 (t0) cc_final: 0.7497 (t0) REVERT: G 343 MET cc_start: 0.8784 (mmm) cc_final: 0.8527 (mmm) REVERT: G 402 MET cc_start: 0.8335 (ttm) cc_final: 0.8016 (mtp) REVERT: K 415 ASP cc_start: 0.7601 (m-30) cc_final: 0.7231 (m-30) REVERT: M 340 ASN cc_start: 0.8497 (m-40) cc_final: 0.8282 (m-40) outliers start: 0 outliers final: 0 residues processed: 533 average time/residue: 0.1886 time to fit residues: 140.9628 Evaluate side-chains 267 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.1980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 287 HIS D 395 ASN B 270 GLN B 370 GLN E 270 GLN E 275 ASN E 395 ASN G 340 ASN G 395 ASN I 147 GLN I 340 ASN I 395 ASN K 395 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102640 restraints weight = 28740.720| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.53 r_work: 0.3133 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19348 Z= 0.107 Angle : 0.546 7.941 26201 Z= 0.271 Chirality : 0.039 0.147 2975 Planarity : 0.004 0.035 3297 Dihedral : 7.608 58.004 2863 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.71 % Allowed : 10.27 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.16), residues: 2324 helix: -0.54 (0.13), residues: 1316 sheet: -1.06 (0.43), residues: 126 loop : -1.97 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 93 TYR 0.024 0.001 TYR M 362 PHE 0.012 0.001 PHE G 384 TRP 0.010 0.001 TRP G 388 HIS 0.010 0.002 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00252 (19348) covalent geometry : angle 0.54579 (26201) hydrogen bonds : bond 0.03056 ( 686) hydrogen bonds : angle 3.41384 ( 2058) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 302 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 343 MET cc_start: 0.9293 (mmm) cc_final: 0.8876 (mmm) REVERT: D 352 GLU cc_start: 0.8006 (pm20) cc_final: 0.7726 (mp0) REVERT: D 385 MET cc_start: 0.9168 (tpp) cc_final: 0.8764 (tpp) REVERT: D 398 LEU cc_start: 0.8353 (mt) cc_final: 0.8065 (mt) REVERT: B 109 ILE cc_start: 0.7674 (mt) cc_final: 0.7460 (mt) REVERT: B 362 TYR cc_start: 0.9162 (t80) cc_final: 0.8934 (t80) REVERT: B 385 MET cc_start: 0.9027 (tpp) cc_final: 0.8562 (tpp) REVERT: B 414 ILE cc_start: 0.8977 (mt) cc_final: 0.8662 (mt) REVERT: E 91 LYS cc_start: 0.8623 (mmtp) cc_final: 0.8138 (mtmm) REVERT: E 136 LYS cc_start: 0.8991 (mttt) cc_final: 0.8703 (mmtt) REVERT: G 226 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8219 (tp) REVERT: G 298 ASP cc_start: 0.7771 (p0) cc_final: 0.7506 (p0) REVERT: I 168 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8731 (m) REVERT: I 220 MET cc_start: 0.8420 (mmt) cc_final: 0.8091 (mmt) REVERT: I 276 MET cc_start: 0.7745 (tmm) cc_final: 0.7481 (ppp) REVERT: I 385 MET cc_start: 0.9113 (tpp) cc_final: 0.8809 (tpp) REVERT: K 276 MET cc_start: 0.7275 (tmm) cc_final: 0.6897 (tmm) REVERT: K 338 MET cc_start: 0.8672 (mtp) cc_final: 0.8319 (mtm) REVERT: K 415 ASP cc_start: 0.8037 (m-30) cc_final: 0.7650 (m-30) REVERT: M 178 TYR cc_start: 0.8952 (m-80) cc_final: 0.8703 (m-80) REVERT: M 298 ASP cc_start: 0.7464 (p0) cc_final: 0.7210 (p0) REVERT: M 367 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7900 (mtm110) outliers start: 35 outliers final: 17 residues processed: 329 average time/residue: 0.1451 time to fit residues: 72.1280 Evaluate side-chains 268 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 249 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 39 optimal weight: 50.0000 chunk 128 optimal weight: 1.9990 chunk 200 optimal weight: 0.0070 chunk 53 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 chunk 134 optimal weight: 0.0370 chunk 76 optimal weight: 0.6980 overall best weight: 0.2076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 270 GLN E 275 ASN G 270 GLN I 270 GLN K 270 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104057 restraints weight = 28526.403| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.54 r_work: 0.3158 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19348 Z= 0.084 Angle : 0.495 7.126 26201 Z= 0.243 Chirality : 0.037 0.151 2975 Planarity : 0.004 0.033 3297 Dihedral : 7.004 57.975 2863 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.91 % Allowed : 11.94 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.17), residues: 2324 helix: 0.42 (0.14), residues: 1316 sheet: -0.83 (0.43), residues: 126 loop : -1.66 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 213 TYR 0.027 0.001 TYR M 362 PHE 0.011 0.001 PHE G 384 TRP 0.010 0.001 TRP E 388 HIS 0.010 0.002 HIS G 89 Details of bonding type rmsd covalent geometry : bond 0.00193 (19348) covalent geometry : angle 0.49480 (26201) hydrogen bonds : bond 0.02455 ( 686) hydrogen bonds : angle 3.10142 ( 2058) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 303 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 198 TYR cc_start: 0.9038 (t80) cc_final: 0.8776 (t80) REVERT: D 352 GLU cc_start: 0.7918 (pm20) cc_final: 0.7709 (mp0) REVERT: D 398 LEU cc_start: 0.8327 (mt) cc_final: 0.8121 (mt) REVERT: B 109 ILE cc_start: 0.7761 (mt) cc_final: 0.7470 (mt) REVERT: B 215 MET cc_start: 0.1740 (ttm) cc_final: 0.1434 (ttm) REVERT: B 276 MET cc_start: 0.8057 (ttp) cc_final: 0.7644 (tmm) REVERT: B 362 TYR cc_start: 0.9282 (t80) cc_final: 0.8982 (t80) REVERT: B 394 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8122 (t70) REVERT: B 414 ILE cc_start: 0.8946 (mt) cc_final: 0.8623 (mt) REVERT: E 136 LYS cc_start: 0.9001 (mttt) cc_final: 0.8738 (mmtt) REVERT: E 158 ARG cc_start: 0.8592 (mpp80) cc_final: 0.8216 (mtt90) REVERT: E 355 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8560 (mp) REVERT: G 120 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8224 (tm) REVERT: G 226 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8274 (tp) REVERT: G 379 ARG cc_start: 0.8323 (tpp-160) cc_final: 0.7994 (mmm160) REVERT: I 168 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8747 (m) REVERT: I 220 MET cc_start: 0.8251 (mmt) cc_final: 0.7885 (mmt) REVERT: I 355 LEU cc_start: 0.8810 (tp) cc_final: 0.8516 (mp) REVERT: K 276 MET cc_start: 0.7384 (tmm) cc_final: 0.7057 (tmm) REVERT: K 304 SER cc_start: 0.9207 (t) cc_final: 0.8966 (p) REVERT: K 415 ASP cc_start: 0.7927 (m-30) cc_final: 0.7725 (m-30) outliers start: 39 outliers final: 19 residues processed: 335 average time/residue: 0.1352 time to fit residues: 69.3168 Evaluate side-chains 292 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 226 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 85 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 147 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 24 optimal weight: 0.0040 chunk 210 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN E 287 HIS G 378 GLN M 287 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.102105 restraints weight = 28720.711| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.47 r_work: 0.3113 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19348 Z= 0.114 Angle : 0.521 7.322 26201 Z= 0.255 Chirality : 0.038 0.141 2975 Planarity : 0.003 0.034 3297 Dihedral : 6.977 58.048 2863 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.01 % Allowed : 13.06 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.17), residues: 2324 helix: 0.79 (0.15), residues: 1316 sheet: -0.71 (0.42), residues: 126 loop : -1.45 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 213 TYR 0.027 0.001 TYR M 362 PHE 0.009 0.001 PHE D 384 TRP 0.015 0.001 TRP E 388 HIS 0.010 0.002 HIS G 89 Details of bonding type rmsd covalent geometry : bond 0.00275 (19348) covalent geometry : angle 0.52135 (26201) hydrogen bonds : bond 0.02841 ( 686) hydrogen bonds : angle 3.13069 ( 2058) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 343 MET cc_start: 0.9251 (mmm) cc_final: 0.8892 (mmm) REVERT: D 366 LEU cc_start: 0.8812 (tp) cc_final: 0.8534 (tt) REVERT: B 362 TYR cc_start: 0.9331 (t80) cc_final: 0.9047 (t80) REVERT: B 414 ILE cc_start: 0.9003 (mt) cc_final: 0.8722 (mt) REVERT: E 158 ARG cc_start: 0.8563 (mpp80) cc_final: 0.8311 (mtt90) REVERT: G 362 TYR cc_start: 0.9112 (t80) cc_final: 0.8737 (t80) REVERT: I 168 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8753 (m) REVERT: K 276 MET cc_start: 0.7501 (tmm) cc_final: 0.7218 (tmm) REVERT: K 338 MET cc_start: 0.8845 (mtp) cc_final: 0.8538 (mtm) REVERT: K 415 ASP cc_start: 0.7980 (m-30) cc_final: 0.7761 (m-30) REVERT: M 131 VAL cc_start: 0.8967 (m) cc_final: 0.8689 (t) REVERT: M 220 MET cc_start: 0.8267 (mmm) cc_final: 0.8056 (mmt) outliers start: 41 outliers final: 28 residues processed: 293 average time/residue: 0.1366 time to fit residues: 61.3135 Evaluate side-chains 272 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 67 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 42 optimal weight: 30.0000 chunk 122 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN E 340 ASN I 340 ASN K 363 GLN M 287 HIS M 424 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.096969 restraints weight = 28862.344| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.56 r_work: 0.3052 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19348 Z= 0.172 Angle : 0.571 7.639 26201 Z= 0.283 Chirality : 0.040 0.141 2975 Planarity : 0.004 0.036 3297 Dihedral : 7.125 58.122 2863 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.30 % Allowed : 14.24 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.17), residues: 2324 helix: 0.87 (0.14), residues: 1316 sheet: -0.60 (0.41), residues: 126 loop : -1.27 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 197 TYR 0.025 0.002 TYR M 362 PHE 0.015 0.002 PHE D 129 TRP 0.016 0.001 TRP E 388 HIS 0.010 0.002 HIS G 89 Details of bonding type rmsd covalent geometry : bond 0.00422 (19348) covalent geometry : angle 0.57054 (26201) hydrogen bonds : bond 0.03419 ( 686) hydrogen bonds : angle 3.31082 ( 2058) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: D 366 LEU cc_start: 0.8922 (tp) cc_final: 0.8664 (tt) REVERT: B 276 MET cc_start: 0.8050 (tmm) cc_final: 0.7794 (tmm) REVERT: E 91 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8259 (mtmm) REVERT: E 136 LYS cc_start: 0.9035 (mttm) cc_final: 0.8754 (mmtt) REVERT: E 158 ARG cc_start: 0.8695 (mpp80) cc_final: 0.8399 (mtt90) REVERT: E 385 MET cc_start: 0.8934 (tpp) cc_final: 0.8302 (tpp) REVERT: G 362 TYR cc_start: 0.9191 (t80) cc_final: 0.8947 (t80) REVERT: I 168 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8765 (m) REVERT: I 415 ASP cc_start: 0.7793 (m-30) cc_final: 0.7525 (m-30) REVERT: K 276 MET cc_start: 0.7872 (tmm) cc_final: 0.7473 (tmm) REVERT: K 372 MET cc_start: 0.9111 (mtp) cc_final: 0.8856 (mtp) REVERT: M 131 VAL cc_start: 0.8952 (m) cc_final: 0.8682 (t) REVERT: M 240 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.7843 (mt) REVERT: M 295 MET cc_start: 0.6736 (mmm) cc_final: 0.6353 (mmm) outliers start: 47 outliers final: 32 residues processed: 278 average time/residue: 0.1446 time to fit residues: 61.2122 Evaluate side-chains 262 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 37 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097587 restraints weight = 28488.313| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.55 r_work: 0.3069 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19348 Z= 0.140 Angle : 0.542 8.407 26201 Z= 0.267 Chirality : 0.039 0.140 2975 Planarity : 0.003 0.037 3297 Dihedral : 7.037 58.068 2863 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.25 % Allowed : 13.99 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.17), residues: 2324 helix: 1.07 (0.14), residues: 1316 sheet: -0.41 (0.42), residues: 126 loop : -1.15 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 172 TYR 0.027 0.001 TYR M 362 PHE 0.011 0.001 PHE D 129 TRP 0.014 0.001 TRP E 388 HIS 0.010 0.002 HIS I 89 Details of bonding type rmsd covalent geometry : bond 0.00343 (19348) covalent geometry : angle 0.54209 (26201) hydrogen bonds : bond 0.03093 ( 686) hydrogen bonds : angle 3.29285 ( 2058) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 229 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 352 GLU cc_start: 0.7968 (pm20) cc_final: 0.7602 (mp0) REVERT: D 366 LEU cc_start: 0.8917 (tp) cc_final: 0.8681 (tt) REVERT: E 136 LYS cc_start: 0.9015 (mttm) cc_final: 0.8732 (mmtt) REVERT: E 158 ARG cc_start: 0.8631 (mpp80) cc_final: 0.8371 (mtt90) REVERT: E 385 MET cc_start: 0.8871 (tpp) cc_final: 0.8290 (tpp) REVERT: G 343 MET cc_start: 0.9433 (mmm) cc_final: 0.9201 (mmm) REVERT: I 131 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8650 (t) REVERT: I 168 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8770 (m) REVERT: I 415 ASP cc_start: 0.7774 (m-30) cc_final: 0.7502 (m-30) REVERT: K 276 MET cc_start: 0.7869 (tmm) cc_final: 0.7503 (tmm) REVERT: K 338 MET cc_start: 0.8896 (mtp) cc_final: 0.8618 (mtm) REVERT: K 372 MET cc_start: 0.9093 (mtp) cc_final: 0.8822 (mtp) REVERT: M 131 VAL cc_start: 0.8938 (m) cc_final: 0.8697 (t) REVERT: M 240 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.7895 (mt) REVERT: M 295 MET cc_start: 0.6705 (mmm) cc_final: 0.6328 (mmm) outliers start: 46 outliers final: 33 residues processed: 271 average time/residue: 0.1419 time to fit residues: 58.7736 Evaluate side-chains 266 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 89 HIS Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 129 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 214 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 184 optimal weight: 0.2980 chunk 47 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 120 optimal weight: 0.0370 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN M 287 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099673 restraints weight = 28514.690| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.56 r_work: 0.3099 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19348 Z= 0.099 Angle : 0.514 8.537 26201 Z= 0.251 Chirality : 0.037 0.140 2975 Planarity : 0.003 0.035 3297 Dihedral : 6.909 57.999 2863 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.20 % Allowed : 14.33 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.17), residues: 2324 helix: 1.31 (0.15), residues: 1309 sheet: -0.26 (0.43), residues: 126 loop : -1.07 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 379 TYR 0.026 0.001 TYR M 362 PHE 0.010 0.001 PHE D 384 TRP 0.011 0.001 TRP E 388 HIS 0.009 0.002 HIS I 89 Details of bonding type rmsd covalent geometry : bond 0.00237 (19348) covalent geometry : angle 0.51432 (26201) hydrogen bonds : bond 0.02669 ( 686) hydrogen bonds : angle 3.21088 ( 2058) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 245 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8765 (t) REVERT: D 198 TYR cc_start: 0.9077 (t80) cc_final: 0.8865 (t80) REVERT: D 343 MET cc_start: 0.9231 (mmm) cc_final: 0.8929 (mmm) REVERT: D 352 GLU cc_start: 0.7932 (pm20) cc_final: 0.7581 (mp0) REVERT: D 366 LEU cc_start: 0.8865 (tp) cc_final: 0.8631 (tt) REVERT: B 304 SER cc_start: 0.8879 (t) cc_final: 0.8427 (p) REVERT: E 136 LYS cc_start: 0.8991 (mttm) cc_final: 0.8740 (mmtt) REVERT: E 158 ARG cc_start: 0.8596 (mpp80) cc_final: 0.8357 (mtt90) REVERT: E 357 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.8936 (mtpt) REVERT: E 385 MET cc_start: 0.8819 (tpp) cc_final: 0.8302 (tpp) REVERT: G 343 MET cc_start: 0.9347 (mmm) cc_final: 0.9123 (mmm) REVERT: G 357 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8778 (mtpt) REVERT: G 379 ARG cc_start: 0.8330 (mmp80) cc_final: 0.7859 (mmm160) REVERT: I 95 MET cc_start: 0.8927 (mmp) cc_final: 0.8711 (mmm) REVERT: I 357 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8901 (mtpt) REVERT: K 276 MET cc_start: 0.7744 (tmm) cc_final: 0.7457 (tmm) REVERT: K 338 MET cc_start: 0.8869 (mtp) cc_final: 0.8583 (mtm) REVERT: K 372 MET cc_start: 0.9050 (mtp) cc_final: 0.8759 (mtp) REVERT: M 131 VAL cc_start: 0.8918 (m) cc_final: 0.8716 (t) REVERT: M 240 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7869 (mt) REVERT: M 295 MET cc_start: 0.6768 (mmm) cc_final: 0.6381 (mmm) outliers start: 45 outliers final: 32 residues processed: 284 average time/residue: 0.1496 time to fit residues: 64.7951 Evaluate side-chains 270 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain I residue 89 HIS Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 357 LYS Chi-restraints excluded: chain K residue 89 HIS Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 154 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 213 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 174 optimal weight: 0.0670 chunk 51 optimal weight: 0.6980 chunk 222 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN G 363 GLN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099231 restraints weight = 28583.897| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.56 r_work: 0.3091 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19348 Z= 0.114 Angle : 0.524 8.584 26201 Z= 0.258 Chirality : 0.038 0.139 2975 Planarity : 0.003 0.034 3297 Dihedral : 6.906 58.052 2863 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.20 % Allowed : 14.53 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.17), residues: 2324 helix: 1.39 (0.15), residues: 1309 sheet: -0.27 (0.43), residues: 126 loop : -0.99 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 146 TYR 0.026 0.001 TYR M 362 PHE 0.009 0.001 PHE I 129 TRP 0.011 0.001 TRP E 388 HIS 0.010 0.002 HIS I 89 Details of bonding type rmsd covalent geometry : bond 0.00274 (19348) covalent geometry : angle 0.52383 (26201) hydrogen bonds : bond 0.02791 ( 686) hydrogen bonds : angle 3.23813 ( 2058) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 HIS cc_start: 0.8983 (OUTLIER) cc_final: 0.8614 (p90) REVERT: D 188 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7638 (mtp) REVERT: D 198 TYR cc_start: 0.9109 (t80) cc_final: 0.8842 (t80) REVERT: D 343 MET cc_start: 0.9252 (mmm) cc_final: 0.8902 (mmm) REVERT: D 352 GLU cc_start: 0.7932 (pm20) cc_final: 0.7572 (mp0) REVERT: D 366 LEU cc_start: 0.8889 (tp) cc_final: 0.8644 (tt) REVERT: B 304 SER cc_start: 0.8870 (t) cc_final: 0.8440 (p) REVERT: E 136 LYS cc_start: 0.9003 (mttm) cc_final: 0.8751 (mmtt) REVERT: E 158 ARG cc_start: 0.8573 (mpp80) cc_final: 0.8335 (mtt90) REVERT: E 357 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8940 (mtpt) REVERT: E 385 MET cc_start: 0.8845 (tpp) cc_final: 0.8335 (tpp) REVERT: G 343 MET cc_start: 0.9334 (mmm) cc_final: 0.9111 (mmm) REVERT: G 357 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8791 (mtpt) REVERT: G 379 ARG cc_start: 0.8336 (mmp80) cc_final: 0.7873 (mmm160) REVERT: I 167 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7949 (t70) REVERT: I 357 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8936 (mtpt) REVERT: I 415 ASP cc_start: 0.7762 (m-30) cc_final: 0.7481 (m-30) REVERT: K 276 MET cc_start: 0.7794 (tmm) cc_final: 0.7572 (tmm) REVERT: K 338 MET cc_start: 0.8908 (mtp) cc_final: 0.8635 (mtm) REVERT: K 372 MET cc_start: 0.9060 (mtp) cc_final: 0.8771 (mtp) REVERT: M 240 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8175 (mt) REVERT: M 295 MET cc_start: 0.6844 (mmm) cc_final: 0.6449 (mmm) outliers start: 45 outliers final: 35 residues processed: 270 average time/residue: 0.1401 time to fit residues: 56.9085 Evaluate side-chains 265 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 HIS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain I residue 89 HIS Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 357 LYS Chi-restraints excluded: chain K residue 89 HIS Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 177 optimal weight: 0.5980 chunk 231 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN G 147 GLN M 287 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.129262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098214 restraints weight = 28577.795| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.56 r_work: 0.3071 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19348 Z= 0.136 Angle : 0.540 7.961 26201 Z= 0.266 Chirality : 0.039 0.148 2975 Planarity : 0.003 0.033 3297 Dihedral : 6.964 58.070 2863 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.30 % Allowed : 14.43 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.17), residues: 2324 helix: 1.42 (0.15), residues: 1309 sheet: -0.29 (0.43), residues: 126 loop : -1.00 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 367 TYR 0.024 0.001 TYR M 125 PHE 0.011 0.001 PHE D 129 TRP 0.012 0.001 TRP E 388 HIS 0.010 0.002 HIS I 89 Details of bonding type rmsd covalent geometry : bond 0.00330 (19348) covalent geometry : angle 0.53966 (26201) hydrogen bonds : bond 0.03025 ( 686) hydrogen bonds : angle 3.33025 ( 2058) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 229 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: D 188 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7710 (mtp) REVERT: D 352 GLU cc_start: 0.7935 (pm20) cc_final: 0.7582 (mp0) REVERT: D 366 LEU cc_start: 0.8919 (tp) cc_final: 0.8670 (tt) REVERT: B 304 SER cc_start: 0.8894 (t) cc_final: 0.8470 (p) REVERT: E 136 LYS cc_start: 0.8997 (mttm) cc_final: 0.8752 (mmtt) REVERT: E 158 ARG cc_start: 0.8602 (mpp80) cc_final: 0.8354 (mtt90) REVERT: E 355 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8641 (mp) REVERT: E 357 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.8897 (mtpp) REVERT: E 385 MET cc_start: 0.8868 (tpp) cc_final: 0.8344 (tpp) REVERT: G 357 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8780 (mtpt) REVERT: G 379 ARG cc_start: 0.8344 (mmp80) cc_final: 0.7888 (mmm160) REVERT: I 151 ASP cc_start: 0.7916 (m-30) cc_final: 0.7667 (m-30) REVERT: I 167 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7981 (t70) REVERT: I 357 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8939 (mtpt) REVERT: I 415 ASP cc_start: 0.7781 (m-30) cc_final: 0.7510 (m-30) REVERT: K 240 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8523 (mm) REVERT: K 338 MET cc_start: 0.8924 (mtp) cc_final: 0.8649 (mtm) REVERT: K 372 MET cc_start: 0.9082 (mtp) cc_final: 0.8795 (mtp) REVERT: M 240 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8185 (mt) REVERT: M 295 MET cc_start: 0.6875 (mmm) cc_final: 0.6490 (mmm) outliers start: 47 outliers final: 37 residues processed: 269 average time/residue: 0.1501 time to fit residues: 60.9835 Evaluate side-chains 272 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain I residue 89 HIS Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 357 LYS Chi-restraints excluded: chain K residue 89 HIS Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 87 optimal weight: 0.0000 chunk 204 optimal weight: 0.2980 chunk 182 optimal weight: 0.8980 chunk 171 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 80 optimal weight: 0.0010 chunk 2 optimal weight: 0.0670 chunk 216 optimal weight: 0.8980 chunk 189 optimal weight: 0.4980 chunk 207 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 overall best weight: 0.0906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN E 363 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105080 restraints weight = 28369.586| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.51 r_work: 0.3158 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19348 Z= 0.086 Angle : 0.504 9.680 26201 Z= 0.246 Chirality : 0.036 0.150 2975 Planarity : 0.003 0.043 3297 Dihedral : 6.773 57.935 2863 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.71 % Allowed : 15.17 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.18), residues: 2324 helix: 1.60 (0.15), residues: 1309 sheet: -0.13 (0.44), residues: 126 loop : -0.92 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 267 TYR 0.024 0.001 TYR M 362 PHE 0.010 0.001 PHE G 384 TRP 0.009 0.001 TRP M 388 HIS 0.014 0.002 HIS D 89 Details of bonding type rmsd covalent geometry : bond 0.00193 (19348) covalent geometry : angle 0.50442 (26201) hydrogen bonds : bond 0.02251 ( 686) hydrogen bonds : angle 3.15519 ( 2058) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 276 MET cc_start: 0.7747 (tmm) cc_final: 0.7529 (tmm) REVERT: D 352 GLU cc_start: 0.7884 (pm20) cc_final: 0.7529 (mp0) REVERT: D 366 LEU cc_start: 0.8826 (tp) cc_final: 0.8584 (tt) REVERT: B 91 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8504 (mppt) REVERT: B 304 SER cc_start: 0.8831 (t) cc_final: 0.8405 (p) REVERT: B 362 TYR cc_start: 0.9328 (t80) cc_final: 0.8948 (t80) REVERT: E 355 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8628 (mp) REVERT: E 357 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.8957 (mtpt) REVERT: E 385 MET cc_start: 0.8778 (tpp) cc_final: 0.8383 (tpp) REVERT: G 357 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8741 (mtpp) REVERT: G 379 ARG cc_start: 0.8287 (mmp80) cc_final: 0.7863 (mmm160) REVERT: I 357 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8987 (mtpt) REVERT: K 240 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8375 (mm) REVERT: K 338 MET cc_start: 0.8881 (mtp) cc_final: 0.8615 (mtm) REVERT: K 372 MET cc_start: 0.8955 (mtp) cc_final: 0.8670 (mtp) REVERT: M 231 ASP cc_start: 0.7387 (p0) cc_final: 0.6956 (p0) outliers start: 35 outliers final: 22 residues processed: 280 average time/residue: 0.1394 time to fit residues: 59.3053 Evaluate side-chains 263 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 357 LYS Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 83 optimal weight: 0.0470 chunk 225 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 170 optimal weight: 0.4980 chunk 78 optimal weight: 0.2980 chunk 191 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 189 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.132293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101814 restraints weight = 28707.892| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.54 r_work: 0.3102 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19348 Z= 0.109 Angle : 0.529 8.935 26201 Z= 0.257 Chirality : 0.038 0.150 2975 Planarity : 0.003 0.033 3297 Dihedral : 6.815 58.027 2863 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.61 % Allowed : 15.36 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.18), residues: 2324 helix: 1.55 (0.15), residues: 1316 sheet: -0.12 (0.44), residues: 126 loop : -0.83 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 267 TYR 0.025 0.001 TYR M 362 PHE 0.009 0.001 PHE G 384 TRP 0.010 0.001 TRP E 388 HIS 0.015 0.002 HIS D 89 Details of bonding type rmsd covalent geometry : bond 0.00263 (19348) covalent geometry : angle 0.52874 (26201) hydrogen bonds : bond 0.02634 ( 686) hydrogen bonds : angle 3.23261 ( 2058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3974.69 seconds wall clock time: 69 minutes 3.84 seconds (4143.84 seconds total)