Starting phenix.real_space_refine on Sat Sep 12 22:25:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6i2n_0333/09_2026/6i2n_0333.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i2n_0333/09_2026/6i2n_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6i2n_0333/09_2026/6i2n_0333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i2n_0333/09_2026/6i2n_0333.map" model { file = "/net/cci-nas-00/data/ceres_data/6i2n_0333/09_2026/6i2n_0333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i2n_0333/09_2026/6i2n_0333.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6i2n_0333/09_2026/6i2n_0333.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6i2n_0333/09_2026/6i2n_0333.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 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: 3.00, per 1000 atoms: 0.16 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: 1.60 Conformation dependent library (CDL) restraints added in 774.7 milliseconds 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: 0.41 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: 2.80 Time building geometry restraints manager: 2.09 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: 25111 2.10 - 4.20: 928 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: 11007 14.80 - 29.59: 627 29.59 - 44.39: 161 44.39 - 59.18: 21 59.18 - 73.98: 35 Dihedral angle restraints: 11851 sinusoidal: 5026 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 11848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2076 0.051 - 0.102: 659 0.102 - 0.153: 171 0.153 - 0.204: 48 0.204 - 0.255: 21 Chirality restraints: 2975 Sorted by residual: chirality pdb=" P U L 1 " pdb=" OP1 U L 1 " pdb=" OP2 U L 1 " pdb=" O5' U L 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" P U F 1 " pdb=" OP1 U F 1 " pdb=" OP2 U F 1 " pdb=" O5' U F 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" P U A 1 " pdb=" OP1 U A 1 " pdb=" OP2 U A 1 " pdb=" O5' U A 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (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: 0.07 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.910 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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= 0.285 Angle : 0.977 10.499 26201 Z= 0.509 Chirality : 0.057 0.255 2975 Planarity : 0.007 0.051 3297 Dihedral : 11.326 73.978 7427 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 are 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/Z covalent geometry : bond 0.00690 / 0.28 (19348) covalent geometry : angle 0.97699 / 0.51 (26201) hydrogen bonds : bond 0.06763 / 4.72 ( 686) hydrogen bonds : angle 4.60283 / 3.17 ( 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 : 0.755 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: 0.8842 (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: 0.1863 time to fit residues: 141.0583 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 : 0.802 ------------------------------------------------------------------------------- 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... 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 = 0.3678 r_free = 0.3678 target = 0.133766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102817 restraints weight = 28707.465| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.54 r_work: 0.3133 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19348 Z= 0.107 Angle : 0.549 7.863 26201 Z= 0.271 Chirality : 0.039 0.149 2975 Planarity : 0.004 0.037 3297 Dihedral : 5.359 45.750 2779 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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 are not related in a simple way. whole: -1.69 (0.16), residues: 2324 helix: -0.51 (0.13), residues: 1316 sheet: -1.03 (0.43), residues: 126 loop : -1.96 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 93 TYR 0.026 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 I 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (19348) covalent geometry : angle 0.54857 / 0.27 (26201) hydrogen bonds : bond 0.03008 / 1.94 ( 686) hydrogen bonds : angle 3.40307 / 2.36 ( 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 338 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 303 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 343 MET cc_start: 0.9292 (mmm) cc_final: 0.8875 (mmm) REVERT: D 352 GLU cc_start: 0.8001 (pm20) cc_final: 0.7739 (mp0) REVERT: D 385 MET cc_start: 0.9176 (tpp) cc_final: 0.8771 (tpp) REVERT: D 398 LEU cc_start: 0.8356 (mt) cc_final: 0.8072 (mt) REVERT: B 109 ILE cc_start: 0.7675 (mt) cc_final: 0.7372 (mt) REVERT: B 362 TYR cc_start: 0.9186 (t80) cc_final: 0.8964 (t80) REVERT: B 385 MET cc_start: 0.9021 (tpp) cc_final: 0.8566 (tpp) REVERT: B 414 ILE cc_start: 0.8972 (mt) cc_final: 0.8658 (mt) REVERT: E 91 LYS cc_start: 0.8649 (mmtp) cc_final: 0.8168 (mtmm) REVERT: E 136 LYS cc_start: 0.8991 (mttt) cc_final: 0.8707 (mmtt) REVERT: G 226 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8212 (tp) REVERT: G 298 ASP cc_start: 0.7742 (p0) cc_final: 0.7482 (p0) REVERT: I 168 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8733 (m) REVERT: I 220 MET cc_start: 0.8420 (mmt) cc_final: 0.8093 (mmt) REVERT: I 276 MET cc_start: 0.7762 (tmm) cc_final: 0.7503 (ppp) REVERT: I 385 MET cc_start: 0.9106 (tpp) cc_final: 0.8816 (tpp) REVERT: I 415 ASP cc_start: 0.7825 (m-30) cc_final: 0.7576 (m-30) REVERT: K 276 MET cc_start: 0.7288 (tmm) cc_final: 0.6905 (tmm) REVERT: K 338 MET cc_start: 0.8674 (mtp) cc_final: 0.8326 (mtm) REVERT: K 415 ASP cc_start: 0.8035 (m-30) cc_final: 0.7647 (m-30) REVERT: M 178 TYR cc_start: 0.8957 (m-80) cc_final: 0.8702 (m-80) REVERT: M 298 ASP cc_start: 0.7444 (p0) cc_final: 0.7190 (p0) REVERT: M 367 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7887 (mtm110) outliers start: 35 outliers final: 18 residues processed: 330 average time/residue: 0.1491 time to fit residues: 75.5927 Evaluate side-chains 271 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 168 VAL 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: 0.0980 chunk 39 optimal weight: 40.0000 chunk 128 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 99 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 134 optimal weight: 0.2980 chunk 76 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 270 GLN E 275 ASN ** 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 = 0.3659 r_free = 0.3659 target = 0.132310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101074 restraints weight = 28744.682| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.55 r_work: 0.3107 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19348 Z= 0.108 Angle : 0.525 7.214 26201 Z= 0.257 Chirality : 0.039 0.144 2975 Planarity : 0.004 0.035 3297 Dihedral : 5.052 46.756 2779 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.20 % Allowed : 12.13 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2324 helix: 0.38 (0.14), residues: 1316 sheet: -0.23 (0.46), residues: 112 loop : -1.70 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 213 TYR 0.026 0.001 TYR M 362 PHE 0.011 0.001 PHE G 384 TRP 0.011 0.001 TRP E 388 HIS 0.011 0.002 HIS G 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (19348) covalent geometry : angle 0.52470 / 0.26 (26201) hydrogen bonds : bond 0.02909 / 1.88 ( 686) hydrogen bonds : angle 3.18392 / 2.20 ( 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 303 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 429 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8327 (tp) REVERT: B 276 MET cc_start: 0.8053 (ttp) cc_final: 0.7641 (tmm) REVERT: B 362 TYR cc_start: 0.9297 (t80) cc_final: 0.8971 (t80) REVERT: B 414 ILE cc_start: 0.9001 (mt) cc_final: 0.8724 (mt) REVERT: E 136 LYS cc_start: 0.9038 (mttt) cc_final: 0.8756 (mmtt) REVERT: E 158 ARG cc_start: 0.8639 (mpp80) cc_final: 0.8302 (mtt90) REVERT: E 385 MET cc_start: 0.8671 (tpp) cc_final: 0.8430 (tpp) REVERT: G 226 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8288 (tp) REVERT: I 168 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8737 (m) REVERT: I 385 MET cc_start: 0.9048 (tpp) cc_final: 0.8817 (tpp) REVERT: K 188 MET cc_start: 0.7954 (mmm) cc_final: 0.7672 (mmm) REVERT: K 276 MET cc_start: 0.7524 (tmm) cc_final: 0.7152 (tmm) REVERT: K 338 MET cc_start: 0.8873 (mtp) cc_final: 0.8579 (mtm) REVERT: M 165 PHE cc_start: 0.7777 (m-10) cc_final: 0.7523 (m-10) REVERT: M 367 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7856 (mtm110) outliers start: 45 outliers final: 25 residues processed: 295 average time/residue: 0.1536 time to fit residues: 68.9156 Evaluate side-chains 276 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 D residue 429 LEU 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 E residue 394 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 226 LEU 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 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 318 THR 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 Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 40 optimal weight: 50.0000 chunk 172 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 275 ASN E 340 ASN G 363 GLN G 378 GLN I 363 GLN M 287 HIS M 424 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.128051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.096796 restraints weight = 29332.748| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.55 r_work: 0.3023 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 19348 Z= 0.228 Angle : 0.639 8.269 26201 Z= 0.316 Chirality : 0.043 0.141 2975 Planarity : 0.004 0.041 3297 Dihedral : 5.561 52.410 2779 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.20 % Allowed : 13.94 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2324 helix: 0.43 (0.14), residues: 1316 sheet: -0.88 (0.42), residues: 126 loop : -1.49 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 356 TYR 0.026 0.002 TYR M 362 PHE 0.026 0.002 PHE D 129 TRP 0.013 0.002 TRP E 388 HIS 0.010 0.002 HIS I 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.23 (19348) covalent geometry : angle 0.63855 / 0.32 (26201) hydrogen bonds : bond 0.04038 / 2.61 ( 686) hydrogen bonds : angle 3.54922 / 2.42 ( 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 292 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 343 MET cc_start: 0.9224 (mmm) cc_final: 0.8948 (mmm) REVERT: D 366 LEU cc_start: 0.8934 (tp) cc_final: 0.8683 (tt) REVERT: D 429 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8304 (tp) REVERT: B 215 MET cc_start: 0.1699 (ttm) cc_final: 0.1494 (ttm) REVERT: B 362 TYR cc_start: 0.9337 (t80) cc_final: 0.9002 (t80) REVERT: E 136 LYS cc_start: 0.9011 (mttt) cc_final: 0.8767 (mmtt) REVERT: E 158 ARG cc_start: 0.8672 (mpp80) cc_final: 0.8379 (mtt90) REVERT: E 385 MET cc_start: 0.8984 (tpp) cc_final: 0.8413 (tpp) REVERT: E 415 ASP cc_start: 0.7789 (m-30) cc_final: 0.7582 (m-30) REVERT: G 362 TYR cc_start: 0.9234 (t80) cc_final: 0.8969 (t80) REVERT: I 168 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8750 (m) REVERT: I 275 ASN cc_start: 0.6916 (t0) cc_final: 0.6716 (m110) REVERT: I 276 MET cc_start: 0.8209 (tmm) cc_final: 0.7962 (tmm) REVERT: K 275 ASN cc_start: 0.6755 (t0) cc_final: 0.6512 (m110) REVERT: K 276 MET cc_start: 0.7880 (tmm) cc_final: 0.7400 (tmm) REVERT: K 338 MET cc_start: 0.8978 (mtp) cc_final: 0.8714 (mtm) REVERT: M 295 MET cc_start: 0.6793 (mmm) cc_final: 0.6454 (mmm) REVERT: M 367 ARG cc_start: 0.8228 (ttp-110) cc_final: 0.7854 (mtm110) outliers start: 45 outliers final: 30 residues processed: 285 average time/residue: 0.1537 time to fit residues: 66.6053 Evaluate side-chains 262 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 D residue 429 LEU Chi-restraints excluded: chain B residue 130 VAL 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 219 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 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 348 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 67 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 147 GLN B 375 GLN E 275 ASN M 287 HIS M 395 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.128014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.096645 restraints weight = 28740.319| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.57 r_work: 0.3050 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3552 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= 0.142 Angle : 0.550 7.044 26201 Z= 0.269 Chirality : 0.039 0.141 2975 Planarity : 0.004 0.039 3297 Dihedral : 5.157 48.597 2779 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.50 % Allowed : 14.33 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2324 helix: 0.81 (0.14), residues: 1316 sheet: -0.07 (0.44), residues: 112 loop : -1.36 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 213 TYR 0.026 0.001 TYR M 125 PHE 0.012 0.001 PHE D 129 TRP 0.012 0.001 TRP G 388 HIS 0.010 0.002 HIS I 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (19348) covalent geometry : angle 0.55044 / 0.27 (26201) hydrogen bonds : bond 0.03179 / 2.05 ( 686) hydrogen bonds : angle 3.28849 / 2.26 ( 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 294 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 243 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 343 MET cc_start: 0.9182 (mmm) cc_final: 0.8843 (mmm) REVERT: D 429 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8287 (tp) REVERT: B 215 MET cc_start: 0.1721 (ttm) cc_final: 0.1498 (ttm) REVERT: B 362 TYR cc_start: 0.9334 (t80) cc_final: 0.8965 (t80) REVERT: E 136 LYS cc_start: 0.9029 (mttt) cc_final: 0.8763 (mmtt) REVERT: E 158 ARG cc_start: 0.8615 (mpp80) cc_final: 0.8346 (mtt90) REVERT: E 385 MET cc_start: 0.9033 (tpp) cc_final: 0.8553 (tpp) REVERT: E 415 ASP cc_start: 0.7683 (m-30) cc_final: 0.7443 (m-30) REVERT: G 343 MET cc_start: 0.9417 (mmm) cc_final: 0.9191 (mmm) REVERT: G 362 TYR cc_start: 0.9185 (t80) cc_final: 0.8973 (t80) REVERT: G 405 GLU cc_start: 0.8342 (tt0) cc_final: 0.8120 (tt0) REVERT: I 168 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8756 (m) REVERT: I 280 GLU cc_start: 0.8034 (mp0) cc_final: 0.7554 (tt0) REVERT: K 276 MET cc_start: 0.7813 (tmm) cc_final: 0.7384 (tmm) REVERT: K 338 MET cc_start: 0.8889 (mtp) cc_final: 0.8647 (mtm) REVERT: M 240 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.7907 (mt) REVERT: M 295 MET cc_start: 0.6723 (mmm) cc_final: 0.6431 (mmm) REVERT: M 367 ARG cc_start: 0.8238 (ttp-110) cc_final: 0.7859 (mtm110) outliers start: 51 outliers final: 31 residues processed: 287 average time/residue: 0.1516 time to fit residues: 66.3869 Evaluate side-chains 265 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 D residue 429 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 B residue 374 ILE 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 219 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain I residue 89 HIS 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 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 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: 4.9990 chunk 22 optimal weight: 0.0980 chunk 212 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 164 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3606 r_free = 0.3606 target = 0.128437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097261 restraints weight = 28580.645| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.55 r_work: 0.3059 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3699 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= 0.131 Angle : 0.542 7.607 26201 Z= 0.265 Chirality : 0.039 0.139 2975 Planarity : 0.003 0.039 3297 Dihedral : 5.067 48.746 2779 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.74 % Allowed : 14.33 % Favored : 82.93 % 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 are not related in a simple way. whole: 0.21 (0.17), residues: 2324 helix: 1.09 (0.14), residues: 1309 sheet: 0.12 (0.45), residues: 112 loop : -1.27 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 213 TYR 0.028 0.001 TYR M 362 PHE 0.010 0.001 PHE G 384 TRP 0.012 0.001 TRP E 388 HIS 0.010 0.002 HIS I 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (19348) covalent geometry : angle 0.54167 / 0.27 (26201) hydrogen bonds : bond 0.03065 / 1.99 ( 686) hydrogen bonds : angle 3.28409 / 2.24 ( 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 294 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.8687 (p-80) REVERT: D 188 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7739 (mtt) REVERT: D 366 LEU cc_start: 0.8890 (tp) cc_final: 0.8653 (tt) REVERT: D 429 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8284 (tp) REVERT: B 215 MET cc_start: 0.1714 (ttm) cc_final: 0.1486 (ttm) REVERT: B 276 MET cc_start: 0.8257 (ttp) cc_final: 0.7822 (tmm) REVERT: B 362 TYR cc_start: 0.9340 (t80) cc_final: 0.9008 (t80) REVERT: E 136 LYS cc_start: 0.9030 (mttt) cc_final: 0.8720 (mmtt) REVERT: E 158 ARG cc_start: 0.8585 (mpp80) cc_final: 0.8331 (mtt90) REVERT: E 385 MET cc_start: 0.9055 (tpp) cc_final: 0.8537 (tpp) REVERT: E 415 ASP cc_start: 0.7554 (m-30) cc_final: 0.7305 (m-30) REVERT: G 357 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8838 (mtpp) REVERT: I 92 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8025 (pm20) REVERT: I 168 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8755 (m) REVERT: I 357 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8987 (mtpt) REVERT: K 90 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8620 (pp) REVERT: K 276 MET cc_start: 0.7879 (tmm) cc_final: 0.7511 (tmm) REVERT: K 338 MET cc_start: 0.8891 (mtp) cc_final: 0.8653 (mtm) REVERT: M 131 VAL cc_start: 0.8936 (m) cc_final: 0.8658 (t) REVERT: M 240 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.7920 (mt) REVERT: M 295 MET cc_start: 0.6812 (mmm) cc_final: 0.6485 (mmm) REVERT: M 367 ARG cc_start: 0.8263 (ttp-110) cc_final: 0.7881 (mtm110) outliers start: 56 outliers final: 38 residues processed: 286 average time/residue: 0.1538 time to fit residues: 67.0176 Evaluate side-chains 280 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 D residue 429 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 131 VAL 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 B residue 425 GLU 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 219 VAL Chi-restraints excluded: chain G residue 226 LEU 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 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 I residue 357 LYS Chi-restraints excluded: chain K residue 90 LEU 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 92 GLU 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: 0.8980 chunk 117 optimal weight: 0.9990 chunk 214 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 184 optimal weight: 0.7980 chunk 47 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 275 ASN M 287 HIS M 395 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097425 restraints weight = 28674.255| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.51 r_work: 0.3049 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19348 Z= 0.146 Angle : 0.561 8.890 26201 Z= 0.274 Chirality : 0.040 0.139 2975 Planarity : 0.004 0.040 3297 Dihedral : 5.122 49.516 2779 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.64 % Allowed : 14.97 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.17), residues: 2324 helix: 1.18 (0.14), residues: 1309 sheet: 0.18 (0.46), residues: 112 loop : -1.21 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 379 TYR 0.025 0.001 TYR M 362 PHE 0.010 0.001 PHE K 129 TRP 0.010 0.001 TRP G 388 HIS 0.012 0.002 HIS K 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (19348) covalent geometry : angle 0.56083 / 0.27 (26201) hydrogen bonds : bond 0.03176 / 2.06 ( 686) hydrogen bonds : angle 3.34421 / 2.29 ( 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 294 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 240 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 89 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.8674 (p-80) REVERT: D 131 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8806 (t) REVERT: D 188 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7791 (mtt) REVERT: D 343 MET cc_start: 0.9188 (mmm) cc_final: 0.8835 (mmm) REVERT: D 366 LEU cc_start: 0.8909 (tp) cc_final: 0.8685 (tt) REVERT: D 398 LEU cc_start: 0.8414 (mt) cc_final: 0.8180 (mt) REVERT: D 429 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8297 (tp) REVERT: B 215 MET cc_start: 0.2138 (ttm) cc_final: 0.1865 (ttm) REVERT: B 276 MET cc_start: 0.8195 (ttp) cc_final: 0.7792 (tmm) REVERT: B 362 TYR cc_start: 0.9338 (t80) cc_final: 0.8970 (t80) REVERT: E 136 LYS cc_start: 0.9031 (mttt) cc_final: 0.8724 (mmtt) REVERT: E 158 ARG cc_start: 0.8579 (mpp80) cc_final: 0.8318 (mtt90) REVERT: E 385 MET cc_start: 0.9031 (tpp) cc_final: 0.8540 (tpp) REVERT: E 415 ASP cc_start: 0.7574 (m-30) cc_final: 0.7322 (m-30) REVERT: G 357 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8856 (mtpp) REVERT: G 362 TYR cc_start: 0.9098 (t80) cc_final: 0.8890 (t80) REVERT: G 379 ARG cc_start: 0.8359 (mmp80) cc_final: 0.7919 (mmm160) REVERT: I 92 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8090 (pm20) REVERT: I 168 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8760 (m) REVERT: I 357 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8987 (mtpt) REVERT: K 90 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8616 (pp) REVERT: K 276 MET cc_start: 0.7825 (tmm) cc_final: 0.7488 (tmm) REVERT: K 338 MET cc_start: 0.8903 (mtp) cc_final: 0.8667 (mtm) REVERT: M 131 VAL cc_start: 0.8934 (m) cc_final: 0.8689 (t) REVERT: M 240 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.7852 (mt) REVERT: M 295 MET cc_start: 0.6877 (mmm) cc_final: 0.6572 (mmm) REVERT: M 385 MET cc_start: 0.9051 (tpp) cc_final: 0.8845 (tpp) outliers start: 54 outliers final: 37 residues processed: 288 average time/residue: 0.1535 time to fit residues: 67.3277 Evaluate side-chains 276 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 131 VAL 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 D residue 429 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 131 VAL 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 B residue 425 GLU 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 219 VAL Chi-restraints excluded: chain G residue 226 LEU 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 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 I residue 357 LYS Chi-restraints excluded: chain K residue 89 HIS Chi-restraints excluded: chain K residue 90 LEU 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: 0.8980 chunk 229 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 363 GLN E 275 ASN ** 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 = 0.3593 r_free = 0.3593 target = 0.127516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096213 restraints weight = 28824.270| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.57 r_work: 0.3036 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.004 0.035 19348 Z= 0.156 Angle : 0.570 8.315 26201 Z= 0.279 Chirality : 0.040 0.141 2975 Planarity : 0.004 0.040 3297 Dihedral : 5.158 49.209 2779 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.89 % Allowed : 14.63 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2324 helix: 1.22 (0.14), residues: 1309 sheet: 0.17 (0.46), residues: 112 loop : -1.18 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 267 TYR 0.026 0.001 TYR M 362 PHE 0.010 0.001 PHE I 129 TRP 0.010 0.001 TRP G 388 HIS 0.012 0.002 HIS K 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (19348) covalent geometry : angle 0.57050 / 0.28 (26201) hydrogen bonds : bond 0.03262 / 2.11 ( 686) hydrogen bonds : angle 3.39506 / 2.33 ( 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 291 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 232 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8795 (t) REVERT: D 188 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7869 (mtt) REVERT: D 240 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8582 (mt) REVERT: D 343 MET cc_start: 0.9172 (mmm) cc_final: 0.8795 (mmm) REVERT: D 352 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: D 366 LEU cc_start: 0.8912 (tp) cc_final: 0.8687 (tt) REVERT: D 398 LEU cc_start: 0.8446 (mt) cc_final: 0.8197 (mt) REVERT: D 429 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8295 (tp) REVERT: B 362 TYR cc_start: 0.9347 (t80) cc_final: 0.8960 (t80) REVERT: E 136 LYS cc_start: 0.9036 (mttt) cc_final: 0.8723 (mmtt) REVERT: E 158 ARG cc_start: 0.8602 (mpp80) cc_final: 0.8346 (mtt90) REVERT: E 385 MET cc_start: 0.9089 (tpp) cc_final: 0.8566 (tpp) REVERT: E 415 ASP cc_start: 0.7611 (m-30) cc_final: 0.7342 (m-30) REVERT: G 357 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8847 (mtpp) REVERT: G 362 TYR cc_start: 0.9121 (t80) cc_final: 0.8859 (t80) REVERT: G 379 ARG cc_start: 0.8423 (mmp80) cc_final: 0.8019 (mmm160) REVERT: I 92 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8199 (pm20) REVERT: I 168 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8760 (m) REVERT: I 357 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9010 (mtpt) REVERT: K 90 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8567 (pp) REVERT: K 240 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8673 (mm) REVERT: K 276 MET cc_start: 0.7794 (tmm) cc_final: 0.7591 (tmm) REVERT: M 240 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.7856 (mt) REVERT: M 295 MET cc_start: 0.6856 (mmm) cc_final: 0.6541 (mmm) REVERT: M 385 MET cc_start: 0.9068 (tpp) cc_final: 0.8868 (tpp) outliers start: 59 outliers final: 39 residues processed: 283 average time/residue: 0.1499 time to fit residues: 64.8241 Evaluate side-chains 277 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 188 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain B residue 116 THR 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 B residue 425 GLU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 240 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 219 VAL Chi-restraints excluded: chain G residue 226 LEU 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 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 I residue 357 LYS Chi-restraints excluded: chain K residue 89 HIS Chi-restraints excluded: chain K residue 90 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 177 optimal weight: 0.6980 chunk 231 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 76 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3606 r_free = 0.3606 target = 0.128626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.097258 restraints weight = 28585.982| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.58 r_work: 0.3052 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19348 Z= 0.139 Angle : 0.560 9.627 26201 Z= 0.274 Chirality : 0.040 0.142 2975 Planarity : 0.004 0.040 3297 Dihedral : 5.074 48.513 2779 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.79 % Allowed : 14.82 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2324 helix: 1.28 (0.14), residues: 1309 sheet: 0.21 (0.46), residues: 112 loop : -1.15 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 267 TYR 0.024 0.001 TYR M 125 PHE 0.009 0.001 PHE G 384 TRP 0.010 0.001 TRP G 388 HIS 0.012 0.002 HIS K 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (19348) covalent geometry : angle 0.56025 / 0.27 (26201) hydrogen bonds : bond 0.03094 / 2.00 ( 686) hydrogen bonds : angle 3.40423 / 2.34 ( 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 292 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 235 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8787 (t) REVERT: D 188 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7802 (mtt) REVERT: D 198 TYR cc_start: 0.9147 (t80) cc_final: 0.8908 (t80) REVERT: D 240 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8568 (mt) REVERT: D 343 MET cc_start: 0.9189 (mmm) cc_final: 0.8804 (mmm) REVERT: D 352 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: D 366 LEU cc_start: 0.8909 (tp) cc_final: 0.8679 (tt) REVERT: D 398 LEU cc_start: 0.8422 (mt) cc_final: 0.8173 (mt) REVERT: D 429 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8290 (tp) REVERT: B 362 TYR cc_start: 0.9363 (t80) cc_final: 0.8930 (t80) REVERT: E 136 LYS cc_start: 0.9026 (mttt) cc_final: 0.8706 (mmtt) REVERT: E 158 ARG cc_start: 0.8582 (mpp80) cc_final: 0.8336 (mtt90) REVERT: E 385 MET cc_start: 0.9031 (tpp) cc_final: 0.8548 (tpp) REVERT: E 415 ASP cc_start: 0.7600 (m-30) cc_final: 0.7324 (m-30) REVERT: G 107 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9021 (tp) REVERT: G 357 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8903 (mtpp) REVERT: G 362 TYR cc_start: 0.9120 (t80) cc_final: 0.8762 (t80) REVERT: G 379 ARG cc_start: 0.8332 (mmp80) cc_final: 0.7926 (mmm160) REVERT: I 168 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8763 (m) REVERT: I 357 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9105 (mtpp) REVERT: K 90 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8547 (pp) REVERT: K 146 ARG cc_start: 0.8695 (ttm-80) cc_final: 0.8374 (ttp80) REVERT: K 240 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8567 (mm) REVERT: M 231 ASP cc_start: 0.7689 (p0) cc_final: 0.7303 (p0) REVERT: M 240 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7751 (mt) REVERT: M 295 MET cc_start: 0.6817 (mmm) cc_final: 0.6494 (mmm) REVERT: M 357 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8693 (ttmt) REVERT: M 367 ARG cc_start: 0.8132 (ttp-110) cc_final: 0.7881 (mtm110) outliers start: 57 outliers final: 38 residues processed: 284 average time/residue: 0.1519 time to fit residues: 66.0753 Evaluate side-chains 283 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 188 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain B residue 116 THR 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 B residue 425 GLU Chi-restraints excluded: chain E residue 168 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 107 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 226 LEU 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 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 I residue 357 LYS Chi-restraints excluded: chain K residue 89 HIS Chi-restraints excluded: chain K residue 90 LEU 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 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 Chi-restraints excluded: chain M residue 357 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 87 optimal weight: 0.0970 chunk 204 optimal weight: 0.5980 chunk 182 optimal weight: 0.0010 chunk 171 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 80 optimal weight: 0.1980 chunk 2 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 275 ASN I 270 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 = 0.3635 r_free = 0.3635 target = 0.131498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.101292 restraints weight = 28622.614| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.46 r_work: 0.3096 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19348 Z= 0.098 Angle : 0.538 10.443 26201 Z= 0.260 Chirality : 0.038 0.143 2975 Planarity : 0.003 0.037 3297 Dihedral : 4.804 45.662 2779 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.25 % Allowed : 15.46 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2324 helix: 1.44 (0.15), residues: 1309 sheet: 0.28 (0.46), residues: 112 loop : -1.06 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 267 TYR 0.021 0.001 TYR M 125 PHE 0.011 0.001 PHE G 384 TRP 0.010 0.001 TRP G 388 HIS 0.011 0.002 HIS K 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (19348) covalent geometry : angle 0.53756 / 0.26 (26201) hydrogen bonds : bond 0.02593 / 1.68 ( 686) hydrogen bonds : angle 3.29561 / 2.28 ( 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 295 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8759 (t) REVERT: D 188 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7589 (mtt) REVERT: D 240 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8543 (mt) REVERT: D 343 MET cc_start: 0.9185 (mmm) cc_final: 0.8817 (mmm) REVERT: D 352 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: D 366 LEU cc_start: 0.8881 (tp) cc_final: 0.8638 (tt) REVERT: D 398 LEU cc_start: 0.8329 (mt) cc_final: 0.8119 (mt) REVERT: D 429 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8277 (tp) REVERT: B 304 SER cc_start: 0.8833 (t) cc_final: 0.8435 (p) REVERT: B 362 TYR cc_start: 0.9344 (t80) cc_final: 0.8950 (t80) REVERT: E 136 LYS cc_start: 0.9001 (mttt) cc_final: 0.8716 (mmtt) REVERT: E 385 MET cc_start: 0.8941 (tpp) cc_final: 0.8464 (tpp) REVERT: E 415 ASP cc_start: 0.7541 (m-30) cc_final: 0.7284 (m-30) REVERT: G 287 HIS cc_start: 0.8059 (t-90) cc_final: 0.7856 (t-90) REVERT: G 357 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8903 (mtpp) REVERT: G 379 ARG cc_start: 0.8315 (mmp80) cc_final: 0.7872 (mmm160) REVERT: K 146 ARG cc_start: 0.8756 (ttm-80) cc_final: 0.8428 (ttp80) REVERT: K 240 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8417 (mm) REVERT: K 379 ARG cc_start: 0.8578 (mmp-170) cc_final: 0.8306 (mmm160) REVERT: M 231 ASP cc_start: 0.7634 (p0) cc_final: 0.7208 (p0) REVERT: M 240 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8187 (mt) REVERT: M 295 MET cc_start: 0.6802 (mmm) cc_final: 0.6491 (mmm) REVERT: M 367 ARG cc_start: 0.8141 (ttp-110) cc_final: 0.7901 (mtm110) outliers start: 46 outliers final: 30 residues processed: 286 average time/residue: 0.1539 time to fit residues: 67.0173 Evaluate side-chains 276 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 238 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 188 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 226 LEU 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 131 VAL 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 226 LEU Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 130 VAL 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 83 optimal weight: 0.0020 chunk 225 optimal weight: 0.0870 chunk 100 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 191 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 189 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 overall best weight: 0.3766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3633 r_free = 0.3633 target = 0.131470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100916 restraints weight = 28593.825| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.50 r_work: 0.3086 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19348 Z= 0.103 Angle : 0.552 11.432 26201 Z= 0.265 Chirality : 0.038 0.144 2975 Planarity : 0.003 0.037 3297 Dihedral : 4.761 45.682 2779 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.01 % Allowed : 15.61 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2324 helix: 1.48 (0.15), residues: 1309 sheet: 0.38 (0.46), residues: 112 loop : -1.01 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 267 TYR 0.021 0.001 TYR M 362 PHE 0.010 0.001 PHE G 384 TRP 0.010 0.001 TRP G 388 HIS 0.012 0.002 HIS K 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.10 (19348) covalent geometry : angle 0.55221 / 0.27 (26201) hydrogen bonds : bond 0.02635 / 1.71 ( 686) hydrogen bonds : angle 3.28164 / 2.27 ( 2058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4157.66 seconds wall clock time: 72 minutes 26.23 seconds (4346.23 seconds total)