Starting phenix.real_space_refine on Mon Jun 16 16:32:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i2n_0333/06_2025/6i2n_0333.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i2n_0333/06_2025/6i2n_0333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6i2n_0333/06_2025/6i2n_0333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i2n_0333/06_2025/6i2n_0333.map" model { file = "/net/cci-nas-00/data/ceres_data/6i2n_0333/06_2025/6i2n_0333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i2n_0333/06_2025/6i2n_0333.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18970 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "B" 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: E, D, G, I, K, M, C, F, H, J, L, U Time building chain proxies: 7.68, per 1000 atoms: 0.40 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: 4.58 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.69 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: 5.48 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5038 1.33 - 1.45: 3200 1.45 - 1.57: 10872 1.57 - 1.69: 35 1.69 - 1.80: 203 Bond restraints: 19348 Sorted by residual: bond pdb=" C PHE G 129 " pdb=" N VAL G 130 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.42e-02 4.96e+03 2.37e+00 bond pdb=" C PHE E 129 " pdb=" N VAL E 130 " ideal model delta sigma weight residual 1.330 1.309 0.022 1.42e-02 4.96e+03 2.34e+00 bond pdb=" C PHE K 129 " pdb=" N VAL K 130 " ideal model delta sigma weight residual 1.330 1.309 0.022 1.42e-02 4.96e+03 2.30e+00 bond pdb=" C PHE I 129 " pdb=" N VAL I 130 " ideal model delta sigma weight residual 1.330 1.309 0.021 1.42e-02 4.96e+03 2.28e+00 bond pdb=" C PHE D 129 " pdb=" N VAL D 130 " ideal model delta sigma weight residual 1.330 1.309 0.021 1.42e-02 4.96e+03 2.24e+00 ... (remaining 19343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 25153 2.10 - 4.20: 886 4.20 - 6.30: 92 6.30 - 8.40: 56 8.40 - 10.50: 14 Bond angle restraints: 26201 Sorted by residual: angle pdb=" N VAL G 131 " pdb=" CA VAL G 131 " pdb=" C VAL G 131 " ideal model delta sigma weight residual 108.88 119.38 -10.50 2.16e+00 2.14e-01 2.36e+01 angle pdb=" N VAL E 131 " pdb=" CA VAL E 131 " pdb=" C VAL E 131 " ideal model delta sigma weight residual 108.88 119.37 -10.49 2.16e+00 2.14e-01 2.36e+01 angle pdb=" N VAL D 131 " pdb=" CA VAL D 131 " pdb=" C VAL D 131 " ideal model delta sigma weight residual 108.88 119.36 -10.48 2.16e+00 2.14e-01 2.36e+01 angle pdb=" N VAL K 131 " pdb=" CA VAL K 131 " pdb=" C VAL K 131 " ideal model delta sigma weight residual 108.88 119.35 -10.47 2.16e+00 2.14e-01 2.35e+01 angle pdb=" N VAL I 131 " pdb=" CA VAL I 131 " pdb=" C VAL I 131 " ideal model delta sigma weight residual 108.88 119.34 -10.46 2.16e+00 2.14e-01 2.35e+01 ... (remaining 26196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 11049 14.80 - 29.59: 634 29.59 - 44.39: 169 44.39 - 59.18: 48 59.18 - 73.98: 35 Dihedral angle restraints: 11935 sinusoidal: 5110 harmonic: 6825 Sorted by residual: dihedral pdb=" CA PHE I 165 " pdb=" C PHE I 165 " pdb=" N GLU I 166 " pdb=" CA GLU I 166 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE E 165 " pdb=" C PHE E 165 " pdb=" N GLU E 166 " pdb=" CA GLU E 166 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE G 165 " pdb=" C PHE G 165 " pdb=" N GLU G 166 " pdb=" CA GLU G 166 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 11932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1739 0.039 - 0.078: 875 0.078 - 0.117: 238 0.117 - 0.157: 81 0.157 - 0.196: 42 Chirality restraints: 2975 Sorted by residual: chirality pdb=" CG LEU G 413 " pdb=" CB LEU G 413 " pdb=" CD1 LEU G 413 " pdb=" CD2 LEU G 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CG LEU E 413 " pdb=" CB LEU E 413 " pdb=" CD1 LEU E 413 " pdb=" CD2 LEU E 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CG LEU M 413 " pdb=" CB LEU M 413 " pdb=" CD1 LEU M 413 " pdb=" CD2 LEU M 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 2972 not shown) Planarity restraints: 3297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 131 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO G 132 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO G 132 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 132 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 131 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO M 132 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO M 132 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO M 132 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 131 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO E 132 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 132 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 132 " -0.029 5.00e-02 4.00e+02 ... (remaining 3294 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6062 2.84 - 3.35: 18066 3.35 - 3.87: 30532 3.87 - 4.38: 35559 4.38 - 4.90: 60406 Nonbonded interactions: 150625 Sorted by model distance: nonbonded pdb=" OD1 ASP E 88 " pdb=" OH TYR E 98 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASP B 88 " pdb=" OH TYR B 98 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASP D 88 " pdb=" OH TYR D 98 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASP M 88 " pdb=" OH TYR M 98 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASP K 88 " pdb=" OH TYR K 98 " model vdw 2.323 3.040 ... (remaining 150620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.23 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'U' } 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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 39.080 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 19348 Z= 0.284 Angle : 0.970 10.499 26201 Z= 0.508 Chirality : 0.053 0.196 2975 Planarity : 0.007 0.051 3297 Dihedral : 11.929 73.978 7511 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.004 TRP E 119 HIS 0.018 0.003 HIS K 89 PHE 0.023 0.004 PHE M 384 TYR 0.028 0.003 TYR B 178 ARG 0.006 0.001 ARG E 197 Details of bonding type rmsd hydrogen bonds : bond 0.06763 ( 686) hydrogen bonds : angle 4.60283 ( 2058) covalent geometry : bond 0.00689 (19348) covalent geometry : angle 0.97011 (26201) *********************** 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 : 2.092 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: 0.8528 (t) REVERT: B 109 ILE cc_start: 0.7388 (mt) cc_final: 0.6783 (mt) REVERT: B 406 LEU cc_start: 0.9048 (tm) cc_final: 0.8843 (tp) REVERT: E 88 ASP cc_start: 0.7881 (t70) cc_final: 0.6469 (t0) REVERT: G 88 ASP cc_start: 0.7383 (t70) cc_final: 0.6585 (t0) REVERT: G 183 ASN cc_start: 0.7801 (t0) cc_final: 0.7495 (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: 0.8011 (mtp) REVERT: K 415 ASP cc_start: 0.7601 (m-30) cc_final: 0.7232 (m-30) REVERT: M 340 ASN cc_start: 0.8497 (m-40) cc_final: 0.8283 (m-40) outliers start: 0 outliers final: 0 residues processed: 533 average time/residue: 0.4033 time to fit residues: 301.4895 Evaluate side-chains 263 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.6980 chunk 175 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 210 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 287 HIS D 395 ASN B 270 GLN B 370 GLN E 270 GLN E 275 ASN E 395 ASN G 270 GLN G 340 ASN G 395 ASN I 147 GLN I 340 ASN I 395 ASN K 395 ASN M 287 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100808 restraints weight = 28708.551| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.50 r_work: 0.3100 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2491 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= 0.138 Angle : 0.575 7.903 26201 Z= 0.285 Chirality : 0.040 0.151 2975 Planarity : 0.005 0.037 3297 Dihedral : 7.622 57.929 2863 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.76 % Allowed : 10.27 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2324 helix: -0.53 (0.13), residues: 1316 sheet: -1.04 (0.43), residues: 126 loop : -1.94 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 388 HIS 0.010 0.002 HIS I 89 PHE 0.013 0.002 PHE G 384 TYR 0.026 0.001 TYR M 362 ARG 0.005 0.000 ARG K 93 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 686) hydrogen bonds : angle 3.43202 ( 2058) covalent geometry : bond 0.00333 (19348) covalent geometry : angle 0.57497 (26201) *********************** 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 323 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 343 MET cc_start: 0.9279 (mmm) cc_final: 0.8891 (mmm) REVERT: D 352 GLU cc_start: 0.8050 (pm20) cc_final: 0.7697 (mp0) REVERT: D 398 LEU cc_start: 0.8409 (mt) cc_final: 0.8105 (mt) REVERT: B 362 TYR cc_start: 0.9240 (t80) cc_final: 0.8948 (t80) REVERT: B 385 MET cc_start: 0.9029 (tpp) cc_final: 0.8722 (tpp) REVERT: B 414 ILE cc_start: 0.9009 (mt) cc_final: 0.8702 (mt) REVERT: E 91 LYS cc_start: 0.8633 (mmtp) cc_final: 0.8155 (mtmm) REVERT: E 136 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8702 (mmtt) REVERT: G 226 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8246 (tp) REVERT: G 298 ASP cc_start: 0.7947 (p0) cc_final: 0.7729 (p0) REVERT: I 151 ASP cc_start: 0.7823 (m-30) cc_final: 0.7600 (m-30) REVERT: I 168 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8726 (m) REVERT: I 276 MET cc_start: 0.7815 (tmm) cc_final: 0.7578 (ppp) REVERT: I 352 GLU cc_start: 0.8420 (pm20) cc_final: 0.8168 (pm20) REVERT: I 385 MET cc_start: 0.9080 (tpp) cc_final: 0.8799 (tpp) REVERT: I 415 ASP cc_start: 0.7819 (m-30) cc_final: 0.7585 (m-30) REVERT: K 338 MET cc_start: 0.8742 (mtp) cc_final: 0.8407 (mtm) REVERT: K 415 ASP cc_start: 0.8046 (m-30) cc_final: 0.7656 (m-30) REVERT: M 178 TYR cc_start: 0.8968 (m-80) cc_final: 0.8678 (m-80) REVERT: M 298 ASP cc_start: 0.7425 (p0) cc_final: 0.7170 (p0) REVERT: M 367 ARG cc_start: 0.8195 (ttp-110) cc_final: 0.7902 (mtm110) outliers start: 36 outliers final: 17 residues processed: 315 average time/residue: 0.3245 time to fit residues: 153.9072 Evaluate side-chains 267 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 248 time to evaluate : 2.181 ------------------------------------------------------------------------------- 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 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 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 168 optimal weight: 0.0170 chunk 53 optimal weight: 20.0000 chunk 68 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 181 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 270 GLN E 275 ASN ** E 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 GLN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.099690 restraints weight = 28594.644| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.56 r_work: 0.3101 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2936 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= 0.112 Angle : 0.529 7.400 26201 Z= 0.260 Chirality : 0.038 0.151 2975 Planarity : 0.004 0.035 3297 Dihedral : 7.114 58.028 2863 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.30 % Allowed : 12.08 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2324 helix: 0.33 (0.14), residues: 1316 sheet: -0.19 (0.45), residues: 112 loop : -1.70 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 388 HIS 0.010 0.002 HIS G 89 PHE 0.011 0.001 PHE G 384 TYR 0.025 0.001 TYR M 362 ARG 0.005 0.000 ARG D 213 Details of bonding type rmsd hydrogen bonds : bond 0.02921 ( 686) hydrogen bonds : angle 3.22255 ( 2058) covalent geometry : bond 0.00271 (19348) covalent geometry : angle 0.52874 (26201) *********************** 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 299 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 429 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8271 (tp) REVERT: B 230 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8659 (ttpp) REVERT: B 362 TYR cc_start: 0.9303 (t80) cc_final: 0.8996 (t80) REVERT: B 414 ILE cc_start: 0.8992 (mt) cc_final: 0.8710 (mt) REVERT: E 91 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8229 (mtmm) REVERT: E 136 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8744 (mmtt) REVERT: E 385 MET cc_start: 0.8743 (tpp) cc_final: 0.8453 (tpp) REVERT: G 226 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8255 (tp) REVERT: I 168 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8760 (m) REVERT: I 385 MET cc_start: 0.9058 (tpp) cc_final: 0.8858 (tpp) REVERT: K 188 MET cc_start: 0.8043 (mmm) cc_final: 0.7665 (mmm) REVERT: K 276 MET cc_start: 0.7568 (tmm) cc_final: 0.7161 (tmm) REVERT: K 338 MET cc_start: 0.8833 (mtp) cc_final: 0.8548 (mtm) REVERT: K 415 ASP cc_start: 0.8030 (m-30) cc_final: 0.7798 (m-30) REVERT: M 165 PHE cc_start: 0.7854 (m-10) cc_final: 0.7581 (m-10) REVERT: M 178 TYR cc_start: 0.9005 (m-80) cc_final: 0.8802 (m-80) REVERT: M 367 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7823 (mtm110) outliers start: 47 outliers final: 27 residues processed: 288 average time/residue: 0.3505 time to fit residues: 153.2053 Evaluate side-chains 279 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 249 time to evaluate : 2.756 ------------------------------------------------------------------------------- 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 241 ILE 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 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 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 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 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 159 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 111 optimal weight: 0.2980 chunk 126 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 226 optimal weight: 0.5980 chunk 230 optimal weight: 0.9990 chunk 210 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 86 optimal weight: 0.0020 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN ** E 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 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 = 0.3646 r_free = 0.3646 target = 0.131261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100145 restraints weight = 28546.901| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.56 r_work: 0.3109 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3223 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= 0.106 Angle : 0.516 6.900 26201 Z= 0.252 Chirality : 0.038 0.142 2975 Planarity : 0.003 0.035 3297 Dihedral : 6.957 58.017 2863 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.25 % Allowed : 13.26 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2324 helix: 0.78 (0.14), residues: 1316 sheet: -0.61 (0.43), residues: 126 loop : -1.39 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 388 HIS 0.010 0.002 HIS I 89 PHE 0.010 0.001 PHE G 384 TYR 0.026 0.001 TYR M 362 ARG 0.004 0.000 ARG D 213 Details of bonding type rmsd hydrogen bonds : bond 0.02763 ( 686) hydrogen bonds : angle 3.12185 ( 2058) covalent geometry : bond 0.00254 (19348) covalent geometry : angle 0.51621 (26201) *********************** 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 310 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 264 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 198 TYR cc_start: 0.9064 (t80) cc_final: 0.8777 (t80) REVERT: D 343 MET cc_start: 0.9204 (mmm) cc_final: 0.8801 (mmm) REVERT: D 352 GLU cc_start: 0.7978 (pm20) cc_final: 0.7643 (mp0) REVERT: D 366 LEU cc_start: 0.8818 (tp) cc_final: 0.8560 (tt) REVERT: D 398 LEU cc_start: 0.8276 (mt) cc_final: 0.8046 (mt) REVERT: D 429 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8237 (tp) REVERT: B 230 LYS cc_start: 0.8975 (ttmm) cc_final: 0.8749 (ttpp) REVERT: B 362 TYR cc_start: 0.9338 (t80) cc_final: 0.9042 (t80) REVERT: B 370 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7712 (mt0) REVERT: B 414 ILE cc_start: 0.8996 (mt) cc_final: 0.8731 (mt) REVERT: E 91 LYS cc_start: 0.8636 (mmtp) cc_final: 0.8216 (mtmm) REVERT: E 158 ARG cc_start: 0.8583 (mpp80) cc_final: 0.8306 (mtt90) REVERT: E 385 MET cc_start: 0.8918 (tpp) cc_final: 0.8452 (tpp) REVERT: E 415 ASP cc_start: 0.7759 (m-30) cc_final: 0.7545 (m-30) REVERT: G 379 ARG cc_start: 0.8339 (tpp-160) cc_final: 0.8050 (mmm160) REVERT: I 95 MET cc_start: 0.9026 (mmp) cc_final: 0.8808 (mmm) REVERT: I 168 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8794 (m) REVERT: I 276 MET cc_start: 0.8164 (tmm) cc_final: 0.7945 (tmm) REVERT: I 280 GLU cc_start: 0.7798 (mp0) cc_final: 0.7567 (tt0) REVERT: K 188 MET cc_start: 0.8207 (mmm) cc_final: 0.7858 (mtm) REVERT: K 276 MET cc_start: 0.7606 (tmm) cc_final: 0.7272 (tmm) REVERT: K 338 MET cc_start: 0.8812 (mtp) cc_final: 0.8530 (mtm) REVERT: K 415 ASP cc_start: 0.7953 (m-30) cc_final: 0.7750 (m-30) REVERT: M 131 VAL cc_start: 0.8932 (m) cc_final: 0.8641 (t) REVERT: M 165 PHE cc_start: 0.7797 (m-10) cc_final: 0.7511 (m-10) REVERT: M 178 TYR cc_start: 0.8997 (m-80) cc_final: 0.8778 (m-80) REVERT: M 367 ARG cc_start: 0.8174 (ttp-110) cc_final: 0.7794 (mtm110) outliers start: 46 outliers final: 29 residues processed: 302 average time/residue: 0.3755 time to fit residues: 171.1656 Evaluate side-chains 276 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 3.983 ------------------------------------------------------------------------------- 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 241 ILE 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 370 GLN Chi-restraints excluded: chain E residue 168 VAL 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 109 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 29 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 139 optimal weight: 0.0170 chunk 120 optimal weight: 0.0570 chunk 96 optimal weight: 1.9990 chunk 182 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN ** E 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 270 GLN M 287 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100489 restraints weight = 28444.081| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.57 r_work: 0.3112 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19348 Z= 0.100 Angle : 0.513 6.963 26201 Z= 0.249 Chirality : 0.037 0.149 2975 Planarity : 0.003 0.035 3297 Dihedral : 6.883 58.019 2863 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.45 % Allowed : 13.75 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2324 helix: 1.06 (0.15), residues: 1316 sheet: -0.41 (0.43), residues: 126 loop : -1.22 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 388 HIS 0.010 0.002 HIS G 89 PHE 0.009 0.001 PHE G 384 TYR 0.025 0.001 TYR M 362 ARG 0.004 0.000 ARG D 213 Details of bonding type rmsd hydrogen bonds : bond 0.02650 ( 686) hydrogen bonds : angle 3.08473 ( 2058) covalent geometry : bond 0.00242 (19348) covalent geometry : angle 0.51250 (26201) *********************** 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 309 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 352 GLU cc_start: 0.7948 (pm20) cc_final: 0.7613 (mp0) REVERT: D 366 LEU cc_start: 0.8823 (tp) cc_final: 0.8581 (tt) REVERT: D 429 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8234 (tp) REVERT: B 215 MET cc_start: 0.2508 (ttm) cc_final: 0.2236 (ttm) REVERT: B 304 SER cc_start: 0.8831 (t) cc_final: 0.8448 (p) REVERT: B 370 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: B 414 ILE cc_start: 0.9001 (mt) cc_final: 0.8743 (mt) REVERT: E 91 LYS cc_start: 0.8594 (mmtp) cc_final: 0.8151 (mtmm) REVERT: E 158 ARG cc_start: 0.8592 (mpp80) cc_final: 0.8277 (mtt90) REVERT: E 385 MET cc_start: 0.8966 (tpp) cc_final: 0.8409 (tpp) REVERT: E 415 ASP cc_start: 0.7679 (m-30) cc_final: 0.7447 (m-30) REVERT: G 343 MET cc_start: 0.9384 (mmm) cc_final: 0.9173 (mmm) REVERT: G 379 ARG cc_start: 0.8359 (tpp-160) cc_final: 0.8038 (mmm160) REVERT: I 168 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8783 (m) REVERT: K 276 MET cc_start: 0.7746 (tmm) cc_final: 0.7416 (tmm) REVERT: K 338 MET cc_start: 0.8812 (mtp) cc_final: 0.8562 (mtm) REVERT: K 415 ASP cc_start: 0.7953 (m-30) cc_final: 0.7751 (m-30) REVERT: M 131 VAL cc_start: 0.8911 (m) cc_final: 0.8666 (t) REVERT: M 165 PHE cc_start: 0.7809 (m-10) cc_final: 0.7536 (m-10) REVERT: M 178 TYR cc_start: 0.8982 (m-80) cc_final: 0.8742 (m-80) REVERT: M 240 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8125 (mt) REVERT: M 367 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7818 (mtm110) outliers start: 50 outliers final: 31 residues processed: 302 average time/residue: 0.3247 time to fit residues: 147.3219 Evaluate side-chains 276 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 2.121 ------------------------------------------------------------------------------- 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 241 ILE 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 348 VAL Chi-restraints excluded: chain B residue 370 GLN 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 E residue 394 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 27 optimal weight: 0.4980 chunk 179 optimal weight: 0.9990 chunk 198 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 155 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 161 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN M 287 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.129653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.098282 restraints weight = 28653.761| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.57 r_work: 0.3079 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3565 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= 0.125 Angle : 0.533 7.855 26201 Z= 0.260 Chirality : 0.038 0.147 2975 Planarity : 0.003 0.036 3297 Dihedral : 6.933 58.065 2863 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.50 % Allowed : 13.41 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2324 helix: 1.15 (0.15), residues: 1316 sheet: -0.23 (0.43), residues: 126 loop : -1.11 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 388 HIS 0.011 0.002 HIS K 89 PHE 0.011 0.001 PHE D 129 TYR 0.028 0.001 TYR M 362 ARG 0.003 0.000 ARG I 146 Details of bonding type rmsd hydrogen bonds : bond 0.02928 ( 686) hydrogen bonds : angle 3.15150 ( 2058) covalent geometry : bond 0.00306 (19348) covalent geometry : angle 0.53263 (26201) *********************** 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 298 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 247 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 198 TYR cc_start: 0.9158 (t80) cc_final: 0.8874 (t80) REVERT: D 352 GLU cc_start: 0.7955 (pm20) cc_final: 0.7612 (mp0) REVERT: D 366 LEU cc_start: 0.8873 (tp) cc_final: 0.8633 (tt) REVERT: D 415 ASP cc_start: 0.7525 (m-30) cc_final: 0.7210 (m-30) REVERT: D 429 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8256 (tp) REVERT: B 304 SER cc_start: 0.8838 (t) cc_final: 0.8438 (p) REVERT: B 370 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7786 (mt0) REVERT: B 424 GLN cc_start: 0.8829 (tp40) cc_final: 0.8446 (tp40) REVERT: E 158 ARG cc_start: 0.8581 (mpp80) cc_final: 0.8321 (mtt90) REVERT: E 355 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8670 (mp) REVERT: E 385 MET cc_start: 0.8983 (tpp) cc_final: 0.8415 (tpp) REVERT: E 415 ASP cc_start: 0.7563 (m-30) cc_final: 0.7321 (m-30) REVERT: G 357 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8805 (mtpt) REVERT: I 168 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8781 (m) REVERT: I 280 GLU cc_start: 0.7854 (mp0) cc_final: 0.7494 (tt0) REVERT: K 276 MET cc_start: 0.7770 (tmm) cc_final: 0.7485 (tmm) REVERT: K 338 MET cc_start: 0.8857 (mtp) cc_final: 0.8618 (mtm) REVERT: K 372 MET cc_start: 0.9123 (mtp) cc_final: 0.8922 (mtp) REVERT: M 131 VAL cc_start: 0.8894 (m) cc_final: 0.8685 (t) REVERT: M 165 PHE cc_start: 0.7901 (m-10) cc_final: 0.7607 (m-10) REVERT: M 178 TYR cc_start: 0.8963 (m-80) cc_final: 0.8744 (m-80) REVERT: M 240 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8176 (mt) REVERT: M 367 ARG cc_start: 0.8223 (ttp-110) cc_final: 0.7848 (mtm110) outliers start: 51 outliers final: 36 residues processed: 290 average time/residue: 0.3361 time to fit residues: 147.0304 Evaluate side-chains 281 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 2.700 ------------------------------------------------------------------------------- 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 241 ILE 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 348 VAL Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 394 ASP 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 G residue 357 LYS Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain K residue 89 HIS Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 277 GLU Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 76 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 191 optimal weight: 0.4980 chunk 190 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 162 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.129205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.097967 restraints weight = 28464.040| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.56 r_work: 0.3074 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3690 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= 0.133 Angle : 0.546 8.808 26201 Z= 0.266 Chirality : 0.038 0.143 2975 Planarity : 0.003 0.035 3297 Dihedral : 6.938 58.100 2863 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.50 % Allowed : 13.94 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2324 helix: 1.25 (0.15), residues: 1316 sheet: -0.24 (0.44), residues: 126 loop : -1.05 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 388 HIS 0.011 0.002 HIS K 89 PHE 0.010 0.001 PHE I 129 TYR 0.028 0.001 TYR M 362 ARG 0.003 0.000 ARG I 146 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 686) hydrogen bonds : angle 3.23276 ( 2058) covalent geometry : bond 0.00323 (19348) covalent geometry : angle 0.54601 (26201) *********************** 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 285 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 131 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8779 (t) REVERT: D 343 MET cc_start: 0.9245 (mmm) cc_final: 0.8986 (mmm) REVERT: D 352 GLU cc_start: 0.7949 (pm20) cc_final: 0.7611 (mp0) REVERT: D 366 LEU cc_start: 0.8884 (tp) cc_final: 0.8654 (tt) REVERT: D 415 ASP cc_start: 0.7504 (m-30) cc_final: 0.7184 (m-30) REVERT: D 429 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8270 (tp) REVERT: B 304 SER cc_start: 0.8835 (t) cc_final: 0.8448 (p) REVERT: B 370 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: E 158 ARG cc_start: 0.8579 (mpp80) cc_final: 0.8343 (mtt90) REVERT: E 357 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8941 (mtpt) REVERT: E 385 MET cc_start: 0.8980 (tpp) cc_final: 0.8423 (tpp) REVERT: E 415 ASP cc_start: 0.7566 (m-30) cc_final: 0.7315 (m-30) REVERT: G 343 MET cc_start: 0.9381 (mmm) cc_final: 0.9111 (mmm) REVERT: G 357 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8818 (mtpt) REVERT: G 379 ARG cc_start: 0.8461 (tpp-160) cc_final: 0.8098 (mmm160) REVERT: I 168 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8782 (m) REVERT: K 240 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8585 (mm) REVERT: K 276 MET cc_start: 0.7774 (tmm) cc_final: 0.7500 (tmm) REVERT: K 338 MET cc_start: 0.8861 (mtp) cc_final: 0.8625 (mtm) REVERT: K 372 MET cc_start: 0.9102 (mtp) cc_final: 0.8844 (mtp) REVERT: M 165 PHE cc_start: 0.7945 (m-10) cc_final: 0.7657 (m-10) REVERT: M 240 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.7909 (mt) REVERT: M 367 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7840 (mtm110) outliers start: 51 outliers final: 37 residues processed: 279 average time/residue: 0.3159 time to fit residues: 132.6936 Evaluate side-chains 270 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 241 ILE 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 348 VAL Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain I residue 89 HIS Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 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 100 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 154 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 83 optimal weight: 0.9980 chunk 224 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN M 287 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.129096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097846 restraints weight = 28661.180| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.57 r_work: 0.3069 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19348 Z= 0.132 Angle : 0.543 8.217 26201 Z= 0.265 Chirality : 0.038 0.143 2975 Planarity : 0.003 0.034 3297 Dihedral : 6.930 58.071 2863 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.59 % Allowed : 14.14 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2324 helix: 1.33 (0.15), residues: 1316 sheet: -0.22 (0.44), residues: 126 loop : -0.98 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 388 HIS 0.010 0.002 HIS I 89 PHE 0.010 0.001 PHE D 129 TYR 0.026 0.001 TYR M 125 ARG 0.004 0.000 ARG I 146 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 686) hydrogen bonds : angle 3.25462 ( 2058) covalent geometry : bond 0.00321 (19348) covalent geometry : angle 0.54292 (26201) *********************** 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 285 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 198 TYR cc_start: 0.9148 (t80) cc_final: 0.8902 (t80) REVERT: D 352 GLU cc_start: 0.7943 (pm20) cc_final: 0.7595 (mp0) REVERT: D 366 LEU cc_start: 0.8898 (tp) cc_final: 0.8671 (tt) REVERT: D 415 ASP cc_start: 0.7516 (m-30) cc_final: 0.7220 (m-30) REVERT: D 429 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8262 (tp) REVERT: B 304 SER cc_start: 0.8775 (t) cc_final: 0.8415 (p) REVERT: E 158 ARG cc_start: 0.8563 (mpp80) cc_final: 0.8325 (mtt90) REVERT: E 357 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.8894 (mtpp) REVERT: E 385 MET cc_start: 0.9001 (tpp) cc_final: 0.8473 (tpp) REVERT: E 415 ASP cc_start: 0.7575 (m-30) cc_final: 0.7326 (m-30) REVERT: G 343 MET cc_start: 0.9343 (mmm) cc_final: 0.9098 (mmm) REVERT: G 357 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8815 (mtpt) REVERT: I 357 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8955 (mtpt) REVERT: K 240 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8564 (mm) REVERT: K 338 MET cc_start: 0.8899 (mtp) cc_final: 0.8687 (mtm) REVERT: K 372 MET cc_start: 0.9110 (mtp) cc_final: 0.8844 (mtp) REVERT: M 165 PHE cc_start: 0.7957 (m-10) cc_final: 0.7664 (m-10) REVERT: M 240 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8193 (mt) REVERT: M 367 ARG cc_start: 0.8226 (ttp-110) cc_final: 0.7855 (mtm110) outliers start: 53 outliers final: 38 residues processed: 277 average time/residue: 0.3423 time to fit residues: 141.9665 Evaluate side-chains 270 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 2.280 ------------------------------------------------------------------------------- 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 241 ILE 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 276 MET Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 357 LYS Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 300 GLU 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 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 100 ASN 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 87 optimal weight: 0.3980 chunk 186 optimal weight: 4.9990 chunk 101 optimal weight: 0.0050 chunk 65 optimal weight: 0.8980 chunk 213 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 97 optimal weight: 0.0370 chunk 7 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.3672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100311 restraints weight = 28464.457| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.48 r_work: 0.3104 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3899 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= 0.101 Angle : 0.526 9.770 26201 Z= 0.255 Chirality : 0.037 0.142 2975 Planarity : 0.003 0.036 3297 Dihedral : 6.830 58.003 2863 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.01 % Allowed : 14.43 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2324 helix: 1.51 (0.15), residues: 1309 sheet: -0.15 (0.44), residues: 126 loop : -0.95 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 388 HIS 0.013 0.002 HIS K 89 PHE 0.010 0.001 PHE G 384 TYR 0.024 0.001 TYR M 362 ARG 0.008 0.000 ARG K 267 Details of bonding type rmsd hydrogen bonds : bond 0.02579 ( 686) hydrogen bonds : angle 3.16357 ( 2058) covalent geometry : bond 0.00238 (19348) covalent geometry : angle 0.52600 (26201) *********************** 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 277 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 HIS cc_start: 0.8961 (OUTLIER) cc_final: 0.8636 (p-80) REVERT: D 352 GLU cc_start: 0.7914 (pm20) cc_final: 0.7571 (mp0) REVERT: D 366 LEU cc_start: 0.8857 (tp) cc_final: 0.8622 (tt) REVERT: D 429 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8242 (tp) REVERT: B 304 SER cc_start: 0.8772 (t) cc_final: 0.8430 (p) REVERT: E 385 MET cc_start: 0.8965 (tpp) cc_final: 0.8506 (tpp) REVERT: E 415 ASP cc_start: 0.7552 (m-30) cc_final: 0.7297 (m-30) REVERT: G 343 MET cc_start: 0.9353 (mmm) cc_final: 0.9134 (mmm) REVERT: G 379 ARG cc_start: 0.8313 (tpp-160) cc_final: 0.7977 (mmm160) REVERT: I 280 GLU cc_start: 0.7936 (mp0) cc_final: 0.7644 (tt0) REVERT: K 240 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8468 (mm) REVERT: K 338 MET cc_start: 0.8846 (mtp) cc_final: 0.8618 (mtm) REVERT: K 372 MET cc_start: 0.9068 (mtp) cc_final: 0.8800 (mtp) REVERT: M 165 PHE cc_start: 0.7812 (m-10) cc_final: 0.7516 (m-10) REVERT: M 231 ASP cc_start: 0.7521 (p0) cc_final: 0.7088 (p0) REVERT: M 240 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.7994 (mt) REVERT: M 367 ARG cc_start: 0.8195 (ttp-110) cc_final: 0.7888 (mtm110) outliers start: 41 outliers final: 31 residues processed: 270 average time/residue: 0.3287 time to fit residues: 134.4562 Evaluate side-chains 262 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 2.176 ------------------------------------------------------------------------------- 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 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 276 MET Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 LEU 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 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 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 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 1 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 158 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN E 340 ASN G 147 GLN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.098084 restraints weight = 28565.039| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.53 r_work: 0.3055 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19348 Z= 0.154 Angle : 0.574 8.504 26201 Z= 0.280 Chirality : 0.039 0.144 2975 Planarity : 0.003 0.033 3297 Dihedral : 6.969 58.116 2863 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.05 % Allowed : 14.73 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2324 helix: 1.39 (0.15), residues: 1316 sheet: -0.19 (0.44), residues: 126 loop : -0.91 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 388 HIS 0.012 0.002 HIS K 89 PHE 0.013 0.001 PHE D 129 TYR 0.024 0.001 TYR M 362 ARG 0.007 0.000 ARG K 267 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 686) hydrogen bonds : angle 3.33100 ( 2058) covalent geometry : bond 0.00375 (19348) covalent geometry : angle 0.57396 (26201) ********************** 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 270 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8794 (p-80) REVERT: D 295 MET cc_start: 0.6908 (mmp) cc_final: 0.6594 (mmp) REVERT: D 366 LEU cc_start: 0.8924 (tp) cc_final: 0.8697 (tt) REVERT: D 429 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8270 (tp) REVERT: B 304 SER cc_start: 0.8829 (t) cc_final: 0.8483 (p) REVERT: E 385 MET cc_start: 0.9015 (tpp) cc_final: 0.8508 (tpp) REVERT: E 415 ASP cc_start: 0.7591 (m-30) cc_final: 0.7344 (m-30) REVERT: G 357 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8798 (mtpt) REVERT: I 357 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8984 (mtpt) REVERT: K 240 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8508 (mm) REVERT: K 338 MET cc_start: 0.8912 (mtp) cc_final: 0.8708 (mtm) REVERT: K 372 MET cc_start: 0.9144 (mtp) cc_final: 0.8875 (mtp) REVERT: M 240 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7934 (mt) REVERT: M 367 ARG cc_start: 0.8245 (ttp-110) cc_final: 0.7929 (mtm110) outliers start: 42 outliers final: 34 residues processed: 262 average time/residue: 0.3279 time to fit residues: 128.8515 Evaluate side-chains 262 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 2.183 ------------------------------------------------------------------------------- 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 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 276 MET Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 300 GLU 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 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 100 ASN Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 240 LEU Chi-restraints excluded: chain K residue 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 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 37 optimal weight: 0.0770 chunk 202 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 213 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 ASN ** M 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099442 restraints weight = 28463.505| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.52 r_work: 0.3082 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19348 Z= 0.118 Angle : 0.549 9.266 26201 Z= 0.267 Chirality : 0.038 0.143 2975 Planarity : 0.003 0.033 3297 Dihedral : 6.885 57.991 2863 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.96 % Allowed : 14.97 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.17), residues: 2324 helix: 1.46 (0.15), residues: 1316 sheet: -0.14 (0.44), residues: 126 loop : -0.88 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 388 HIS 0.011 0.002 HIS K 89 PHE 0.010 0.001 PHE M 165 TYR 0.024 0.001 TYR M 125 ARG 0.007 0.000 ARG K 267 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 686) hydrogen bonds : angle 3.28289 ( 2058) covalent geometry : bond 0.00283 (19348) covalent geometry : angle 0.54872 (26201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8900.26 seconds wall clock time: 154 minutes 36.93 seconds (9276.93 seconds total)