Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3081210.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3081210.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3081210.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.28, per 1000 atoms: 0.38 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 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: 0.52 Conformation dependent library (CDL) restraints added in 194.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 512 0.91 - 1.16: 1125 1.16 - 1.41: 641 1.41 - 1.67: 832 1.67 - 1.92: 43 Bond restraints: 3153 Sorted by residual: bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.156 0.222 1.10e-02 8.26e+03 4.09e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.511 -0.190 1.00e-02 1.00e+04 3.61e+02 bond pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 1.330 1.539 -0.209 1.22e-02 6.72e+03 2.94e+02 bond pdb=" CA LEU A 72 " pdb=" C LEU A 72 " ideal model delta sigma weight residual 1.521 1.741 -0.220 1.32e-02 5.74e+03 2.78e+02 bond pdb=" N VAL A 186 " pdb=" CA VAL A 186 " ideal model delta sigma weight residual 1.459 1.251 0.208 1.25e-02 6.40e+03 2.76e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.14: 3403 5.14 - 10.27: 1796 10.27 - 15.41: 522 15.41 - 20.54: 53 20.54 - 25.68: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLU A 163 " pdb=" C GLU A 163 " pdb=" N PHE A 164 " ideal model delta sigma weight residual 122.08 106.03 16.05 1.07e+00 8.73e-01 2.25e+02 angle pdb=" CA ALYS A 93 " pdb=" C ALYS A 93 " pdb=" O ALYS A 93 " ideal model delta sigma weight residual 120.63 136.22 -15.59 1.08e+00 8.57e-01 2.08e+02 angle pdb=" O VAL A 44 " pdb=" C VAL A 44 " pdb=" N GLN A 45 " ideal model delta sigma weight residual 123.10 139.29 -16.19 1.17e+00 7.31e-01 1.91e+02 angle pdb=" O LYS A 12 " pdb=" C LYS A 12 " pdb=" N GLY A 13 " ideal model delta sigma weight residual 122.87 139.41 -16.54 1.23e+00 6.61e-01 1.81e+02 angle pdb=" N SER A 47 " pdb=" CA SER A 47 " pdb=" C SER A 47 " ideal model delta sigma weight residual 111.33 127.40 -16.07 1.21e+00 6.83e-01 1.76e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.25: 1306 17.25 - 34.48: 120 34.48 - 51.72: 34 51.72 - 68.95: 17 68.95 - 86.19: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 151 " pdb=" N LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual -122.60 -145.57 22.97 0 2.50e+00 1.60e-01 8.44e+01 dihedral pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual 122.80 145.17 -22.37 0 2.50e+00 1.60e-01 8.00e+01 dihedral pdb=" C ARG A 98 " pdb=" N ARG A 98 " pdb=" CA ARG A 98 " pdb=" CB ARG A 98 " ideal model delta harmonic sigma weight residual -122.60 -144.13 21.53 0 2.50e+00 1.60e-01 7.42e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 86 0.227 - 0.455: 74 0.455 - 0.682: 55 0.682 - 0.910: 20 0.910 - 1.137: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 7 " pdb=" CB LEU A 7 " pdb=" CD1 LEU A 7 " pdb=" CD2 LEU A 7 " both_signs ideal model delta sigma weight residual False -2.59 -3.73 1.14 2.00e-01 2.50e+01 3.23e+01 chirality pdb=" CA ARG A 98 " pdb=" N ARG A 98 " pdb=" C ARG A 98 " pdb=" CB ARG A 98 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA SER A 57 " pdb=" N SER A 57 " pdb=" C SER A 57 " pdb=" CB SER A 57 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.69e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.076 2.00e-02 2.50e+03 6.41e-02 1.23e+02 pdb=" CG TYR A 139 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.113 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.076 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.024 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.062 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.031 2.00e-02 2.50e+03 5.29e-02 8.38e+01 pdb=" CG ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.062 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.096 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.053 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.029 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.009 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.064 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.007 2.00e-02 2.50e+03 5.28e-02 8.37e+01 pdb=" CG PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.099 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.027 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.045 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.100 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.037 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.028 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 643 2.25 - 2.84: 7583 2.84 - 3.43: 10714 3.43 - 4.01: 15390 4.01 - 4.60: 22239 Nonbonded interactions: 56569 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.663 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.772 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.777 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.804 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.833 2.450 ... (remaining 56564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_3081210_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3623 r_free= 0.2041 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474652 | | target function (ml) not normalized (work): 22060.034690 | | target function (ml) not normalized (free): 1154.222567 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3810 0.2240 4.8544 4.9164| | 2: 3.78 - 3.00 1.00 2430 110 0.3394 0.1703 4.084 4.1463| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.79 2500 142 0.50 48.79 0.83 0.13 6606.59| | 2: 3.78 - 3.00 2430 110 0.93 11.67 1.48 0.26 468.49| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 406.68 max = 12072.81 mean = 3581.12| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.97 mean = 30.50| |phase err.(test): min = 0.00 max = 89.99 mean = 33.40| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.228 1557 Z= 5.393 Angle : 5.341 17.586 2118 Z= 3.715 Chirality : 0.444 1.137 243 Planarity : 0.031 0.085 284 Dihedral : 13.921 86.187 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 35.14 % Peptide Plane: Cis-proline : 18.18 % 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: -3.26 (0.48), residues: 224 helix: -3.12 (0.36), residues: 109 sheet: -0.94 (0.83), residues: 38 loop : -0.82 (0.61), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.099 0.019 ARG A 5 TYR 0.086 0.039 TYR A 139 PHE 0.083 0.029 PHE A 164 HIS 0.076 0.030 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3623 r_free= 0.2041 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474652 | | target function (ml) not normalized (work): 22060.034690 | | target function (ml) not normalized (free): 1154.222567 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3575 0.3653 0.2117 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3575 0.3653 0.2117 n_refl.: 5182 remove outliers: r(all,work,free)=0.2525 0.2550 0.2117 n_refl.: 5178 overall B=-2.80 to atoms: r(all,work,free)=0.2418 0.2439 0.2076 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1579 0.1577 0.1631 n_refl.: 5178 remove outliers: r(all,work,free)=0.1577 0.1574 0.1631 n_refl.: 5177 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4067 445.093 408.304 0.691 1.023 0.398 11.894-9.307 99.02 97 4 0.1952 714.542 695.453 0.973 1.024 0.372 9.237-7.194 100.00 213 7 0.2145 584.353 575.913 1.009 1.022 0.357 7.162-5.571 100.00 427 22 0.2350 438.486 425.289 0.966 1.017 0.294 5.546-4.326 100.00 867 58 0.1389 601.979 594.390 0.996 1.009 0.278 4.315-3.360 100.00 1859 96 0.1309 572.489 566.007 1.046 0.996 0.200 3.356-3.002 100.00 1373 60 0.1634 440.955 432.181 1.032 0.983 0.097 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.5958 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1574 r_free=0.1631 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1574 r_free=0.1631 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.575088 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.885967 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1170 0.1806 0.0636 0.010 1.0 3.2 0.5 0.0 0 9.288 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.70 18.06 6.36 3.013 16.061 1.886 0.018 10.30 17.94 7.63 4.883 16.203 1.886 0.015 Individual atomic B min max mean iso aniso Overall: 1.79 111.50 17.36 5.28 1785 0 Protein: 1.79 111.14 14.67 5.28 1519 0 Water: 4.07 111.50 32.96 N/A 258 0 Other: 16.95 37.05 24.10 N/A 8 0 Chain A: 1.79 111.50 17.36 N/A 1785 0 Histogram: Values Number of atoms 1.79 - 12.76 902 12.76 - 23.73 493 23.73 - 34.70 192 34.70 - 45.67 113 45.67 - 56.64 55 56.64 - 67.62 13 67.62 - 78.59 8 78.59 - 89.56 5 89.56 - 100.53 1 100.53 - 111.50 3 =========================== Idealize ADP of riding H ========================== r_work=0.1030 r_free=0.1794 r_work=0.1024 r_free=0.1800 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1024 r_free = 0.1800 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1018 r_free = 0.1794 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1018 r_free= 0.1794 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014253 | | target function (ls_wunit_k1) not normalized (work): 70.194971 | | target function (ls_wunit_k1) not normalized (free): 10.632548 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1058 0.1018 0.1794 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2102 0.2102 0.2203 n_refl.: 5177 remove outliers: r(all,work,free)=0.2102 0.2102 0.2203 n_refl.: 5177 overall B=-0.98 to atoms: r(all,work,free)=0.2061 0.2059 0.2193 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1053 0.1014 0.1774 n_refl.: 5177 remove outliers: r(all,work,free)=0.1051 0.1012 0.1774 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3425 323.785 306.149 0.663 1.006 0.370 11.894-9.307 99.02 97 4 0.1563 524.271 516.171 0.983 1.008 0.351 9.237-7.194 100.00 213 7 0.1670 428.749 427.800 1.025 1.008 0.317 7.162-5.571 100.00 427 22 0.1613 321.724 317.861 0.986 1.006 0.296 5.546-4.326 100.00 867 58 0.0913 441.682 438.537 1.001 1.004 0.232 4.315-3.360 100.00 1859 96 0.0755 420.044 419.966 1.043 0.999 0.193 3.356-3.002 100.00 1373 60 0.1008 323.536 322.404 1.014 0.995 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.4947 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1012 r_free=0.1774 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1014 r_free=0.1774 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1014 r_free=0.1774 | n_water=258 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.1041 r_free=0.1777 | n_water=246 | time (s): 22.130 (total time: 22.670) Filter (q & B) r_work=0.1040 r_free=0.1774 | n_water=243 | time (s): 1.500 (total time: 24.170) Compute maps r_work=0.1040 r_free=0.1774 | n_water=243 | time (s): 0.450 (total time: 24.620) Filter (map) r_work=0.1335 r_free=0.1864 | n_water=145 | time (s): 1.340 (total time: 25.960) Find peaks r_work=0.1335 r_free=0.1864 | n_water=145 | time (s): 0.410 (total time: 26.370) Add new water r_work=0.1690 r_free=0.2116 | n_water=231 | time (s): 1.550 (total time: 27.920) Refine new water occ: r_work=0.1155 r_free=0.1676 adp: r_work=0.1128 r_free=0.1679 occ: r_work=0.1124 r_free=0.1668 adp: r_work=0.1111 r_free=0.1670 occ: r_work=0.1110 r_free=0.1655 adp: r_work=0.1106 r_free=0.1655 ADP+occupancy (water only), MIN, final r_work=0.1106 r_free=0.1655 r_work=0.1106 r_free=0.1655 | n_water=231 | time (s): 4.760 (total time: 32.680) Filter (q & B) r_work=0.1106 r_free=0.1655 | n_water=231 | time (s): 0.730 (total time: 33.410) Filter (dist only) r_work=0.1112 r_free=0.1642 | n_water=229 | time (s): 18.130 (total time: 51.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.744320 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.767899 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1005 0.1733 0.0728 0.009 1.0 4.5 0.5 0.0 0 11.872 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.05 17.33 7.28 4.655 16.751 2.768 0.014 9.38 17.34 7.97 5.405 17.121 2.768 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.94 16.55 6.42 1756 0 Protein: 0.00 106.94 14.90 6.39 1519 0 Water: 0.00 62.80 27.09 N/A 229 0 Other: 17.03 44.31 27.52 N/A 8 0 Chain A: 0.00 106.94 15.64 N/A 1671 0 Chain S: 2.38 61.13 34.27 N/A 85 0 Histogram: Values Number of atoms 0.00 - 10.69 684 10.69 - 21.39 665 21.39 - 32.08 205 32.08 - 42.78 117 42.78 - 53.47 40 53.47 - 64.16 32 64.16 - 74.86 6 74.86 - 85.55 3 85.55 - 96.25 2 96.25 - 106.94 2 =========================== Idealize ADP of riding H ========================== r_work=0.0938 r_free=0.1734 r_work=0.0934 r_free=0.1731 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0934 r_free = 0.1731 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0931 r_free = 0.1728 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0931 r_free= 0.1728 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.011743 | | target function (ls_wunit_k1) not normalized (work): 57.822432 | | target function (ls_wunit_k1) not normalized (free): 9.744653 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0972 0.0931 0.1728 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2115 0.2118 0.2190 n_refl.: 5176 remove outliers: r(all,work,free)=0.2115 0.2118 0.2190 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2115 0.2118 0.2190 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0972 0.0931 0.1737 n_refl.: 5176 remove outliers: r(all,work,free)=0.0970 0.0929 0.1737 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3176 325.900 305.988 0.659 1.005 0.360 11.894-9.307 99.02 97 4 0.1527 524.271 519.200 0.979 1.007 0.340 9.237-7.194 100.00 213 7 0.1423 428.749 429.919 1.025 1.007 0.304 7.162-5.571 100.00 427 22 0.1376 321.724 319.170 0.997 1.006 0.290 5.546-4.326 100.00 867 58 0.0780 441.682 439.113 1.010 1.003 0.250 4.315-3.360 100.00 1859 96 0.0714 420.044 419.841 1.054 0.999 0.190 3.356-3.002 100.00 1373 60 0.0980 323.536 322.237 1.029 0.995 0.067 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-4.1194 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0929 r_free=0.1737 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0931 r_free=0.1747 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0931 r_free=0.1747 | n_water=229 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.0955 r_free=0.1731 | n_water=223 | time (s): 17.290 (total time: 17.900) Filter (q & B) r_work=0.1009 r_free=0.1756 | n_water=221 | time (s): 1.280 (total time: 19.180) Compute maps r_work=0.1009 r_free=0.1756 | n_water=221 | time (s): 0.610 (total time: 19.790) Filter (map) r_work=0.1264 r_free=0.1850 | n_water=155 | time (s): 1.530 (total time: 21.320) Find peaks r_work=0.1264 r_free=0.1850 | n_water=155 | time (s): 0.590 (total time: 21.910) Add new water r_work=0.1592 r_free=0.2159 | n_water=232 | time (s): 1.770 (total time: 23.680) Refine new water occ: r_work=0.1037 r_free=0.1684 adp: r_work=0.1031 r_free=0.1690 occ: r_work=0.1021 r_free=0.1672 adp: r_work=0.1019 r_free=0.1679 occ: r_work=0.1011 r_free=0.1662 adp: r_work=0.1010 r_free=0.1671 ADP+occupancy (water only), MIN, final r_work=0.1010 r_free=0.1671 r_work=0.1010 r_free=0.1671 | n_water=232 | time (s): 8.940 (total time: 32.620) Filter (q & B) r_work=0.1011 r_free=0.1677 | n_water=230 | time (s): 1.370 (total time: 33.990) Filter (dist only) r_work=0.1011 r_free=0.1677 | n_water=230 | time (s): 16.570 (total time: 50.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.087352 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.250288 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0923 0.1767 0.0844 0.011 1.1 4.5 0.5 0.0 0 0.544 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.23 17.67 8.44 5.368 17.722 0.250 5.147 8.79 18.06 9.26 7.509 17.785 0.250 5.051 Individual atomic B min max mean iso aniso Overall: 0.00 105.56 16.44 9.29 1757 0 Protein: 0.00 105.56 15.09 9.26 1519 0 Water: 0.00 60.94 24.90 N/A 230 0 Other: 16.75 44.06 28.97 N/A 8 0 Chain A: 0.00 105.56 15.80 N/A 1660 0 Chain S: 0.00 60.94 27.34 N/A 97 0 Histogram: Values Number of atoms 0.00 - 10.56 661 10.56 - 21.11 654 21.11 - 31.67 237 31.67 - 42.22 120 42.22 - 52.78 48 52.78 - 63.33 18 63.33 - 73.89 10 73.89 - 84.45 4 84.45 - 95.00 4 95.00 - 105.56 1 =========================== Idealize ADP of riding H ========================== r_work=0.0879 r_free=0.1806 r_work=0.0886 r_free=0.1819 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0886 r_free = 0.1819 target_work(ml) = 5.055 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0875 r_free = 0.1800 target_work(ml) = 5.048 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0875 r_free= 0.1800 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.048195 | | target function (ml) not normalized (work): 24852.265192 | | target function (ml) not normalized (free): 1810.037587 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0922 0.0875 0.1800 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2050 0.2050 0.2182 n_refl.: 5175 remove outliers: r(all,work,free)=0.2050 0.2050 0.2182 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2050 0.2050 0.2182 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0918 0.0872 0.1790 n_refl.: 5175 remove outliers: r(all,work,free)=0.0918 0.0872 0.1790 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3624 325.900 297.179 0.583 0.992 0.328 11.894-9.307 99.02 97 4 0.1874 524.271 513.442 0.951 0.996 0.327 9.237-7.194 100.00 213 7 0.1835 428.749 425.292 1.008 0.998 0.310 7.162-5.571 100.00 427 22 0.1735 321.724 314.244 0.981 0.999 0.290 5.546-4.326 100.00 867 58 0.0901 441.682 435.548 0.997 1.000 0.260 4.315-3.360 100.00 1859 96 0.0578 420.044 419.411 1.047 1.002 0.210 3.356-3.002 100.00 1373 60 0.0609 323.536 323.017 1.021 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-5.9668 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0872 r_free=0.1790 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0873 r_free=0.1788 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0873 r_free=0.1788 | n_water=230 | time (s): 0.480 (total time: 0.480) Filter (dist) r_work=0.0880 r_free=0.1785 | n_water=229 | time (s): 18.630 (total time: 19.110) Filter (q & B) r_work=0.0977 r_free=0.1846 | n_water=224 | time (s): 1.210 (total time: 20.320) Compute maps r_work=0.0977 r_free=0.1846 | n_water=224 | time (s): 0.440 (total time: 20.760) Filter (map) r_work=0.1243 r_free=0.1987 | n_water=157 | time (s): 1.560 (total time: 22.320) Find peaks r_work=0.1243 r_free=0.1987 | n_water=157 | time (s): 0.460 (total time: 22.780) Add new water r_work=0.1564 r_free=0.2327 | n_water=230 | time (s): 1.760 (total time: 24.540) Refine new water r_work=0.1564 r_free=0.2327 | n_water=230 | time (s): 0.100 (total time: 24.640) Filter (q & B) r_work=0.1243 r_free=0.1987 | n_water=157 | time (s): 1.610 (total time: 26.250) Filter (dist only) r_work=0.1266 r_free=0.1979 | n_water=151 | time (s): 12.440 (total time: 38.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.431933 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.300449 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1110 0.2033 0.0923 0.011 1.1 5.1 0.5 0.0 0 0.716 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.10 20.33 9.23 7.190 17.776 0.300 5.357 10.48 20.13 9.65 8.408 17.836 0.300 5.275 Individual atomic B min max mean iso aniso Overall: 0.00 103.80 16.12 10.51 1678 0 Protein: 0.00 103.80 15.30 10.48 1519 0 Water: 0.00 56.08 23.78 N/A 151 0 Other: 12.19 46.77 28.04 N/A 8 0 Chain A: 0.00 103.80 15.87 N/A 1641 0 Chain S: 3.13 56.08 27.34 N/A 37 0 Histogram: Values Number of atoms 0.00 - 10.38 642 10.38 - 20.76 603 20.76 - 31.14 245 31.14 - 41.52 107 41.52 - 51.90 45 51.90 - 62.28 15 62.28 - 72.66 10 72.66 - 83.04 5 83.04 - 93.42 4 93.42 - 103.80 2 =========================== Idealize ADP of riding H ========================== r_work=0.1048 r_free=0.2013 r_work=0.1052 r_free=0.2016 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1052 r_free = 0.2016 target_work(ml) = 5.279 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1050 r_free = 0.2013 target_work(ml) = 5.277 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1050 r_free= 0.2013 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.276759 | | target function (ml) not normalized (work): 25977.484572 | | target function (ml) not normalized (free): 1699.619721 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1098 0.1050 0.2013 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2312 0.2306 0.2533 n_refl.: 5175 remove outliers: r(all,work,free)=0.2312 0.2306 0.2533 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2312 0.2306 0.2533 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1084 0.1036 0.1999 n_refl.: 5175 remove outliers: r(all,work,free)=0.1084 0.1036 0.1999 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3827 325.900 296.906 0.674 0.995 0.360 11.894-9.307 99.02 97 4 0.1714 524.271 509.686 1.025 0.998 0.355 9.237-7.194 100.00 213 7 0.1907 428.749 423.322 1.048 1.000 0.350 7.162-5.571 100.00 427 22 0.1757 321.724 317.159 1.029 1.000 0.320 5.546-4.326 100.00 867 58 0.1051 441.682 434.818 1.025 1.001 0.280 4.315-3.360 100.00 1859 96 0.0760 420.044 418.145 1.098 1.002 0.240 3.356-3.002 100.00 1373 60 0.0848 323.536 322.371 1.089 1.002 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-6.5603 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1036 r_free=0.1999 After: r_work=0.1039 r_free=0.1999 ================================== NQH flips ================================== r_work=0.1039 r_free=0.1999 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1039 r_free=0.1999 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1039 r_free=0.1999 | n_water=151 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.1054 r_free=0.1998 | n_water=148 | time (s): 12.940 (total time: 13.410) Filter (q & B) r_work=0.1081 r_free=0.1974 | n_water=147 | time (s): 1.730 (total time: 15.140) Compute maps r_work=0.1081 r_free=0.1974 | n_water=147 | time (s): 0.500 (total time: 15.640) Filter (map) r_work=0.1112 r_free=0.1950 | n_water=136 | time (s): 2.100 (total time: 17.740) Find peaks r_work=0.1112 r_free=0.1950 | n_water=136 | time (s): 0.510 (total time: 18.250) Add new water r_work=0.1430 r_free=0.2270 | n_water=206 | time (s): 1.520 (total time: 19.770) Refine new water occ: r_work=0.1113 r_free=0.1976 adp: r_work=0.1114 r_free=0.2002 occ: r_work=0.1097 r_free=0.1962 adp: r_work=0.1099 r_free=0.1983 occ: r_work=0.1081 r_free=0.1942 adp: r_work=0.1083 r_free=0.1961 ADP+occupancy (water only), MIN, final r_work=0.1083 r_free=0.1961 r_work=0.1083 r_free=0.1961 | n_water=206 | time (s): 11.460 (total time: 31.230) Filter (q & B) r_work=0.1084 r_free=0.1971 | n_water=202 | time (s): 1.760 (total time: 32.990) Filter (dist only) r_work=0.1082 r_free=0.1958 | n_water=200 | time (s): 15.880 (total time: 48.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.130669 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.239705 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1047 0.2069 0.1022 0.011 1.2 8.0 0.5 0.0 0 0.565 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.47 20.69 10.22 7.985 18.111 0.240 5.223 10.17 20.60 10.43 8.565 18.118 0.240 5.166 Individual atomic B min max mean iso aniso Overall: 0.00 101.81 16.78 11.13 1727 0 Protein: 0.00 101.81 15.51 11.11 1519 0 Water: 1.24 57.39 25.98 N/A 200 0 Other: 11.89 48.33 28.06 N/A 8 0 Chain A: 0.00 101.81 15.99 N/A 1634 0 Chain S: 1.24 57.39 30.74 N/A 93 0 Histogram: Values Number of atoms 0.00 - 10.18 625 10.18 - 20.36 594 20.36 - 30.54 287 30.54 - 40.72 115 40.72 - 50.90 60 50.90 - 61.08 19 61.08 - 71.26 14 71.26 - 81.45 5 81.45 - 91.63 4 91.63 - 101.81 4 =========================== Idealize ADP of riding H ========================== r_work=0.1017 r_free=0.2060 r_work=0.1021 r_free=0.2060 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1021 r_free = 0.2060 target_work(ml) = 5.169 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0979 r_free = 0.2006 target_work(ml) = 5.139 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0979 r_free= 0.2006 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.138684 | | target function (ml) not normalized (work): 25297.739602 | | target function (ml) not normalized (free): 1813.819453 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1286 0.1981 5.574 6.1424| | 2: 3.78 - 3.00 1.00 2430 110 0.0605 0.2048 4.6921 8.5601| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.91 12.51 1.00 0.95 13354.17| | 2: 3.78 - 3.00 2430 110 0.98 3.43 1.01 0.98 1671.61| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 1189.16 max = 21463.75 mean = 7587.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.63 mean = 8.03| |phase err.(test): min = 0.00 max = 88.97 mean = 8.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1031 0.0979 0.2006 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2244 0.2243 0.2353 n_refl.: 5175 remove outliers: r(all,work,free)=0.2244 0.2243 0.2353 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2244 0.2243 0.2353 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1027 0.0976 0.1993 n_refl.: 5175 remove outliers: r(all,work,free)=0.1027 0.0976 0.1993 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.4012 325.900 290.675 0.602 0.986 0.330 11.894-9.307 99.02 97 4 0.1767 524.271 510.261 0.989 0.991 0.340 9.237-7.194 100.00 213 7 0.2152 428.749 416.714 1.022 0.994 0.324 7.162-5.571 100.00 427 22 0.1973 321.724 314.850 0.996 0.996 0.310 5.546-4.326 100.00 867 58 0.1048 441.682 436.259 1.014 0.999 0.270 4.315-3.360 100.00 1859 96 0.0675 420.044 418.634 1.091 1.002 0.240 3.356-3.002 100.00 1373 60 0.0610 323.536 323.809 1.080 1.006 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.2113 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3623 0.2041 0.081 5.341 8.8 119.3 19.9 258 0.000 1_bss: 0.1574 0.1631 0.081 5.341 6.0 116.5 17.1 258 0.000 1_settarget: 0.1574 0.1631 0.081 5.341 6.0 116.5 17.1 258 0.000 1_nqh: 0.1574 0.1631 0.081 5.341 6.0 116.5 17.1 258 0.000 1_weight: 0.1574 0.1631 0.081 5.341 6.0 116.5 17.1 258 0.000 1_xyzrec: 0.1170 0.1806 0.010 0.961 6.0 116.5 17.1 258 0.210 1_adp: 0.1030 0.1794 0.010 0.961 1.8 111.5 17.4 258 0.210 1_regHadp: 0.1024 0.1800 0.010 0.961 1.8 111.5 17.4 258 0.210 1_occ: 0.1018 0.1794 0.010 0.961 1.8 111.5 17.4 258 0.210 2_bss: 0.1012 0.1774 0.010 0.961 0.8 110.5 16.4 258 0.210 2_settarget: 0.1012 0.1774 0.010 0.961 0.8 110.5 16.4 258 0.210 2_updatecdl: 0.1012 0.1774 0.010 0.989 0.8 110.5 16.4 258 0.210 2_nqh: 0.1014 0.1774 0.010 0.989 0.8 110.5 16.4 258 0.213 2_sol: 0.1112 0.1642 0.010 0.989 0.8 110.2 15.8 229 n/a 2_weight: 0.1112 0.1642 0.010 0.989 0.8 110.2 15.8 229 n/a 2_xyzrec: 0.1005 0.1733 0.009 1.002 0.8 110.2 15.8 229 n/a 2_adp: 0.0938 0.1734 0.009 1.002 0.0 106.9 16.5 229 n/a 2_regHadp: 0.0934 0.1731 0.009 1.002 0.0 106.9 16.5 229 n/a 2_occ: 0.0931 0.1728 0.009 1.002 0.0 106.9 16.5 229 n/a 3_bss: 0.0929 0.1737 0.009 1.002 0.0 106.9 16.5 229 n/a 3_settarget: 0.0929 0.1737 0.009 1.002 0.0 106.9 16.5 229 n/a 3_updatecdl: 0.0929 0.1737 0.009 1.007 0.0 106.9 16.5 229 n/a 3_nqh: 0.0931 0.1747 0.009 1.007 0.0 106.9 16.5 229 n/a 3_sol: 0.1011 0.1677 0.009 1.007 0.0 106.9 16.3 230 n/a 3_weight: 0.1011 0.1677 0.009 1.007 0.0 106.9 16.3 230 n/a 3_xyzrec: 0.0923 0.1767 0.011 1.088 0.0 106.9 16.3 230 n/a 3_adp: 0.0879 0.1806 0.011 1.088 0.0 105.6 16.4 230 n/a 3_regHadp: 0.0886 0.1819 0.011 1.088 0.0 105.6 16.4 230 n/a 3_occ: 0.0875 0.1800 0.011 1.088 0.0 105.6 16.4 230 n/a 4_bss: 0.0872 0.1790 0.011 1.088 0.0 105.6 16.4 230 n/a 4_settarget: 0.0872 0.1790 0.011 1.088 0.0 105.6 16.4 230 n/a 4_updatecdl: 0.0872 0.1790 0.011 1.089 0.0 105.6 16.4 230 n/a 4_nqh: 0.0873 0.1788 0.011 1.089 0.0 105.6 16.4 230 n/a 4_sol: 0.1266 0.1979 0.011 1.089 0.0 105.6 16.0 151 n/a 4_weight: 0.1266 0.1979 0.011 1.089 0.0 105.6 16.0 151 n/a 4_xyzrec: 0.1110 0.2033 0.011 1.100 0.0 105.6 16.0 151 n/a 4_adp: 0.1048 0.2013 0.011 1.100 0.0 103.8 16.1 151 n/a 4_regHadp: 0.1052 0.2016 0.011 1.100 0.0 103.8 16.1 151 n/a 4_occ: 0.1050 0.2013 0.011 1.100 0.0 103.8 16.1 151 n/a 5_bss: 0.1036 0.1999 0.011 1.100 0.0 103.8 16.1 151 n/a 5_settarget: 0.1036 0.1999 0.011 1.100 0.0 103.8 16.1 151 n/a 5_updatecdl: 0.1036 0.1999 0.011 1.113 0.0 103.8 16.1 151 n/a 5_setrh: 0.1039 0.1999 0.011 1.113 0.0 103.8 16.1 151 n/a 5_nqh: 0.1039 0.1999 0.011 1.113 0.0 103.8 16.1 151 n/a 5_sol: 0.1082 0.1958 0.011 1.113 0.0 103.8 16.8 200 n/a 5_weight: 0.1082 0.1958 0.011 1.113 0.0 103.8 16.8 200 n/a 5_xyzrec: 0.1047 0.2069 0.011 1.187 0.0 103.8 16.8 200 n/a 5_adp: 0.1017 0.2060 0.011 1.187 0.0 101.8 16.8 200 n/a 5_regHadp: 0.1021 0.2060 0.011 1.187 0.0 101.8 16.8 200 n/a 5_occ: 0.0979 0.2006 0.011 1.187 0.0 101.8 16.8 200 n/a end: 0.0976 0.1993 0.011 1.187 0.0 101.8 16.8 200 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3081210_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3081210_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0700 Refinement macro-cycles (run) : 455.4100 Write final files (write_after_run_outputs) : 10.3400 Total : 468.8200 Total CPU time: 8.14 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:30 PST -0800 (1735492710.58 s) Start R-work = 0.1574, R-free = 0.1631 Final R-work = 0.0976, R-free = 0.1993 =============================================================================== Job complete usr+sys time: 497.76 seconds wall clock time: 8 minutes 40.70 seconds (520.70 seconds total)