Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2348261.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_2348261.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2348261.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 1 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: 1.79, per 1000 atoms: 0.53 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: 0.34 Conformation dependent library (CDL) restraints added in 194.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 609 0.93 - 1.19: 1053 1.19 - 1.45: 737 1.45 - 1.72: 738 1.72 - 1.98: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALYS A 175 " pdb=" CA ALYS A 175 " ideal model delta sigma weight residual 1.459 1.219 0.240 1.23e-02 6.61e+03 3.80e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.462 -0.228 1.19e-02 7.06e+03 3.67e+02 bond pdb=" N ILE A 152 " pdb=" CA ILE A 152 " ideal model delta sigma weight residual 1.459 1.695 -0.236 1.27e-02 6.20e+03 3.46e+02 bond pdb=" C VAL A 181 " pdb=" O VAL A 181 " ideal model delta sigma weight residual 1.237 1.440 -0.203 1.19e-02 7.06e+03 2.91e+02 bond pdb=" CA SER A 121 " pdb=" C SER A 121 " ideal model delta sigma weight residual 1.524 1.305 0.218 1.30e-02 5.92e+03 2.82e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.89: 3308 4.89 - 9.78: 1855 9.78 - 14.67: 527 14.67 - 19.56: 82 19.56 - 24.45: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 114.50 132.51 -18.01 1.16e+00 7.43e-01 2.41e+02 angle pdb=" O AASN A 76 " pdb=" C AASN A 76 " pdb=" N LEU A 77 " ideal model delta sigma weight residual 122.12 105.97 16.15 1.06e+00 8.90e-01 2.32e+02 angle pdb=" O PRO A 54 " pdb=" C PRO A 54 " pdb=" N ASP A 55 " ideal model delta sigma weight residual 123.00 105.52 17.48 1.22e+00 6.72e-01 2.05e+02 angle pdb=" CA ALYS A 93 " pdb=" C ALYS A 93 " pdb=" O ALYS A 93 " ideal model delta sigma weight residual 120.90 135.17 -14.27 1.07e+00 8.73e-01 1.78e+02 angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 109.37 13.23 1.00e+00 1.00e+00 1.75e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.24: 1285 16.24 - 32.48: 131 32.48 - 48.72: 43 48.72 - 64.95: 18 64.95 - 81.19: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CA THR A 110 " pdb=" CB THR A 110 " ideal model delta harmonic sigma weight residual 123.40 144.81 -21.41 0 2.50e+00 1.60e-01 7.33e+01 dihedral pdb=" C ILE A 168 " pdb=" N ILE A 168 " pdb=" CA ILE A 168 " pdb=" CB ILE A 168 " ideal model delta harmonic sigma weight residual -122.00 -142.24 20.24 0 2.50e+00 1.60e-01 6.56e+01 dihedral pdb=" N LYS A 62 " pdb=" C LYS A 62 " pdb=" CA LYS A 62 " pdb=" CB LYS A 62 " ideal model delta harmonic sigma weight residual 122.80 142.92 -20.12 0 2.50e+00 1.60e-01 6.47e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.207: 104 0.207 - 0.414: 74 0.414 - 0.620: 38 0.620 - 0.827: 23 0.827 - 1.034: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.49 1.03 2.00e-01 2.50e+01 2.67e+01 chirality pdb=" CA ALA A 104 " pdb=" N ALA A 104 " pdb=" C ALA A 104 " pdb=" CB ALA A 104 " both_signs ideal model delta sigma weight residual False 2.48 3.49 -1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.41 -0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.058 9.50e-02 1.11e+02 7.06e-02 1.04e+02 pdb=" NE ARG A 28 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.092 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " 0.107 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " 0.052 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.053 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.115 2.00e-02 2.50e+03 5.78e-02 1.00e+02 pdb=" CG PHE A 164 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.064 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.031 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.027 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.014 2.00e-02 2.50e+03 5.76e-02 9.94e+01 pdb=" CG TYR A 141 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.113 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.091 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.044 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.031 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.046 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.061 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.007 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 664 2.26 - 2.84: 7701 2.84 - 3.43: 10651 3.43 - 4.01: 15373 4.01 - 4.60: 22153 Nonbonded interactions: 56542 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.670 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.756 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.809 2.450 nonbonded pdb="HD22BASN A 76 " pdb=" HB2 PHE A 119 " model vdw sym.op. 1.845 2.270 -y,x-y-1,z+1/3 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.847 2.450 ... (remaining 56537 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_2348261_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= 0.3620 r_free= 0.1980 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.471102 | | target function (ml) not normalized (work): 22042.534899 | | target function (ml) not normalized (free): 1145.817044 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3818 0.2179 4.8546 4.8823| | 2: 3.78 - 3.00 1.00 2430 110 0.3379 0.1644 4.0765 4.1139| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.49 49.01 0.83 0.13 6620.28| | 2: 3.78 - 3.00 2430 110 0.94 11.24 1.48 0.26 446.26| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 374.09 max = 12074.51 mean = 3577.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.39| |phase err.(test): min = 0.00 max = 89.97 mean = 33.35| |-----------------------------------------------------------------------------| ----------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 0.258 1557 Z= 5.390 Angle : 5.224 18.008 2118 Z= 3.706 Chirality : 0.371 1.034 243 Planarity : 0.032 0.089 284 Dihedral : 13.767 81.187 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 3.11 % Allowed : 1.86 % Favored : 95.03 % Cbeta Deviations : 29.19 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.25 (0.49), residues: 224 helix: -2.33 (0.41), residues: 102 sheet: -1.05 (0.91), residues: 28 loop : -0.30 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.111 0.028 ARG A 27 TYR 0.107 0.036 TYR A 141 PHE 0.121 0.037 PHE A 164 HIS 0.065 0.033 HIS A 138 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= 0.3620 r_free= 0.1980 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.471102 | | target function (ml) not normalized (work): 22042.534899 | | target function (ml) not normalized (free): 1145.817044 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3578 0.3656 0.2061 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3578 0.3656 0.2061 n_refl.: 5182 remove outliers: r(all,work,free)=0.2522 0.2548 0.2061 n_refl.: 5178 overall B=-2.84 to atoms: r(all,work,free)=0.2413 0.2436 0.2023 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1562 0.1564 0.1534 n_refl.: 5178 remove outliers: r(all,work,free)=0.1556 0.1557 0.1534 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 97.87 87 5 0.3842 453.419 401.469 0.654 1.076 0.400 11.894-9.307 99.02 97 4 0.1958 714.246 690.369 0.931 1.071 0.393 9.237-7.194 100.00 213 7 0.2147 584.111 574.191 0.962 1.063 0.364 7.162-5.571 100.00 427 22 0.2347 438.305 423.729 0.932 1.049 0.295 5.546-4.326 100.00 867 58 0.1405 601.730 594.277 0.979 1.027 0.243 4.315-3.360 100.00 1859 96 0.1315 572.252 565.534 1.057 0.989 0.224 3.356-3.002 100.00 1373 60 0.1550 440.772 435.440 1.070 0.951 0.043 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9559 b_overall=-3.6207 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1557 r_free=0.1534 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1558 r_free=0.1526 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.795142 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.662112 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 0.1158 0.1785 0.0627 0.010 1.0 3.2 0.5 0.0 0 9.398 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 17.85 6.27 3.013 16.014 1.662 0.018 10.23 17.79 7.56 4.715 16.232 1.662 0.015 Individual atomic B min max mean iso aniso Overall: 2.20 111.45 17.45 5.06 1785 0 Protein: 2.20 111.27 14.77 5.05 1519 0 Water: 4.02 111.45 33.04 N/A 258 0 Other: 17.24 36.34 23.93 N/A 8 0 Chain A: 2.20 111.45 17.45 N/A 1785 0 Histogram: Values Number of atoms 2.20 - 13.12 921 13.12 - 24.05 481 24.05 - 34.97 188 34.97 - 45.90 107 45.90 - 56.83 59 56.83 - 67.75 12 67.75 - 78.68 8 78.68 - 89.60 5 89.60 - 100.53 1 100.53 - 111.45 3 =========================== Idealize ADP of riding H ========================== r_work=0.1023 r_free=0.1779 r_work=0.1017 r_free=0.1783 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1017 r_free = 0.1783 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1012 r_free = 0.1785 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.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1012 r_free= 0.1785 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014006 | | target function (ls_wunit_k1) not normalized (work): 68.949268 | | target function (ls_wunit_k1) not normalized (free): 10.778890 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1052 0.1012 0.1785 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2095 0.2093 0.2225 n_refl.: 5175 remove outliers: r(all,work,free)=0.2095 0.2093 0.2225 n_refl.: 5175 overall B=-0.98 to atoms: r(all,work,free)=0.2054 0.2051 0.2214 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1054 0.1015 0.1791 n_refl.: 5175 remove outliers: r(all,work,free)=0.1052 0.1012 0.1791 n_refl.: 5174 ======================== 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 94.79 86 5 0.3288 329.178 310.660 0.666 1.011 0.370 11.894-9.307 99.02 97 4 0.1504 522.902 515.289 0.983 1.012 0.361 9.237-7.194 100.00 213 7 0.1671 427.630 427.321 1.022 1.011 0.341 7.162-5.571 100.00 427 22 0.1616 320.884 317.752 0.981 1.008 0.299 5.546-4.326 100.00 867 58 0.0911 440.529 437.700 0.997 1.005 0.207 4.315-3.360 100.00 1859 96 0.0769 418.948 418.723 1.045 0.998 0.204 3.356-3.002 100.00 1373 60 0.1003 322.691 320.943 1.018 0.992 0.043 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.4860 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1012 r_free=0.1791 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1015 r_free=0.1799 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1015 r_free=0.1799 | n_water=258 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.1046 r_free=0.1800 | n_water=245 | time (s): 17.760 (total time: 18.310) Filter (q & B) r_work=0.1047 r_free=0.1802 | n_water=243 | time (s): 1.690 (total time: 20.000) Compute maps r_work=0.1047 r_free=0.1802 | n_water=243 | time (s): 0.610 (total time: 20.610) Filter (map) r_work=0.1346 r_free=0.1878 | n_water=144 | time (s): 1.310 (total time: 21.920) Find peaks r_work=0.1346 r_free=0.1878 | n_water=144 | time (s): 0.380 (total time: 22.300) Add new water r_work=0.1690 r_free=0.2164 | n_water=227 | time (s): 1.240 (total time: 23.540) Refine new water occ: r_work=0.1168 r_free=0.1685 adp: r_work=0.1145 r_free=0.1684 occ: r_work=0.1141 r_free=0.1671 adp: r_work=0.1141 r_free=0.1671 occ: r_work=0.1141 r_free=0.1671 adp: r_work=0.1141 r_free=0.1671 ADP+occupancy (water only), MIN, final r_work=0.1141 r_free=0.1671 r_work=0.1141 r_free=0.1671 | n_water=227 | time (s): 5.210 (total time: 28.750) Filter (q & B) r_work=0.1141 r_free=0.1671 | n_water=227 | time (s): 1.200 (total time: 29.950) Filter (dist only) r_work=0.1145 r_free=0.1652 | n_water=224 | time (s): 17.080 (total time: 47.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.644018 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.876929 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 0.1028 0.1841 0.0814 0.009 1.0 4.5 0.5 0.6 0 11.322 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.28 18.41 8.14 4.528 16.560 2.877 0.014 9.58 18.50 8.92 5.370 16.867 2.877 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 107.96 16.00 6.31 1751 0 Protein: 0.00 107.96 14.76 6.29 1519 0 Water: 0.00 63.54 24.13 N/A 224 0 Other: 13.74 37.31 24.93 N/A 8 0 Chain A: 0.00 107.96 15.52 N/A 1669 0 Chain S: 3.56 47.01 25.84 N/A 82 0 Histogram: Values Number of atoms 0.00 - 10.80 691 10.80 - 21.59 667 21.59 - 32.39 229 32.39 - 43.19 104 43.19 - 53.98 28 53.98 - 64.78 21 64.78 - 75.58 4 75.58 - 86.37 3 86.37 - 97.17 2 97.17 - 107.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.0958 r_free=0.1850 r_work=0.0955 r_free=0.1848 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0955 r_free = 0.1848 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0952 r_free = 0.1830 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0952 r_free= 0.1830 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.012247 | | target function (ls_wunit_k1) not normalized (work): 60.281704 | | target function (ls_wunit_k1) not normalized (free): 10.463230 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0996 0.0952 0.1830 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2117 0.2118 0.2242 n_refl.: 5174 remove outliers: r(all,work,free)=0.2117 0.2118 0.2242 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2117 0.2118 0.2242 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0994 0.0950 0.1838 n_refl.: 5174 remove outliers: r(all,work,free)=0.0994 0.0950 0.1838 n_refl.: 5174 ======================== 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 94.79 86 5 0.3262 329.178 312.760 0.661 1.008 0.360 11.894-9.307 99.02 97 4 0.1503 522.902 518.970 0.984 1.009 0.350 9.237-7.194 100.00 213 7 0.1476 427.630 429.123 1.022 1.009 0.304 7.162-5.571 100.00 427 22 0.1388 320.884 318.793 0.991 1.007 0.290 5.546-4.326 100.00 867 58 0.0804 440.529 437.993 1.004 1.004 0.240 4.315-3.360 100.00 1859 96 0.0735 418.948 418.577 1.052 0.999 0.220 3.356-3.002 100.00 1373 60 0.0995 322.691 321.337 1.024 0.995 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.9281 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0950 r_free=0.1838 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0950 r_free=0.1842 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0950 r_free=0.1842 | n_water=224 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.0965 r_free=0.1829 | n_water=220 | time (s): 16.050 (total time: 16.710) Filter (q & B) r_work=0.1025 r_free=0.1872 | n_water=218 | time (s): 1.510 (total time: 18.220) Compute maps r_work=0.1025 r_free=0.1872 | n_water=218 | time (s): 0.530 (total time: 18.750) Filter (map) r_work=0.1266 r_free=0.1833 | n_water=154 | time (s): 2.180 (total time: 20.930) Find peaks r_work=0.1266 r_free=0.1833 | n_water=154 | time (s): 0.440 (total time: 21.370) Add new water r_work=0.1696 r_free=0.2193 | n_water=244 | time (s): 1.440 (total time: 22.810) Refine new water occ: r_work=0.1062 r_free=0.1768 adp: r_work=0.1057 r_free=0.1768 occ: r_work=0.1046 r_free=0.1758 adp: r_work=0.1046 r_free=0.1758 occ: r_work=0.1037 r_free=0.1751 adp: r_work=0.1037 r_free=0.1753 ADP+occupancy (water only), MIN, final r_work=0.1037 r_free=0.1753 r_work=0.1037 r_free=0.1753 | n_water=244 | time (s): 8.990 (total time: 31.800) Filter (q & B) r_work=0.1037 r_free=0.1759 | n_water=242 | time (s): 1.320 (total time: 33.120) Filter (dist only) r_work=0.1050 r_free=0.1774 | n_water=241 | time (s): 19.640 (total time: 52.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.107064 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.221659 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 0.0955 0.1859 0.0904 0.011 1.1 4.2 0.5 0.0 0 0.554 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.55 18.59 9.04 5.280 17.507 0.222 5.159 9.10 18.66 9.56 7.064 17.536 0.222 5.066 Individual atomic B min max mean iso aniso Overall: 0.00 107.80 16.21 8.71 1768 0 Protein: 0.00 107.80 14.93 8.71 1519 0 Water: 0.54 57.76 23.95 N/A 241 0 Other: 14.77 39.91 25.87 N/A 8 0 Chain A: 0.00 107.80 15.57 N/A 1651 0 Chain S: 0.54 50.17 25.29 N/A 117 0 Histogram: Values Number of atoms 0.00 - 10.78 696 10.78 - 21.56 647 21.56 - 32.34 252 32.34 - 43.12 110 43.12 - 53.90 33 53.90 - 64.68 14 64.68 - 75.46 9 75.46 - 86.24 2 86.24 - 97.02 4 97.02 - 107.80 1 =========================== Idealize ADP of riding H ========================== r_work=0.0910 r_free=0.1866 r_work=0.0915 r_free=0.1878 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0915 r_free = 0.1878 target_work(ml) = 5.070 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0900 r_free = 0.1855 target_work(ml) = 5.060 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0900 r_free= 0.1855 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.059964 | | target function (ml) not normalized (work): 24905.144796 | | target function (ml) not normalized (free): 1852.430017 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0948 0.0900 0.1855 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2088 0.2094 0.2150 n_refl.: 5174 remove outliers: r(all,work,free)=0.2088 0.2094 0.2150 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2088 0.2094 0.2150 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0938 0.0891 0.1839 n_refl.: 5174 remove outliers: r(all,work,free)=0.0936 0.0888 0.1839 n_refl.: 5173 ======================== 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 93.75 85 5 0.3687 331.403 294.355 0.590 0.995 0.340 11.894-9.307 99.02 97 4 0.1850 522.902 508.704 0.951 0.997 0.340 9.237-7.194 100.00 213 7 0.1921 427.630 420.621 1.000 0.999 0.300 7.162-5.571 100.00 427 22 0.1877 320.884 311.437 0.975 0.999 0.254 5.546-4.326 100.00 867 58 0.0923 440.529 435.288 1.000 1.000 0.230 4.315-3.360 100.00 1859 96 0.0588 418.948 418.679 1.056 1.002 0.220 3.356-3.002 100.00 1373 60 0.0580 322.691 322.313 1.025 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.2110 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0888 r_free=0.1839 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0890 r_free=0.1835 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0890 r_free=0.1835 | n_water=241 | time (s): 0.480 (total time: 0.480) Filter (dist) r_work=0.0905 r_free=0.1826 | n_water=238 | time (s): 18.870 (total time: 19.350) Filter (q & B) r_work=0.0940 r_free=0.1860 | n_water=237 | time (s): 1.320 (total time: 20.670) Compute maps r_work=0.0940 r_free=0.1860 | n_water=237 | time (s): 0.550 (total time: 21.220) Filter (map) r_work=0.1219 r_free=0.1919 | n_water=166 | time (s): 1.650 (total time: 22.870) Find peaks r_work=0.1219 r_free=0.1919 | n_water=166 | time (s): 0.430 (total time: 23.300) Add new water r_work=0.1512 r_free=0.2161 | n_water=242 | time (s): 1.180 (total time: 24.480) Refine new water occ: r_work=0.1001 r_free=0.1822 adp: r_work=0.0999 r_free=0.1821 occ: r_work=0.0990 r_free=0.1808 adp: r_work=0.0991 r_free=0.1811 occ: r_work=0.0983 r_free=0.1800 adp: r_work=0.0984 r_free=0.1802 ADP+occupancy (water only), MIN, final r_work=0.0984 r_free=0.1802 r_work=0.0984 r_free=0.1802 | n_water=242 | time (s): 9.190 (total time: 33.670) Filter (q & B) r_work=0.0986 r_free=0.1811 | n_water=237 | time (s): 1.640 (total time: 35.310) Filter (dist only) r_work=0.1000 r_free=0.1827 | n_water=234 | time (s): 19.590 (total time: 54.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.061773 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.199653 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 0.0911 0.1925 0.1013 0.011 1.1 5.4 0.5 0.0 0 0.531 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.11 19.25 10.13 6.798 17.699 0.200 5.042 8.84 19.47 10.63 8.054 17.852 0.200 4.972 Individual atomic B min max mean iso aniso Overall: 0.00 107.44 16.53 10.46 1761 0 Protein: 0.00 107.44 15.40 10.45 1519 0 Water: 0.00 55.00 23.51 N/A 234 0 Other: 13.75 39.85 27.00 N/A 8 0 Chain A: 0.00 107.44 15.91 N/A 1642 0 Chain S: 1.61 55.00 25.14 N/A 119 0 Histogram: Values Number of atoms 0.00 - 10.74 675 10.74 - 21.49 639 21.49 - 32.23 261 32.23 - 42.98 113 42.98 - 53.72 39 53.72 - 64.47 15 64.47 - 75.21 5 75.21 - 85.95 9 85.95 - 96.70 4 96.70 - 107.44 1 =========================== Idealize ADP of riding H ========================== r_work=0.0884 r_free=0.1947 r_work=0.0888 r_free=0.1951 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0888 r_free = 0.1951 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0880 r_free = 0.1937 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5173 (all), 4.87 % free)-------------| | | | r_work= 0.0880 r_free= 0.1937 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 4.970611 | | target function (ml) not normalized (work): 24460.376900 | | target function (ml) not normalized (free): 2236.379638 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0934 0.0880 0.1937 n_refl.: 5173 re-set all scales: r(all,work,free)=0.2070 0.2067 0.2279 n_refl.: 5173 remove outliers: r(all,work,free)=0.2070 0.2067 0.2279 n_refl.: 5173 overall B=-0.00 to atoms: r(all,work,free)=0.2070 0.2067 0.2279 n_refl.: 5173 bulk-solvent and scaling: r(all,work,free)=0.0933 0.0879 0.1937 n_refl.: 5173 remove outliers: r(all,work,free)=0.0933 0.0879 0.1937 n_refl.: 5173 ======================== 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 93.75 85 5 0.3943 331.403 297.673 0.586 0.987 0.330 11.894-9.307 99.02 97 4 0.1976 522.902 507.128 0.948 0.991 0.320 9.237-7.194 100.00 213 7 0.1993 427.630 418.801 1.000 0.994 0.310 7.162-5.571 100.00 427 22 0.2020 320.884 310.689 0.983 0.996 0.259 5.546-4.326 100.00 867 58 0.0989 440.529 435.195 1.012 0.999 0.230 4.315-3.360 100.00 1859 96 0.0558 418.948 418.386 1.073 1.002 0.220 3.356-3.002 100.00 1373 60 0.0449 322.691 322.528 1.043 1.005 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.0414 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0879 r_free=0.1937 After: r_work=0.0883 r_free=0.1937 ================================== NQH flips ================================== r_work=0.0883 r_free=0.1937 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=0.0883 r_free=0.1938 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0883 r_free=0.1938 | n_water=234 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.0916 r_free=0.1921 | n_water=228 | time (s): 18.250 (total time: 18.750) Filter (q & B) r_work=0.0980 r_free=0.1969 | n_water=226 | time (s): 1.500 (total time: 20.250) Compute maps r_work=0.0980 r_free=0.1969 | n_water=226 | time (s): 0.530 (total time: 20.780) Filter (map) r_work=0.1247 r_free=0.2050 | n_water=161 | time (s): 1.530 (total time: 22.310) Find peaks r_work=0.1247 r_free=0.2050 | n_water=161 | time (s): 0.390 (total time: 22.700) Add new water r_work=0.1513 r_free=0.2221 | n_water=225 | time (s): 1.740 (total time: 24.440) Refine new water occ: r_work=0.1008 r_free=0.1906 adp: r_work=0.1003 r_free=0.1907 occ: r_work=0.0996 r_free=0.1896 adp: r_work=0.0996 r_free=0.1902 occ: r_work=0.0991 r_free=0.1890 adp: r_work=0.0990 r_free=0.1896 ADP+occupancy (water only), MIN, final r_work=0.0990 r_free=0.1896 r_work=0.0990 r_free=0.1896 | n_water=225 | time (s): 13.700 (total time: 38.140) Filter (q & B) r_work=0.0990 r_free=0.1899 | n_water=223 | time (s): 1.900 (total time: 40.040) Filter (dist only) r_work=0.0997 r_free=0.1904 | n_water=222 | time (s): 18.010 (total time: 58.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.991088 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.195618 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 0.0936 0.1912 0.0976 0.010 1.1 6.4 0.5 0.0 0 0.496 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.36 19.12 9.76 7.961 18.093 0.196 5.052 9.12 19.17 10.06 8.709 18.206 0.196 4.991 Individual atomic B min max mean iso aniso Overall: 0.00 108.08 16.71 11.45 1749 0 Protein: 0.00 108.08 15.77 11.45 1519 0 Water: 0.23 55.70 22.77 N/A 222 0 Other: 15.09 42.62 28.79 N/A 8 0 Chain A: 0.00 108.08 16.17 N/A 1632 0 Chain S: 0.52 55.60 24.32 N/A 117 0 Histogram: Values Number of atoms 0.00 - 10.81 669 10.81 - 21.62 629 21.62 - 32.42 279 32.42 - 43.23 97 43.23 - 54.04 40 54.04 - 64.85 15 64.85 - 75.66 6 75.66 - 86.47 8 86.47 - 97.27 4 97.27 - 108.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.0912 r_free=0.1917 r_work=0.0915 r_free=0.1925 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0915 r_free = 0.1925 target_work(ml) = 4.996 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0908 r_free = 0.1916 target_work(ml) = 4.991 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5173 (all), 4.87 % free)-------------| | | | r_work= 0.0908 r_free= 0.1916 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.991458 | | target function (ml) not normalized (work): 24562.966276 | | target function (ml) not normalized (free): 2201.936755 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2491 142 0.1277 0.1871 5.5408 6.1791| | 2: 3.78 - 3.00 1.00 2430 110 0.0458 0.1993 4.4284 12.041| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2491 142 0.92 12.14 1.00 0.98 12940.03| | 2: 3.78 - 3.00 2430 110 0.99 2.17 1.00 1.00 1019.54| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 661.99 max = 21462.55 mean = 7053.67| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.86 mean = 7.22| |phase err.(test): min = 0.00 max = 87.45 mean = 7.25| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0959 0.0908 0.1916 n_refl.: 5173 re-set all scales: r(all,work,free)=0.2129 0.2127 0.2284 n_refl.: 5173 remove outliers: r(all,work,free)=0.2129 0.2127 0.2284 n_refl.: 5173 overall B=-0.00 to atoms: r(all,work,free)=0.2129 0.2127 0.2284 n_refl.: 5173 bulk-solvent and scaling: r(all,work,free)=0.0958 0.0907 0.1925 n_refl.: 5173 remove outliers: r(all,work,free)=0.0958 0.0907 0.1925 n_refl.: 5173 ======================== 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 93.75 85 5 0.3859 331.403 299.984 0.602 0.988 0.328 11.894-9.307 99.02 97 4 0.1953 522.902 508.535 0.954 0.994 0.318 9.237-7.194 100.00 213 7 0.2063 427.630 418.728 0.999 0.997 0.294 7.162-5.571 100.00 427 22 0.2083 320.884 309.768 0.982 0.998 0.280 5.546-4.326 100.00 867 58 0.1051 440.529 434.460 1.011 1.000 0.230 4.315-3.360 100.00 1859 96 0.0587 418.948 418.283 1.087 1.002 0.230 3.356-3.002 100.00 1373 60 0.0439 322.691 322.739 1.059 1.003 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.5938 ================= 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 : 0.3620 0.1980 0.081 5.224 8.8 119.3 19.9 258 0.000 1_bss: 0.1557 0.1534 0.081 5.224 6.0 116.5 17.0 258 0.000 1_settarget: 0.1557 0.1534 0.081 5.224 6.0 116.5 17.0 258 0.000 1_nqh: 0.1558 0.1526 0.081 5.224 6.0 116.5 17.0 258 0.006 1_weight: 0.1558 0.1526 0.081 5.224 6.0 116.5 17.0 258 0.006 1_xyzrec: 0.1158 0.1785 0.010 0.970 6.0 116.5 17.0 258 0.219 1_adp: 0.1023 0.1779 0.010 0.970 2.2 111.5 17.5 258 0.219 1_regHadp: 0.1017 0.1783 0.010 0.970 2.2 111.5 17.5 258 0.219 1_occ: 0.1012 0.1785 0.010 0.970 2.2 111.5 17.5 258 0.219 2_bss: 0.1012 0.1791 0.010 0.970 1.2 110.5 16.5 258 0.219 2_settarget: 0.1012 0.1791 0.010 0.970 1.2 110.5 16.5 258 0.219 2_updatecdl: 0.1012 0.1791 0.010 0.993 1.2 110.5 16.5 258 0.219 2_nqh: 0.1015 0.1799 0.010 0.993 1.2 110.5 16.5 258 0.214 2_sol: 0.1145 0.1652 0.010 0.993 1.2 110.3 15.4 224 n/a 2_weight: 0.1145 0.1652 0.010 0.993 1.2 110.3 15.4 224 n/a 2_xyzrec: 0.1028 0.1841 0.009 0.988 1.2 110.3 15.4 224 n/a 2_adp: 0.0958 0.1850 0.009 0.988 0.0 108.0 16.0 224 n/a 2_regHadp: 0.0955 0.1848 0.009 0.988 0.0 108.0 16.0 224 n/a 2_occ: 0.0952 0.1830 0.009 0.988 0.0 108.0 16.0 224 n/a 3_bss: 0.0950 0.1838 0.009 0.988 0.0 108.0 16.0 224 n/a 3_settarget: 0.0950 0.1838 0.009 0.988 0.0 108.0 16.0 224 n/a 3_updatecdl: 0.0950 0.1838 0.009 0.995 0.0 108.0 16.0 224 n/a 3_nqh: 0.0950 0.1842 0.009 0.995 0.0 108.0 16.0 224 n/a 3_sol: 0.1050 0.1774 0.009 0.995 0.0 108.0 16.2 241 n/a 3_weight: 0.1050 0.1774 0.009 0.995 0.0 108.0 16.2 241 n/a 3_xyzrec: 0.0955 0.1859 0.011 1.057 0.0 108.0 16.2 241 n/a 3_adp: 0.0910 0.1866 0.011 1.057 0.0 107.8 16.2 241 n/a 3_regHadp: 0.0915 0.1878 0.011 1.057 0.0 107.8 16.2 241 n/a 3_occ: 0.0900 0.1855 0.011 1.057 0.0 107.8 16.2 241 n/a 4_bss: 0.0888 0.1839 0.011 1.057 0.0 107.8 16.2 241 n/a 4_settarget: 0.0888 0.1839 0.011 1.057 0.0 107.8 16.2 241 n/a 4_updatecdl: 0.0888 0.1839 0.011 1.069 0.0 107.8 16.2 241 n/a 4_nqh: 0.0890 0.1835 0.011 1.069 0.0 107.8 16.2 241 n/a 4_sol: 0.1000 0.1827 0.011 1.069 0.0 107.8 16.2 234 n/a 4_weight: 0.1000 0.1827 0.011 1.069 0.0 107.8 16.2 234 n/a 4_xyzrec: 0.0911 0.1925 0.011 1.082 0.0 107.8 16.2 234 n/a 4_adp: 0.0884 0.1947 0.011 1.082 0.0 107.4 16.5 234 n/a 4_regHadp: 0.0888 0.1951 0.011 1.082 0.0 107.4 16.5 234 n/a 4_occ: 0.0880 0.1937 0.011 1.082 0.0 107.4 16.5 234 n/a 5_bss: 0.0879 0.1937 0.011 1.082 0.0 107.4 16.5 234 n/a 5_settarget: 0.0879 0.1937 0.011 1.082 0.0 107.4 16.5 234 n/a 5_updatecdl: 0.0879 0.1937 0.011 1.086 0.0 107.4 16.5 234 n/a 5_setrh: 0.0883 0.1937 0.011 1.086 0.0 107.4 16.5 234 n/a 5_nqh: 0.0883 0.1938 0.011 1.086 0.0 107.4 16.5 234 n/a 5_sol: 0.0997 0.1904 0.011 1.086 0.0 107.4 16.5 222 n/a 5_weight: 0.0997 0.1904 0.011 1.086 0.0 107.4 16.5 222 n/a 5_xyzrec: 0.0936 0.1912 0.010 1.149 0.0 107.4 16.5 222 n/a 5_adp: 0.0912 0.1917 0.010 1.149 0.0 108.1 16.7 222 n/a 5_regHadp: 0.0915 0.1925 0.010 1.149 0.0 108.1 16.7 222 n/a 5_occ: 0.0908 0.1916 0.010 1.149 0.0 108.1 16.7 222 n/a end: 0.0907 0.1925 0.010 1.149 0.0 108.1 16.7 222 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2348261_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2348261_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6300 Refinement macro-cycles (run) : 473.1600 Write final files (write_after_run_outputs) : 10.4900 Total : 487.2800 Total CPU time: 8.50 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:51 PST -0800 (1735492731.40 s) Start R-work = 0.1557, R-free = 0.1534 Final R-work = 0.0907, R-free = 0.1925 =============================================================================== Job complete usr+sys time: 519.70 seconds wall clock time: 9 minutes 2.13 seconds (542.13 seconds total)