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_8008321.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_8008321.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8008321.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: 1.73, per 1000 atoms: 0.51 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: 0.44 Conformation dependent library (CDL) restraints added in 106.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 533 0.92 - 1.17: 1104 1.17 - 1.43: 667 1.43 - 1.69: 824 1.69 - 1.94: 25 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 104 " pdb=" CA ALA A 104 " ideal model delta sigma weight residual 1.455 1.703 -0.248 1.25e-02 6.40e+03 3.95e+02 bond pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 1.246 1.419 -0.173 9.20e-03 1.18e+04 3.52e+02 bond pdb=" N THR A 34 " pdb=" CA THR A 34 " ideal model delta sigma weight residual 1.458 1.241 0.216 1.22e-02 6.72e+03 3.15e+02 bond pdb=" C ILE A 21 " pdb=" O ILE A 21 " ideal model delta sigma weight residual 1.242 1.091 0.151 8.60e-03 1.35e+04 3.07e+02 bond pdb=" C ARG A 98 " pdb=" N ALYS A 99 " ideal model delta sigma weight residual 1.333 1.566 -0.233 1.38e-02 5.25e+03 2.85e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 3184 4.72 - 9.43: 1852 9.43 - 14.15: 610 14.15 - 18.87: 118 18.87 - 23.59: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA AGLU A 90 " pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 120.82 137.50 -16.68 1.05e+00 9.07e-01 2.52e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.35 134.89 -13.54 9.20e-01 1.18e+00 2.17e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 121.53 109.25 12.28 8.70e-01 1.32e+00 1.99e+02 angle pdb=" O ALA A 165 " pdb=" C ALA A 165 " pdb=" N LEU A 166 " ideal model delta sigma weight residual 122.15 106.84 15.31 1.14e+00 7.69e-01 1.80e+02 angle pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 109.00 95.79 13.21 1.00e+00 1.00e+00 1.74e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.44: 1318 18.44 - 36.88: 121 36.88 - 55.31: 30 55.31 - 73.75: 10 73.75 - 92.19: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -141.50 18.90 0 2.50e+00 1.60e-01 5.72e+01 dihedral pdb=" N SER A 47 " pdb=" C SER A 47 " pdb=" CA SER A 47 " pdb=" CB SER A 47 " ideal model delta harmonic sigma weight residual 122.80 104.37 18.43 0 2.50e+00 1.60e-01 5.43e+01 dihedral pdb=" C GLU A 116 " pdb=" N GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual -122.60 -141.02 18.42 0 2.50e+00 1.60e-01 5.43e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.222: 95 0.222 - 0.440: 77 0.440 - 0.658: 49 0.658 - 0.877: 16 0.877 - 1.095: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA SER A 47 " pdb=" N SER A 47 " pdb=" C SER A 47 " pdb=" CB SER A 47 " both_signs ideal model delta sigma weight residual False 2.51 3.61 -1.09 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA ALA A 56 " pdb=" N ALA A 56 " pdb=" C ALA A 56 " pdb=" CB ALA A 56 " both_signs ideal model delta sigma weight residual False 2.48 3.48 -1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.58 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.057 2.00e-02 2.50e+03 7.67e-02 1.77e+02 pdb=" CG PHE A 162 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.102 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.076 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.080 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.126 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.066 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.072 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.098 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.111 2.00e-02 2.50e+03 6.98e-02 1.46e+02 pdb=" CG PHE A 119 " -0.094 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.074 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.137 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.022 2.00e-02 2.50e+03 6.61e-02 1.31e+02 pdb=" CG ATYR A 67 " -0.027 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.103 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.045 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.038 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.083 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.110 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.055 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.016 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.34: 1194 2.34 - 2.90: 8151 2.90 - 3.47: 10475 3.47 - 4.03: 15175 4.03 - 4.60: 21550 Nonbonded interactions: 56545 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.770 2.100 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.792 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.815 2.100 nonbonded pdb=" O ALA A 6 " pdb=" H THR A 34 " model vdw 1.830 2.450 nonbonded pdb=" H CYS A 46 " pdb=" O VAL A 50 " model vdw 1.849 2.450 ... (remaining 56540 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_8008321_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= 0.3617 r_free= 0.2018 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.465419 | | target function (ml) not normalized (work): 22014.514208 | | target function (ml) not normalized (free): 1146.485160 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3801 0.2283 4.8501 4.9138| | 2: 3.78 - 3.00 1.00 2430 110 0.3393 0.1570 4.0697 4.0793| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.83 0.83 0.13 6609.39| | 2: 3.78 - 3.00 2430 110 0.94 11.19 1.48 0.26 443.31| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 373.71 max = 12073.15 mean = 3570.12| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.28| |phase err.(test): min = 0.00 max = 90.00 mean = 33.43| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.248 1557 Z= 5.441 Angle : 5.290 21.328 2118 Z= 3.740 Chirality : 0.390 1.095 243 Planarity : 0.030 0.100 284 Dihedral : 14.300 92.188 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 30.27 % 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: -2.21 (0.48), residues: 224 helix: -2.26 (0.39), residues: 108 sheet: -0.87 (0.87), residues: 28 loop : -0.24 (0.58), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.019 ARG A 156 TYR 0.064 0.029 TYR A 139 PHE 0.119 0.062 PHE A 164 HIS 0.045 0.027 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= 0.3617 r_free= 0.2018 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.465419 | | target function (ml) not normalized (work): 22014.514208 | | target function (ml) not normalized (free): 1146.485160 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3572 0.3649 0.2141 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3572 0.3649 0.2141 n_refl.: 5182 remove outliers: r(all,work,free)=0.2527 0.2549 0.2141 n_refl.: 5178 overall B=-2.62 to atoms: r(all,work,free)=0.2426 0.2446 0.2097 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1562 0.1562 0.1576 n_refl.: 5178 remove outliers: r(all,work,free)=0.1558 0.1557 0.1576 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 98.94 88 5 0.3853 449.628 405.683 0.653 1.053 0.406 11.894-9.307 99.02 97 4 0.1855 714.270 684.266 0.917 1.051 0.379 9.237-7.194 100.00 213 7 0.2181 584.131 572.066 0.945 1.046 0.364 7.162-5.571 100.00 427 22 0.2313 438.319 420.847 0.915 1.036 0.294 5.546-4.326 100.00 867 58 0.1386 601.750 592.127 0.954 1.019 0.235 4.315-3.360 100.00 1859 96 0.1319 572.271 567.154 1.027 0.991 0.210 3.356-3.002 100.00 1373 60 0.1580 440.787 435.866 1.038 0.963 0.053 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-4.5449 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1557 r_free=0.1576 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1558 r_free=0.1577 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.088113 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.759191 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 0.1164 0.1803 0.0638 0.010 1.0 2.6 0.5 0.0 0 9.544 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 18.03 6.38 3.013 16.241 1.759 0.018 10.21 17.94 7.73 4.949 16.517 1.759 0.015 Individual atomic B min max mean iso aniso Overall: 2.46 111.68 17.79 5.29 1785 0 Protein: 2.46 111.52 15.10 5.29 1519 0 Water: 4.25 111.68 33.41 N/A 258 0 Other: 18.29 35.39 24.98 N/A 8 0 Chain A: 2.46 111.68 17.79 N/A 1785 0 Histogram: Values Number of atoms 2.46 - 13.38 908 13.38 - 24.31 491 24.31 - 35.23 191 35.23 - 46.15 106 46.15 - 57.07 57 57.07 - 67.99 15 67.99 - 78.92 8 78.92 - 89.84 5 89.84 - 100.76 1 100.76 - 111.68 3 =========================== Idealize ADP of riding H ========================== r_work=0.1021 r_free=0.1794 r_work=0.1015 r_free=0.1803 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1015 r_free = 0.1803 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 = 0.1018 r_free = 0.1792 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1018 r_free= 0.1792 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014158 | | target function (ls_wunit_k1) not normalized (work): 69.715142 | | target function (ls_wunit_k1) not normalized (free): 10.655674 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1057 0.1018 0.1792 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2113 0.2111 0.2245 n_refl.: 5176 remove outliers: r(all,work,free)=0.2113 0.2111 0.2245 n_refl.: 5176 overall B=-0.95 to atoms: r(all,work,free)=0.2071 0.2068 0.2232 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1057 0.1019 0.1777 n_refl.: 5176 remove outliers: r(all,work,free)=0.1057 0.1019 0.1777 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 0.3312 319.369 299.381 0.642 1.014 0.376 11.894-9.307 99.02 97 4 0.1551 507.344 499.705 0.942 1.015 0.351 9.237-7.194 100.00 213 7 0.1724 414.906 413.818 0.982 1.013 0.341 7.162-5.571 100.00 427 22 0.1629 311.337 307.996 0.946 1.010 0.301 5.546-4.326 100.00 867 58 0.0919 427.421 424.381 0.965 1.005 0.212 4.315-3.360 100.00 1859 96 0.0768 406.482 406.489 1.017 0.997 0.203 3.356-3.002 100.00 1373 60 0.1000 313.090 311.625 1.000 0.989 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.2765 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1019 r_free=0.1777 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1019 r_free=0.1777 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1019 r_free=0.1777 | n_water=258 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1039 r_free=0.1789 | n_water=249 | time (s): 20.500 (total time: 21.100) Filter (q & B) r_work=0.1038 r_free=0.1791 | n_water=246 | time (s): 1.740 (total time: 22.840) Compute maps r_work=0.1038 r_free=0.1791 | n_water=246 | time (s): 0.490 (total time: 23.330) Filter (map) r_work=0.1341 r_free=0.1856 | n_water=147 | time (s): 1.950 (total time: 25.280) Find peaks r_work=0.1341 r_free=0.1856 | n_water=147 | time (s): 0.600 (total time: 25.880) Add new water r_work=0.1690 r_free=0.2139 | n_water=234 | time (s): 1.580 (total time: 27.460) Refine new water occ: r_work=0.1140 r_free=0.1696 adp: r_work=0.1113 r_free=0.1696 occ: r_work=0.1110 r_free=0.1680 adp: r_work=0.1098 r_free=0.1682 occ: r_work=0.1099 r_free=0.1669 adp: r_work=0.1095 r_free=0.1676 ADP+occupancy (water only), MIN, final r_work=0.1095 r_free=0.1676 r_work=0.1095 r_free=0.1676 | n_water=234 | time (s): 4.300 (total time: 31.760) Filter (q & B) r_work=0.1095 r_free=0.1676 | n_water=234 | time (s): 1.140 (total time: 32.900) Filter (dist only) r_work=0.1105 r_free=0.1679 | n_water=230 | time (s): 18.260 (total time: 51.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.403175 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.705634 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 0.0998 0.1824 0.0827 0.009 1.0 3.5 0.5 0.0 0 11.202 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.98 18.24 8.27 4.691 17.206 2.706 0.013 9.29 18.52 9.23 5.459 17.649 2.706 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.14 17.06 6.48 1757 0 Protein: 0.00 108.14 15.46 6.45 1519 0 Water: 0.00 63.01 27.24 N/A 230 0 Other: 18.28 40.54 28.04 N/A 8 0 Chain A: 0.00 108.14 16.27 N/A 1671 0 Chain S: 0.36 61.65 32.43 N/A 86 0 Histogram: Values Number of atoms 0.00 - 10.81 626 10.81 - 21.63 718 21.63 - 32.44 210 32.44 - 43.26 115 43.26 - 54.07 49 54.07 - 64.89 25 64.89 - 75.70 6 75.70 - 86.52 3 86.52 - 97.33 3 97.33 - 108.14 2 =========================== Idealize ADP of riding H ========================== r_work=0.0929 r_free=0.1852 r_work=0.0927 r_free=0.1854 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0927 r_free = 0.1854 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0921 r_free = 0.1830 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= 0.0921 r_free= 0.1830 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011569 | | target function (ls_wunit_k1) not normalized (work): 56.966954 | | target function (ls_wunit_k1) not normalized (free): 10.255218 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0967 0.0921 0.1830 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2150 0.2157 0.2177 n_refl.: 5176 remove outliers: r(all,work,free)=0.2150 0.2157 0.2177 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2150 0.2157 0.2177 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0969 0.0924 0.1836 n_refl.: 5176 remove outliers: r(all,work,free)=0.0965 0.0919 0.1836 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 0.3037 318.786 300.216 0.672 1.009 0.360 11.894-9.307 99.02 97 4 0.1377 507.344 503.815 0.993 1.010 0.350 9.237-7.194 100.00 213 7 0.1466 414.906 413.098 1.024 1.009 0.346 7.162-5.571 100.00 427 22 0.1428 311.337 308.559 0.995 1.008 0.300 5.546-4.326 100.00 867 58 0.0783 427.421 425.021 1.013 1.005 0.240 4.315-3.360 100.00 1859 96 0.0713 406.482 406.283 1.067 1.000 0.200 3.356-3.002 100.00 1373 60 0.0940 313.090 312.100 1.048 0.995 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-4.7766 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0919 r_free=0.1836 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 3 r_work=0.0925 r_free=0.1837 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0925 r_free=0.1837 | n_water=230 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0942 r_free=0.1832 | n_water=226 | time (s): 19.500 (total time: 20.010) Filter (q & B) r_work=0.0980 r_free=0.1856 | n_water=224 | time (s): 1.280 (total time: 21.290) Compute maps r_work=0.0980 r_free=0.1856 | n_water=224 | time (s): 0.450 (total time: 21.740) Filter (map) r_work=0.1232 r_free=0.1903 | n_water=156 | time (s): 1.500 (total time: 23.240) Find peaks r_work=0.1232 r_free=0.1903 | n_water=156 | time (s): 0.420 (total time: 23.660) Add new water r_work=0.1633 r_free=0.2275 | n_water=245 | time (s): 1.390 (total time: 25.050) Refine new water occ: r_work=0.1043 r_free=0.1794 adp: r_work=0.1042 r_free=0.1803 occ: r_work=0.1029 r_free=0.1781 adp: r_work=0.1029 r_free=0.1793 occ: r_work=0.1018 r_free=0.1769 adp: r_work=0.1017 r_free=0.1777 ADP+occupancy (water only), MIN, final r_work=0.1017 r_free=0.1777 r_work=0.1017 r_free=0.1777 | n_water=245 | time (s): 11.510 (total time: 36.560) Filter (q & B) r_work=0.1017 r_free=0.1782 | n_water=244 | time (s): 1.250 (total time: 37.810) Filter (dist only) r_work=0.1022 r_free=0.1799 | n_water=242 | time (s): 19.050 (total time: 56.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.076653 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.222548 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 0.0924 0.1908 0.0984 0.011 1.1 3.5 0.5 0.6 0 0.538 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.24 19.08 9.84 5.438 18.335 0.223 5.101 8.78 19.16 10.38 7.256 18.378 0.223 4.999 Individual atomic B min max mean iso aniso Overall: 0.00 107.77 17.01 8.96 1769 0 Protein: 0.00 107.77 15.66 8.93 1519 0 Water: 0.00 59.32 25.12 N/A 242 0 Other: 13.93 43.39 28.28 N/A 8 0 Chain A: 0.00 107.77 16.39 N/A 1659 0 Chain S: 0.00 59.32 26.43 N/A 110 0 Histogram: Values Number of atoms 0.00 - 10.78 640 10.78 - 21.55 681 21.55 - 32.33 250 32.33 - 43.11 128 43.11 - 53.88 33 53.88 - 64.66 20 64.66 - 75.44 9 75.44 - 86.21 3 86.21 - 96.99 4 96.99 - 107.77 1 =========================== Idealize ADP of riding H ========================== r_work=0.0878 r_free=0.1916 r_work=0.0883 r_free=0.1925 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0883 r_free = 0.1925 target_work(ml) = 5.003 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0871 r_free = 0.1913 target_work(ml) = 4.996 | | occupancies: max = 1.00 min = 0.26 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= 0.0871 r_free= 0.1913 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.995616 | | target function (ml) not normalized (work): 24588.422576 | | target function (ml) not normalized (free): 1939.145527 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0924 0.0871 0.1913 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2041 0.2043 0.2156 n_refl.: 5174 remove outliers: r(all,work,free)=0.2041 0.2043 0.2156 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2041 0.2043 0.2156 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0913 0.0861 0.1897 n_refl.: 5174 remove outliers: r(all,work,free)=0.0913 0.0861 0.1897 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 0.3633 318.786 290.068 0.610 0.993 0.334 11.894-9.307 99.02 97 4 0.1768 507.344 494.070 0.953 0.996 0.330 9.237-7.194 100.00 213 7 0.1888 414.906 406.673 0.999 0.998 0.315 7.162-5.571 100.00 427 22 0.1787 311.337 301.574 0.978 0.999 0.280 5.546-4.326 100.00 867 58 0.0899 427.421 422.630 1.002 1.000 0.230 4.315-3.360 100.00 1859 96 0.0570 406.482 405.826 1.062 1.002 0.200 3.356-3.002 100.00 1373 60 0.0562 313.090 312.756 1.041 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.7251 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0861 r_free=0.1897 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.0861 r_free=0.1900 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0861 r_free=0.1900 | n_water=242 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.0871 r_free=0.1911 | n_water=240 | time (s): 18.710 (total time: 19.370) Filter (q & B) r_work=0.0955 r_free=0.1878 | n_water=237 | time (s): 1.890 (total time: 21.260) Compute maps r_work=0.0955 r_free=0.1878 | n_water=237 | time (s): 0.470 (total time: 21.730) Filter (map) r_work=0.1245 r_free=0.1911 | n_water=161 | time (s): 1.660 (total time: 23.390) Find peaks r_work=0.1245 r_free=0.1911 | n_water=161 | time (s): 0.570 (total time: 23.960) Add new water r_work=0.1569 r_free=0.2288 | n_water=242 | time (s): 1.770 (total time: 25.730) Refine new water r_work=0.1569 r_free=0.2288 | n_water=242 | time (s): 0.060 (total time: 25.790) Filter (q & B) r_work=0.1245 r_free=0.1911 | n_water=161 | time (s): 1.490 (total time: 27.280) Filter (dist only) r_work=0.1257 r_free=0.1864 | n_water=157 | time (s): 11.440 (total time: 38.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.425139 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.288204 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 0.1106 0.1906 0.0801 0.012 1.1 4.5 0.5 0.0 0 0.713 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.06 19.06 8.01 7.003 18.321 0.288 5.314 10.48 19.02 8.54 8.365 18.363 0.288 5.227 Individual atomic B min max mean iso aniso Overall: 0.00 105.57 16.64 10.41 1684 0 Protein: 0.00 105.57 15.79 10.39 1519 0 Water: 0.95 53.01 24.29 N/A 157 0 Other: 13.46 44.75 27.90 N/A 8 0 Chain A: 0.00 105.57 16.42 N/A 1643 0 Chain S: 5.30 47.22 25.28 N/A 41 0 Histogram: Values Number of atoms 0.00 - 10.56 623 10.56 - 21.11 632 21.11 - 31.67 248 31.67 - 42.23 99 42.23 - 52.78 46 52.78 - 63.34 14 63.34 - 73.90 10 73.90 - 84.46 6 84.46 - 95.01 3 95.01 - 105.57 3 =========================== Idealize ADP of riding H ========================== r_work=0.1048 r_free=0.1902 r_work=0.1052 r_free=0.1905 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1052 r_free = 0.1905 target_work(ml) = 5.230 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1051 r_free = 0.1896 target_work(ml) = 5.228 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.1051 r_free= 0.1896 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.227809 | | target function (ml) not normalized (work): 25731.273482 | | target function (ml) not normalized (free): 1718.308673 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1094 0.1051 0.1896 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2334 0.2331 0.2478 n_refl.: 5174 remove outliers: r(all,work,free)=0.2334 0.2331 0.2478 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2334 0.2331 0.2478 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.1080 0.1035 0.1905 n_refl.: 5174 remove outliers: r(all,work,free)=0.1080 0.1035 0.1905 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 0.3668 318.786 292.321 0.671 1.000 0.359 11.894-9.307 99.02 97 4 0.1590 507.344 497.368 0.974 1.002 0.353 9.237-7.194 100.00 213 7 0.2026 414.906 406.116 0.990 1.003 0.348 7.162-5.571 100.00 427 22 0.1854 311.337 304.093 0.982 1.002 0.310 5.546-4.326 100.00 867 58 0.1096 427.421 422.245 0.993 1.002 0.260 4.315-3.360 100.00 1859 96 0.0752 406.482 404.852 1.073 1.000 0.220 3.356-3.002 100.00 1373 60 0.0794 313.090 311.808 1.069 0.999 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.3264 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1035 r_free=0.1905 After: r_work=0.1038 r_free=0.1906 ================================== NQH flips ================================== r_work=0.1038 r_free=0.1906 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1038 r_free=0.1906 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1038 r_free=0.1906 | n_water=157 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.1064 r_free=0.1913 | n_water=152 | time (s): 13.430 (total time: 13.920) Filter (q & B) r_work=0.1086 r_free=0.1937 | n_water=151 | time (s): 1.200 (total time: 15.120) Compute maps r_work=0.1086 r_free=0.1937 | n_water=151 | time (s): 0.430 (total time: 15.550) Filter (map) r_work=0.1121 r_free=0.1926 | n_water=141 | time (s): 1.440 (total time: 16.990) Find peaks r_work=0.1121 r_free=0.1926 | n_water=141 | time (s): 0.530 (total time: 17.520) Add new water r_work=0.1401 r_free=0.2161 | n_water=203 | time (s): 1.620 (total time: 19.140) Refine new water occ: r_work=0.1120 r_free=0.1929 adp: r_work=0.1120 r_free=0.1939 occ: r_work=0.1105 r_free=0.1915 adp: r_work=0.1105 r_free=0.1927 occ: r_work=0.1089 r_free=0.1904 adp: r_work=0.1090 r_free=0.1914 ADP+occupancy (water only), MIN, final r_work=0.1090 r_free=0.1914 r_work=0.1090 r_free=0.1914 | n_water=203 | time (s): 13.600 (total time: 32.740) Filter (q & B) r_work=0.1090 r_free=0.1909 | n_water=199 | time (s): 1.440 (total time: 34.180) Filter (dist only) r_work=0.1089 r_free=0.1913 | n_water=198 | time (s): 16.040 (total time: 50.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.200713 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.254304 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 0.1037 0.1970 0.0933 0.011 1.3 8.6 0.5 0.6 0 0.600 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.37 19.70 9.33 7.954 18.652 0.254 5.171 10.10 19.97 9.87 8.886 18.650 0.254 5.110 Individual atomic B min max mean iso aniso Overall: 0.00 105.34 17.17 11.51 1725 0 Protein: 0.00 105.34 15.94 11.49 1519 0 Water: 1.81 59.60 26.20 N/A 198 0 Other: 10.42 42.15 26.67 N/A 8 0 Chain A: 0.00 105.34 16.47 N/A 1636 0 Chain S: 3.24 59.60 29.95 N/A 89 0 Histogram: Values Number of atoms 0.00 - 10.53 613 10.53 - 21.07 633 21.07 - 31.60 259 31.60 - 42.13 120 42.13 - 52.67 55 52.67 - 63.20 20 63.20 - 73.74 11 73.74 - 84.27 8 84.27 - 94.80 3 94.80 - 105.34 3 =========================== Idealize ADP of riding H ========================== r_work=0.1010 r_free=0.1997 r_work=0.1015 r_free=0.2000 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1015 r_free = 0.2000 target_work(ml) = 5.116 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0983 r_free = 0.1976 target_work(ml) = 5.095 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0983 r_free= 0.1976 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.095488 | | target function (ml) not normalized (work): 25079.991116 | | target function (ml) not normalized (free): 1846.605827 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1310 0.1953 5.5554 6.1427| | 2: 3.78 - 3.00 1.00 2430 110 0.0584 0.2015 4.6238 8.8576| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2492 142 0.91 12.72 0.99 0.95 12824.73| | 2: 3.78 - 3.00 2430 110 0.98 3.12 1.01 0.98 1475.97| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 1023.37 max = 20647.88 mean = 7221.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.56 mean = 7.98| |phase err.(test): min = 0.00 max = 82.57 mean = 7.24| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1033 0.0983 0.1976 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2292 0.2288 0.2486 n_refl.: 5174 remove outliers: r(all,work,free)=0.2292 0.2288 0.2486 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2292 0.2288 0.2486 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.1026 0.0978 0.1962 n_refl.: 5174 remove outliers: r(all,work,free)=0.1026 0.0978 0.1962 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 0.3836 318.786 280.157 0.641 0.990 0.330 11.894-9.307 99.02 97 4 0.1792 507.344 493.666 1.030 0.994 0.350 9.237-7.194 100.00 213 7 0.2187 414.906 404.517 1.060 0.996 0.350 7.162-5.571 100.00 427 22 0.2010 311.337 305.843 1.038 0.998 0.270 5.546-4.326 100.00 867 58 0.1092 427.421 421.364 1.063 1.000 0.244 4.315-3.360 100.00 1859 96 0.0677 406.482 405.885 1.161 1.003 0.230 3.356-3.002 100.00 1373 60 0.0565 313.090 312.704 1.153 1.006 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-9.2439 ================= 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 : 0.3617 0.2018 0.080 5.290 8.8 119.3 19.9 258 0.000 1_bss: 0.1557 0.1576 0.080 5.290 6.2 116.7 17.3 258 0.000 1_settarget: 0.1557 0.1576 0.080 5.290 6.2 116.7 17.3 258 0.000 1_nqh: 0.1558 0.1577 0.080 5.290 6.2 116.7 17.3 258 0.003 1_weight: 0.1558 0.1577 0.080 5.290 6.2 116.7 17.3 258 0.003 1_xyzrec: 0.1164 0.1803 0.010 0.974 6.2 116.7 17.3 258 0.198 1_adp: 0.1021 0.1794 0.010 0.974 2.5 111.7 17.8 258 0.198 1_regHadp: 0.1015 0.1803 0.010 0.974 2.5 111.7 17.8 258 0.198 1_occ: 0.1018 0.1792 0.010 0.974 2.5 111.7 17.8 258 0.198 2_bss: 0.1019 0.1777 0.010 0.974 1.5 110.7 16.8 258 0.198 2_settarget: 0.1019 0.1777 0.010 0.974 1.5 110.7 16.8 258 0.198 2_updatecdl: 0.1019 0.1777 0.010 0.996 1.5 110.7 16.8 258 0.198 2_nqh: 0.1019 0.1777 0.010 0.996 1.5 110.7 16.8 258 0.201 2_sol: 0.1105 0.1679 0.010 0.996 1.0 110.6 16.2 230 n/a 2_weight: 0.1105 0.1679 0.010 0.996 1.0 110.6 16.2 230 n/a 2_xyzrec: 0.0998 0.1824 0.009 0.975 1.0 110.6 16.2 230 n/a 2_adp: 0.0929 0.1852 0.009 0.975 0.0 108.1 17.1 230 n/a 2_regHadp: 0.0927 0.1854 0.009 0.975 0.0 108.1 17.1 230 n/a 2_occ: 0.0921 0.1830 0.009 0.975 0.0 108.1 17.1 230 n/a 3_bss: 0.0919 0.1836 0.009 0.975 0.0 108.1 17.1 230 n/a 3_settarget: 0.0919 0.1836 0.009 0.975 0.0 108.1 17.1 230 n/a 3_updatecdl: 0.0919 0.1836 0.009 0.982 0.0 108.1 17.1 230 n/a 3_nqh: 0.0925 0.1837 0.009 0.982 0.0 108.1 17.1 230 n/a 3_sol: 0.1022 0.1799 0.009 0.982 0.0 108.1 16.9 242 n/a 3_weight: 0.1022 0.1799 0.009 0.982 0.0 108.1 16.9 242 n/a 3_xyzrec: 0.0924 0.1908 0.011 1.065 0.0 108.1 16.9 242 n/a 3_adp: 0.0878 0.1916 0.011 1.065 0.0 107.8 17.0 242 n/a 3_regHadp: 0.0883 0.1925 0.011 1.065 0.0 107.8 17.0 242 n/a 3_occ: 0.0871 0.1913 0.011 1.065 0.0 107.8 17.0 242 n/a 4_bss: 0.0861 0.1897 0.011 1.065 0.0 107.8 17.0 242 n/a 4_settarget: 0.0861 0.1897 0.011 1.065 0.0 107.8 17.0 242 n/a 4_updatecdl: 0.0861 0.1897 0.011 1.077 0.0 107.8 17.0 242 n/a 4_nqh: 0.0861 0.1900 0.011 1.077 0.0 107.8 17.0 242 n/a 4_sol: 0.1257 0.1864 0.011 1.077 0.0 107.8 16.6 157 n/a 4_weight: 0.1257 0.1864 0.011 1.077 0.0 107.8 16.6 157 n/a 4_xyzrec: 0.1106 0.1906 0.012 1.105 0.0 107.8 16.6 157 n/a 4_adp: 0.1048 0.1902 0.012 1.105 0.0 105.6 16.6 157 n/a 4_regHadp: 0.1052 0.1905 0.012 1.105 0.0 105.6 16.6 157 n/a 4_occ: 0.1051 0.1896 0.012 1.105 0.0 105.6 16.6 157 n/a 5_bss: 0.1035 0.1905 0.012 1.105 0.0 105.6 16.6 157 n/a 5_settarget: 0.1035 0.1905 0.012 1.105 0.0 105.6 16.6 157 n/a 5_updatecdl: 0.1035 0.1905 0.012 1.118 0.0 105.6 16.6 157 n/a 5_setrh: 0.1038 0.1906 0.012 1.118 0.0 105.6 16.6 157 n/a 5_nqh: 0.1038 0.1906 0.012 1.118 0.0 105.6 16.6 157 n/a 5_sol: 0.1089 0.1913 0.012 1.118 0.0 105.6 17.2 198 n/a 5_weight: 0.1089 0.1913 0.012 1.118 0.0 105.6 17.2 198 n/a 5_xyzrec: 0.1037 0.1970 0.011 1.268 0.0 105.6 17.2 198 n/a 5_adp: 0.1010 0.1997 0.011 1.268 0.0 105.3 17.2 198 n/a 5_regHadp: 0.1015 0.2000 0.011 1.268 0.0 105.3 17.2 198 n/a 5_occ: 0.0983 0.1976 0.011 1.268 0.0 105.3 17.2 198 n/a end: 0.0978 0.1962 0.011 1.268 0.0 105.3 17.2 198 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8008321_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8008321_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9100 Refinement macro-cycles (run) : 460.3700 Write final files (write_after_run_outputs) : 11.0000 Total : 474.2800 Total CPU time: 8.27 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:37 PST -0800 (1735492717.46 s) Start R-work = 0.1557, R-free = 0.1576 Final R-work = 0.0978, R-free = 0.1962 =============================================================================== Job complete usr+sys time: 505.64 seconds wall clock time: 8 minutes 47.69 seconds (527.69 seconds total)