Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4811713.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4811713.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4811713.pdb" 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" } 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: 1.33, per 1000 atoms: 0.39 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: 0.51 Conformation dependent library (CDL) restraints added in 210.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 408 0.89 - 1.16: 1214 1.16 - 1.42: 658 1.42 - 1.68: 840 1.68 - 1.95: 33 Bond restraints: 3153 Sorted by residual: bond pdb=" CA THR A 34 " pdb=" C THR A 34 " ideal model delta sigma weight residual 1.523 1.283 0.240 1.23e-02 6.61e+03 3.80e+02 bond pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 1.334 1.099 0.236 1.33e-02 5.65e+03 3.14e+02 bond pdb=" C GLN A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 1.335 1.528 -0.193 1.09e-02 8.42e+03 3.13e+02 bond pdb=" C LEU A 112 " pdb=" O LEU A 112 " ideal model delta sigma weight residual 1.237 1.439 -0.203 1.16e-02 7.43e+03 3.06e+02 bond pdb=" CA TYR A 141 " pdb=" C TYR A 141 " ideal model delta sigma weight residual 1.524 1.741 -0.217 1.25e-02 6.40e+03 3.01e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 3236 4.88 - 9.75: 1905 9.75 - 14.63: 533 14.63 - 19.51: 98 19.51 - 24.38: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.12 139.86 -17.74 1.06e+00 8.90e-01 2.80e+02 angle pdb=" OD1AASN A 97 " pdb=" CG AASN A 97 " pdb=" ND2AASN A 97 " ideal model delta sigma weight residual 122.60 138.54 -15.94 1.00e+00 1.00e+00 2.54e+02 angle pdb=" OD1 ASN A 135 " pdb=" CG ASN A 135 " pdb=" ND2 ASN A 135 " ideal model delta sigma weight residual 122.60 108.18 14.42 1.00e+00 1.00e+00 2.08e+02 angle pdb=" C LEU A 72 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " ideal model delta sigma weight residual 120.21 107.69 12.52 9.60e-01 1.09e+00 1.70e+02 angle pdb=" CA LYS A 89 " pdb=" C LYS A 89 " pdb=" O LYS A 89 " ideal model delta sigma weight residual 120.98 107.15 13.84 1.10e+00 8.26e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 1307 17.50 - 35.00: 121 35.00 - 52.49: 37 52.49 - 69.99: 14 69.99 - 87.48: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C SER A 83 " pdb=" N SER A 83 " pdb=" CA SER A 83 " pdb=" CB SER A 83 " ideal model delta harmonic sigma weight residual -122.60 -144.03 21.43 0 2.50e+00 1.60e-01 7.35e+01 dihedral pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CA VAL A 35 " pdb=" CB VAL A 35 " ideal model delta harmonic sigma weight residual 123.40 104.80 18.60 0 2.50e+00 1.60e-01 5.54e+01 dihedral pdb=" C ILE A 31 " pdb=" N ILE A 31 " pdb=" CA ILE A 31 " pdb=" CB ILE A 31 " ideal model delta harmonic sigma weight residual -122.00 -139.73 17.73 0 2.50e+00 1.60e-01 5.03e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.215: 98 0.215 - 0.429: 75 0.429 - 0.643: 43 0.643 - 0.857: 20 0.857 - 1.071: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -3.70 1.07 2.00e-01 2.50e+01 2.87e+01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.47 -1.02 2.00e-01 2.50e+01 2.62e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.71 -0.92 2.00e-01 2.50e+01 2.13e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 45 " -0.018 2.00e-02 2.50e+03 8.86e-02 1.18e+02 pdb=" CD GLN A 45 " -0.135 2.00e-02 2.50e+03 pdb=" OE1 GLN A 45 " 0.100 2.00e-02 2.50e+03 pdb=" NE2 GLN A 45 " 0.065 2.00e-02 2.50e+03 pdb="HE21 GLN A 45 " 0.079 2.00e-02 2.50e+03 pdb="HE22 GLN A 45 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.030 2.00e-02 2.50e+03 5.99e-02 1.08e+02 pdb=" CG TYR A 141 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.112 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.072 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.066 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.084 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.092 2.00e-02 2.50e+03 5.81e-02 1.01e+02 pdb=" CG PHE A 119 " -0.122 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.060 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.045 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.008 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 705 2.26 - 2.85: 7714 2.85 - 3.43: 10703 3.43 - 4.02: 15316 4.02 - 4.60: 22151 Nonbonded interactions: 56589 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.681 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.753 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.824 2.100 nonbonded pdb=" O VAL A 51 " pdb=" H ACYS A 53 " model vdw sym.op. 1.826 2.450 x-y,-y,-z-4/3 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.835 2.450 ... (remaining 56584 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_4811713_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= 0.3613 r_free= 0.2027 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.465004 | | target function (ml) not normalized (work): 22012.471456 | | target function (ml) not normalized (free): 1154.258370 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3787 0.2190 4.8504 4.9031| | 2: 3.78 - 3.00 1.00 2430 110 0.3401 0.1751 4.0685 4.1638| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.65 0.83 0.13 6595.84| | 2: 3.78 - 3.00 2430 110 0.94 11.30 1.48 0.26 443.16| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 374.11 max = 12047.54 mean = 3563.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.24| |phase err.(test): min = 0.00 max = 90.00 mean = 33.15| |-----------------------------------------------------------------------------| ----------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 0.246 1557 Z= 5.331 Angle : 5.362 18.216 2118 Z= 3.708 Chirality : 0.400 1.071 243 Planarity : 0.032 0.088 284 Dihedral : 13.917 87.482 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 1.86 % Favored : 96.89 % Cbeta Deviations : 35.14 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.47), residues: 224 helix: -2.61 (0.39), residues: 109 sheet: -0.63 (0.78), residues: 28 loop : -0.13 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.105 0.033 ARG A 156 TYR 0.093 0.036 TYR A 141 PHE 0.115 0.031 PHE A 119 HIS 0.077 0.029 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3613 r_free= 0.2027 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.465004 | | target function (ml) not normalized (work): 22012.471456 | | target function (ml) not normalized (free): 1154.258370 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3569 0.3645 0.2130 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3569 0.3645 0.2130 n_refl.: 5182 remove outliers: r(all,work,free)=0.2525 0.2550 0.2130 n_refl.: 5178 overall B=-2.50 to atoms: r(all,work,free)=0.2427 0.2448 0.2093 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1552 0.1546 0.1662 n_refl.: 5178 remove outliers: r(all,work,free)=0.1548 0.1541 0.1662 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 0.3799 449.908 407.337 0.640 1.047 0.396 11.894-9.307 99.02 97 4 0.1845 714.714 695.156 0.920 1.045 0.372 9.237-7.194 100.00 213 7 0.2187 584.495 574.543 0.951 1.040 0.374 7.162-5.571 100.00 427 22 0.2266 438.592 426.322 0.920 1.031 0.356 5.546-4.326 100.00 867 58 0.1360 602.125 595.869 0.955 1.017 0.234 4.315-3.360 100.00 1859 96 0.1306 572.627 566.943 1.022 0.993 0.188 3.356-3.002 100.00 1373 60 0.1573 441.062 433.222 1.025 0.969 0.077 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9174 b_overall=-4.3452 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1541 r_free=0.1662 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1541 r_free=0.1662 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.521186 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.710548 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 0.1162 0.1790 0.0628 0.009 1.0 3.5 0.5 0.0 0 9.261 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 17.90 6.28 3.013 16.354 1.711 0.018 10.30 18.02 7.72 4.752 16.552 1.711 0.015 Individual atomic B min max mean iso aniso Overall: 2.41 111.79 17.76 5.15 1785 0 Protein: 2.41 111.74 15.04 5.15 1519 0 Water: 4.36 111.79 33.56 N/A 258 0 Other: 16.35 38.39 23.93 N/A 8 0 Chain A: 2.41 111.79 17.76 N/A 1785 0 Histogram: Values Number of atoms 2.41 - 13.34 909 13.34 - 24.28 493 24.28 - 35.22 188 35.22 - 46.16 109 46.16 - 57.10 54 57.10 - 68.04 14 68.04 - 78.98 8 78.98 - 89.92 5 89.92 - 100.85 1 100.85 - 111.79 4 =========================== Idealize ADP of riding H ========================== r_work=0.1030 r_free=0.1802 r_work=0.1022 r_free=0.1807 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1022 r_free = 0.1807 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 = 0.1021 r_free = 0.1814 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.18 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= 0.1021 r_free= 0.1814 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014238 | | target function (ls_wunit_k1) not normalized (work): 70.109371 | | target function (ls_wunit_k1) not normalized (free): 10.661422 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1061 0.1021 0.1814 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2121 0.2120 0.2237 n_refl.: 5176 remove outliers: r(all,work,free)=0.2121 0.2120 0.2237 n_refl.: 5176 overall B=-1.09 to atoms: r(all,work,free)=0.2074 0.2071 0.2224 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1062 0.1023 0.1804 n_refl.: 5176 remove outliers: r(all,work,free)=0.1062 0.1023 0.1804 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 0.3301 318.689 311.333 0.704 0.997 0.376 11.894-9.307 99.02 97 4 0.1497 506.263 497.880 0.995 1.000 0.346 9.237-7.194 100.00 213 7 0.1692 414.022 412.872 1.031 1.000 0.336 7.162-5.571 100.00 427 22 0.1682 310.673 306.188 0.992 1.000 0.332 5.546-4.326 100.00 867 58 0.0924 426.511 422.721 1.003 1.000 0.197 4.315-3.360 100.00 1859 96 0.0769 405.616 405.514 1.051 0.999 0.184 3.356-3.002 100.00 1373 60 0.1007 312.423 311.188 1.021 0.999 0.062 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.9180 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1023 r_free=0.1804 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1025 r_free=0.1805 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1025 r_free=0.1805 | n_water=258 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.1050 r_free=0.1781 | n_water=249 | time (s): 19.220 (total time: 19.720) Filter (q & B) r_work=0.1050 r_free=0.1775 | n_water=245 | time (s): 1.580 (total time: 21.300) Compute maps r_work=0.1050 r_free=0.1775 | n_water=245 | time (s): 0.510 (total time: 21.810) Filter (map) r_work=0.1389 r_free=0.1825 | n_water=140 | time (s): 1.380 (total time: 23.190) Find peaks r_work=0.1389 r_free=0.1825 | n_water=140 | time (s): 0.430 (total time: 23.620) Add new water r_work=0.1745 r_free=0.2095 | n_water=232 | time (s): 1.370 (total time: 24.990) Refine new water occ: r_work=0.1176 r_free=0.1684 adp: r_work=0.1149 r_free=0.1689 occ: r_work=0.1147 r_free=0.1663 adp: r_work=0.1133 r_free=0.1672 occ: r_work=0.1134 r_free=0.1655 adp: r_work=0.1130 r_free=0.1660 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1660 r_work=0.1130 r_free=0.1660 | n_water=232 | time (s): 8.350 (total time: 33.340) Filter (q & B) r_work=0.1130 r_free=0.1660 | n_water=232 | time (s): 0.950 (total time: 34.290) Filter (dist only) r_work=0.1140 r_free=0.1643 | n_water=228 | time (s): 18.880 (total time: 53.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.776021 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.463993 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 0.1020 0.1768 0.0748 0.009 1.0 3.5 0.5 0.6 0 11.388 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.20 17.68 7.48 4.600 17.008 2.464 0.014 9.53 17.95 8.42 5.481 17.440 2.464 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 106.65 16.88 6.41 1755 0 Protein: 0.00 106.65 15.29 6.40 1519 0 Water: 0.00 62.98 27.23 N/A 228 0 Other: 13.81 37.82 24.03 N/A 8 0 Chain A: 0.00 106.65 16.03 N/A 1664 0 Chain S: 4.01 59.85 32.45 N/A 91 0 Histogram: Values Number of atoms 0.00 - 10.66 640 10.66 - 21.33 695 21.33 - 31.99 215 31.99 - 42.66 120 42.66 - 53.32 41 53.32 - 63.99 28 63.99 - 74.65 8 74.65 - 85.32 3 85.32 - 95.98 3 95.98 - 106.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.0953 r_free=0.1795 r_work=0.0950 r_free=0.1796 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0950 r_free = 0.1796 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0947 r_free = 0.1784 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.19 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= 0.0947 r_free= 0.1784 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ls_wunit_k1) (work): 0.012169 | | target function (ls_wunit_k1) not normalized (work): 59.919596 | | target function (ls_wunit_k1) not normalized (free): 9.529202 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0989 0.0947 0.1784 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2146 0.2154 0.2138 n_refl.: 5176 remove outliers: r(all,work,free)=0.2146 0.2154 0.2138 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2146 0.2154 0.2138 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0987 0.0945 0.1788 n_refl.: 5176 remove outliers: r(all,work,free)=0.0983 0.0940 0.1788 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 0.3086 318.106 299.407 0.664 1.005 0.360 11.894-9.307 99.02 97 4 0.1485 506.263 500.309 0.988 1.007 0.340 9.237-7.194 100.00 213 7 0.1453 414.022 415.259 1.029 1.008 0.320 7.162-5.571 100.00 427 22 0.1493 310.673 307.070 0.998 1.006 0.310 5.546-4.326 100.00 867 58 0.0791 426.511 423.773 1.015 1.004 0.230 4.315-3.360 100.00 1859 96 0.0722 405.616 405.558 1.068 1.000 0.200 3.356-3.002 100.00 1373 60 0.0975 312.423 311.787 1.046 0.996 0.063 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-4.8079 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0940 r_free=0.1788 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0942 r_free=0.1788 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0942 r_free=0.1788 | n_water=228 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.0944 r_free=0.1787 | n_water=227 | time (s): 17.360 (total time: 17.980) Filter (q & B) r_work=0.0973 r_free=0.1816 | n_water=226 | time (s): 1.940 (total time: 19.920) Compute maps r_work=0.0973 r_free=0.1816 | n_water=226 | time (s): 0.520 (total time: 20.440) Filter (map) r_work=0.1252 r_free=0.1833 | n_water=150 | time (s): 1.990 (total time: 22.430) Find peaks r_work=0.1252 r_free=0.1833 | n_water=150 | time (s): 0.610 (total time: 23.040) Add new water r_work=0.1658 r_free=0.2210 | n_water=248 | time (s): 1.620 (total time: 24.660) Refine new water occ: r_work=0.1065 r_free=0.1742 adp: r_work=0.1063 r_free=0.1752 occ: r_work=0.1047 r_free=0.1728 adp: r_work=0.1048 r_free=0.1738 occ: r_work=0.1033 r_free=0.1716 adp: r_work=0.1033 r_free=0.1723 ADP+occupancy (water only), MIN, final r_work=0.1033 r_free=0.1723 r_work=0.1033 r_free=0.1723 | n_water=248 | time (s): 10.230 (total time: 34.890) Filter (q & B) r_work=0.1033 r_free=0.1718 | n_water=246 | time (s): 1.350 (total time: 36.240) Filter (dist only) r_work=0.1041 r_free=0.1733 | n_water=245 | time (s): 19.360 (total time: 55.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.093186 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.249281 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 0.0951 0.1800 0.0849 0.011 1.1 4.5 0.5 0.6 0 0.547 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.51 18.00 8.49 5.386 18.222 0.249 5.119 8.97 18.02 9.05 7.343 18.224 0.249 5.018 Individual atomic B min max mean iso aniso Overall: 0.00 107.61 16.85 9.09 1772 0 Protein: 0.00 107.61 15.42 9.08 1519 0 Water: 0.00 57.98 25.45 N/A 245 0 Other: 14.35 46.59 25.81 N/A 8 0 Chain A: 0.00 107.61 16.08 N/A 1652 0 Chain S: 0.00 57.62 27.43 N/A 120 0 Histogram: Values Number of atoms 0.00 - 10.76 656 10.76 - 21.52 676 21.52 - 32.28 244 32.28 - 43.04 118 43.04 - 53.80 42 53.80 - 64.56 19 64.56 - 75.33 10 75.33 - 86.09 2 86.09 - 96.85 4 96.85 - 107.61 1 =========================== Idealize ADP of riding H ========================== r_work=0.0897 r_free=0.1802 r_work=0.0902 r_free=0.1809 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0902 r_free = 0.1809 target_work(ml) = 5.022 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0889 r_free = 0.1801 target_work(ml) = 5.014 | | occupancies: max = 1.00 min = 0.21 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= 0.0889 r_free= 0.1801 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 5.013996 | | target function (ml) not normalized (work): 24678.888060 | | target function (ml) not normalized (free): 1855.006119 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0935 0.0889 0.1801 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2042 0.2045 0.2119 n_refl.: 5174 remove outliers: r(all,work,free)=0.2042 0.2045 0.2119 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2042 0.2045 0.2119 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0925 0.0880 0.1787 n_refl.: 5174 remove outliers: r(all,work,free)=0.0925 0.0880 0.1787 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 0.3730 318.106 290.177 0.604 0.989 0.336 11.894-9.307 99.02 97 4 0.1805 506.263 492.207 0.956 0.994 0.333 9.237-7.194 100.00 213 7 0.1909 414.022 407.368 1.006 0.996 0.290 7.162-5.571 100.00 427 22 0.1883 310.673 301.154 0.980 0.998 0.280 5.546-4.326 100.00 867 58 0.0901 426.511 421.103 1.008 1.000 0.215 4.315-3.360 100.00 1859 96 0.0587 405.616 405.222 1.067 1.003 0.210 3.356-3.002 100.00 1373 60 0.0570 312.423 312.426 1.046 1.006 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.0236 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0880 r_free=0.1787 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0880 r_free=0.1787 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0880 r_free=0.1787 | n_water=245 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0886 r_free=0.1786 | n_water=244 | time (s): 19.990 (total time: 20.560) Filter (q & B) r_work=0.0955 r_free=0.1837 | n_water=242 | time (s): 1.800 (total time: 22.360) Compute maps r_work=0.0955 r_free=0.1837 | n_water=242 | time (s): 0.500 (total time: 22.860) Filter (map) r_work=0.1258 r_free=0.1868 | n_water=160 | time (s): 1.650 (total time: 24.510) Find peaks r_work=0.1258 r_free=0.1868 | n_water=160 | time (s): 0.540 (total time: 25.050) Add new water r_work=0.1607 r_free=0.2184 | n_water=250 | time (s): 1.910 (total time: 26.960) Refine new water occ: r_work=0.1001 r_free=0.1825 adp: r_work=0.0994 r_free=0.1834 occ: r_work=0.0983 r_free=0.1800 adp: r_work=0.0982 r_free=0.1820 occ: r_work=0.0972 r_free=0.1785 adp: r_work=0.0971 r_free=0.1803 ADP+occupancy (water only), MIN, final r_work=0.0971 r_free=0.1803 r_work=0.0971 r_free=0.1803 | n_water=250 | time (s): 10.350 (total time: 37.310) Filter (q & B) r_work=0.0971 r_free=0.1807 | n_water=248 | time (s): 1.890 (total time: 39.200) Filter (dist only) r_work=0.0978 r_free=0.1793 | n_water=246 | time (s): 19.020 (total time: 58.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.957417 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.221829 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 0.0893 0.1825 0.0932 0.011 1.0 4.5 0.5 0.6 0 0.479 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.93 18.25 9.32 7.077 18.358 0.222 4.970 8.70 18.42 9.72 8.365 18.433 0.222 4.899 Individual atomic B min max mean iso aniso Overall: 0.00 107.82 17.09 10.90 1773 0 Protein: 0.00 107.82 15.76 10.90 1519 0 Water: 0.00 59.77 24.96 N/A 246 0 Other: 14.42 48.95 26.86 N/A 8 0 Chain A: 0.00 107.82 16.35 N/A 1641 0 Chain S: 0.00 55.00 26.23 N/A 132 0 Histogram: Values Number of atoms 0.00 - 10.78 644 10.78 - 21.56 671 21.56 - 32.35 246 32.35 - 43.13 121 43.13 - 53.91 55 53.91 - 64.69 15 64.69 - 75.47 10 75.47 - 86.25 7 86.25 - 97.04 2 97.04 - 107.82 2 =========================== Idealize ADP of riding H ========================== r_work=0.0870 r_free=0.1842 r_work=0.0874 r_free=0.1845 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0874 r_free = 0.1845 target_work(ml) = 4.905 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0862 r_free = 0.1837 target_work(ml) = 4.896 | | occupancies: max = 1.00 min = 0.21 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= 0.0862 r_free= 0.1837 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 4.896443 | | target function (ml) not normalized (work): 24100.294897 | | target function (ml) not normalized (free): 2187.105902 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0910 0.0862 0.1837 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2087 0.2091 0.2163 n_refl.: 5174 remove outliers: r(all,work,free)=0.2087 0.2091 0.2163 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2087 0.2091 0.2163 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0908 0.0860 0.1832 n_refl.: 5174 remove outliers: r(all,work,free)=0.0908 0.0860 0.1832 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 0.3869 318.106 287.189 0.596 0.983 0.305 11.894-9.307 99.02 97 4 0.1923 506.263 491.249 0.989 0.989 0.301 9.237-7.194 100.00 213 7 0.2169 414.022 403.387 1.053 0.993 0.280 7.162-5.571 100.00 427 22 0.2047 310.673 299.647 1.040 0.996 0.280 5.546-4.326 100.00 867 58 0.0949 426.511 420.930 1.072 0.999 0.224 4.315-3.360 100.00 1859 96 0.0531 405.616 405.449 1.142 1.003 0.210 3.356-3.002 100.00 1373 60 0.0412 312.423 312.843 1.122 1.007 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.3733 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0860 r_free=0.1832 After: r_work=0.0863 r_free=0.1831 ================================== NQH flips ================================== r_work=0.0863 r_free=0.1831 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0863 r_free=0.1831 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0863 r_free=0.1831 | n_water=246 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.0884 r_free=0.1836 | n_water=241 | time (s): 20.340 (total time: 20.960) Filter (q & B) r_work=0.0936 r_free=0.1871 | n_water=239 | time (s): 1.950 (total time: 22.910) Compute maps r_work=0.0936 r_free=0.1871 | n_water=239 | time (s): 0.650 (total time: 23.560) Filter (map) r_work=0.1278 r_free=0.1905 | n_water=160 | time (s): 1.490 (total time: 25.050) Find peaks r_work=0.1278 r_free=0.1905 | n_water=160 | time (s): 0.400 (total time: 25.450) Add new water r_work=0.1587 r_free=0.2144 | n_water=241 | time (s): 1.270 (total time: 26.720) Refine new water occ: r_work=0.1004 r_free=0.1834 adp: r_work=0.0999 r_free=0.1838 occ: r_work=0.0991 r_free=0.1828 adp: r_work=0.0991 r_free=0.1835 occ: r_work=0.0982 r_free=0.1823 adp: r_work=0.0982 r_free=0.1827 ADP+occupancy (water only), MIN, final r_work=0.0982 r_free=0.1827 r_work=0.0982 r_free=0.1827 | n_water=241 | time (s): 13.790 (total time: 40.510) Filter (q & B) r_work=0.0982 r_free=0.1832 | n_water=239 | time (s): 1.800 (total time: 42.310) Filter (dist only) r_work=0.0989 r_free=0.1834 | n_water=237 | time (s): 19.670 (total time: 61.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.962099 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.251893 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 0.0927 0.1843 0.0916 0.010 1.1 6.7 0.5 0.0 0 0.481 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.27 18.43 9.16 8.272 18.552 0.252 4.977 9.04 18.49 9.45 9.255 18.624 0.252 4.916 Individual atomic B min max mean iso aniso Overall: 0.00 107.03 17.22 12.19 1764 0 Protein: 0.00 107.03 16.07 12.17 1519 0 Water: 0.00 62.10 24.25 N/A 237 0 Other: 11.99 49.75 27.84 N/A 8 0 Chain A: 0.00 107.03 16.53 N/A 1630 0 Chain S: 0.00 62.10 25.59 N/A 134 0 Histogram: Values Number of atoms 0.00 - 10.70 619 10.70 - 21.41 677 21.41 - 32.11 251 32.11 - 42.81 129 42.81 - 53.51 50 53.51 - 64.22 17 64.22 - 74.92 8 74.92 - 85.62 7 85.62 - 96.33 4 96.33 - 107.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.0904 r_free=0.1849 r_work=0.0907 r_free=0.1847 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0907 r_free = 0.1847 target_work(ml) = 4.922 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0900 r_free = 0.1832 target_work(ml) = 4.916 | | 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= 0.0900 r_free= 0.1832 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.915844 | | target function (ml) not normalized (work): 24195.783559 | | target function (ml) not normalized (free): 2258.932959 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1301 0.1836 5.5285 6.1745| | 2: 3.78 - 3.00 1.00 2430 110 0.0410 0.1826 4.2876 12.565| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.83 1.00 0.89 13526.88| | 2: 3.78 - 3.00 2430 110 0.99 1.73 1.00 0.91 804.82| |alpha: min = 0.88 max = 0.91 mean = 0.90| |beta: min = 502.38 max = 22872.05 mean = 7245.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.76 mean = 7.35| |phase err.(test): min = 0.00 max = 80.86 mean = 7.34| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0947 0.0900 0.1832 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2146 0.2145 0.2257 n_refl.: 5174 remove outliers: r(all,work,free)=0.2146 0.2145 0.2257 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2146 0.2145 0.2257 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0949 0.0903 0.1838 n_refl.: 5174 remove outliers: r(all,work,free)=0.0949 0.0903 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 0.4110 318.106 281.486 0.572 0.981 0.309 11.894-9.307 99.02 97 4 0.1989 506.263 490.752 0.960 0.988 0.308 9.237-7.194 100.00 213 7 0.2260 414.022 402.103 1.010 0.993 0.285 7.162-5.571 100.00 427 22 0.2120 310.673 300.090 1.004 0.995 0.280 5.546-4.326 100.00 867 58 0.1039 426.511 420.093 1.038 0.998 0.223 4.315-3.360 100.00 1859 96 0.0567 405.616 405.608 1.119 1.003 0.216 3.356-3.002 100.00 1373 60 0.0392 312.423 313.062 1.100 1.007 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-9.2957 ================= 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 : 0.3613 0.2027 0.081 5.362 8.8 119.3 19.9 258 0.000 1_bss: 0.1541 0.1662 0.081 5.362 6.3 116.8 17.4 258 0.000 1_settarget: 0.1541 0.1662 0.081 5.362 6.3 116.8 17.4 258 0.000 1_nqh: 0.1541 0.1662 0.081 5.362 6.3 116.8 17.4 258 0.000 1_weight: 0.1541 0.1662 0.081 5.362 6.3 116.8 17.4 258 0.000 1_xyzrec: 0.1162 0.1790 0.009 0.963 6.3 116.8 17.4 258 0.214 1_adp: 0.1030 0.1802 0.009 0.963 2.4 111.8 17.8 258 0.214 1_regHadp: 0.1022 0.1807 0.009 0.963 2.4 111.8 17.8 258 0.214 1_occ: 0.1021 0.1814 0.009 0.963 2.4 111.8 17.8 258 0.214 2_bss: 0.1023 0.1804 0.009 0.963 1.3 110.7 16.7 258 0.214 2_settarget: 0.1023 0.1804 0.009 0.963 1.3 110.7 16.7 258 0.214 2_updatecdl: 0.1023 0.1804 0.010 0.991 1.3 110.7 16.7 258 0.214 2_nqh: 0.1025 0.1805 0.010 0.991 1.3 110.7 16.7 258 0.216 2_sol: 0.1140 0.1643 0.010 0.991 1.0 110.6 16.1 228 n/a 2_weight: 0.1140 0.1643 0.010 0.991 1.0 110.6 16.1 228 n/a 2_xyzrec: 0.1020 0.1768 0.009 0.974 1.0 110.6 16.1 228 n/a 2_adp: 0.0953 0.1795 0.009 0.974 0.0 106.6 16.9 228 n/a 2_regHadp: 0.0950 0.1796 0.009 0.974 0.0 106.6 16.9 228 n/a 2_occ: 0.0947 0.1784 0.009 0.974 0.0 106.6 16.9 228 n/a 3_bss: 0.0940 0.1788 0.009 0.974 0.0 106.6 16.9 228 n/a 3_settarget: 0.0940 0.1788 0.009 0.974 0.0 106.6 16.9 228 n/a 3_updatecdl: 0.0940 0.1788 0.009 0.979 0.0 106.6 16.9 228 n/a 3_nqh: 0.0942 0.1788 0.009 0.979 0.0 106.6 16.9 228 n/a 3_sol: 0.1041 0.1733 0.009 0.979 0.0 106.6 16.8 245 n/a 3_weight: 0.1041 0.1733 0.009 0.979 0.0 106.6 16.8 245 n/a 3_xyzrec: 0.0951 0.1800 0.011 1.054 0.0 106.6 16.8 245 n/a 3_adp: 0.0897 0.1802 0.011 1.054 0.0 107.6 16.9 245 n/a 3_regHadp: 0.0902 0.1809 0.011 1.054 0.0 107.6 16.9 245 n/a 3_occ: 0.0889 0.1801 0.011 1.054 0.0 107.6 16.9 245 n/a 4_bss: 0.0880 0.1787 0.011 1.054 0.0 107.6 16.9 245 n/a 4_settarget: 0.0880 0.1787 0.011 1.054 0.0 107.6 16.9 245 n/a 4_updatecdl: 0.0880 0.1787 0.011 1.063 0.0 107.6 16.9 245 n/a 4_nqh: 0.0880 0.1787 0.011 1.063 0.0 107.6 16.9 245 n/a 4_sol: 0.0978 0.1793 0.011 1.063 0.0 107.6 16.9 246 n/a 4_weight: 0.0978 0.1793 0.011 1.063 0.0 107.6 16.9 246 n/a 4_xyzrec: 0.0893 0.1825 0.011 1.020 0.0 107.6 16.9 246 n/a 4_adp: 0.0870 0.1842 0.011 1.020 0.0 107.8 17.1 246 n/a 4_regHadp: 0.0874 0.1845 0.011 1.020 0.0 107.8 17.1 246 n/a 4_occ: 0.0862 0.1837 0.011 1.020 0.0 107.8 17.1 246 n/a 5_bss: 0.0860 0.1832 0.011 1.020 0.0 107.8 17.1 246 n/a 5_settarget: 0.0860 0.1832 0.011 1.020 0.0 107.8 17.1 246 n/a 5_updatecdl: 0.0860 0.1832 0.011 1.023 0.0 107.8 17.1 246 n/a 5_setrh: 0.0863 0.1831 0.011 1.023 0.0 107.8 17.1 246 n/a 5_nqh: 0.0863 0.1831 0.011 1.023 0.0 107.8 17.1 246 n/a 5_sol: 0.0989 0.1834 0.011 1.023 0.0 107.8 17.1 237 n/a 5_weight: 0.0989 0.1834 0.011 1.023 0.0 107.8 17.1 237 n/a 5_xyzrec: 0.0927 0.1843 0.010 1.094 0.0 107.8 17.1 237 n/a 5_adp: 0.0904 0.1849 0.010 1.094 0.0 107.0 17.2 237 n/a 5_regHadp: 0.0907 0.1847 0.010 1.094 0.0 107.0 17.2 237 n/a 5_occ: 0.0900 0.1832 0.010 1.094 0.0 107.0 17.2 237 n/a end: 0.0903 0.1838 0.010 1.094 0.0 107.0 17.2 237 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4811713_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4811713_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2300 Refinement macro-cycles (run) : 504.0200 Write final files (write_after_run_outputs) : 9.0300 Total : 516.2800 Total CPU time: 8.95 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:17 PST -0800 (1735492757.84 s) Start R-work = 0.1541, R-free = 0.1662 Final R-work = 0.0903, R-free = 0.1838 =============================================================================== Job complete usr+sys time: 543.84 seconds wall clock time: 9 minutes 25.29 seconds (565.29 seconds total)