Starting phenix.refine on Sun Dec 29 09:24:41 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=2 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 { 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 = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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" } 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: 1.60, per 1000 atoms: 0.47 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: 0.32 Conformation dependent library (CDL) restraints added in 136.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.46 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 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2785 r_free= 0.1820 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.410366 | | target function (ml) not normalized (work): 71637.581172 | | target function (ml) not normalized (free): 3262.673774 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3190 0.2144 7.6311 5.0183| | 2: 3.63 - 2.88 1.00 2711 122 0.2649 0.1807 4.3175 4.3312| | 3: 2.88 - 2.52 1.00 2682 148 0.2534 0.1616 4.1769 4.1757| | 4: 2.52 - 2.29 1.00 2661 139 0.2529 0.1546 3.467 3.6237| | 5: 2.29 - 2.13 1.00 2678 122 0.2698 0.1539 3.4014 3.4802| | 6: 2.13 - 2.00 1.00 2692 117 0.2729 0.1765 3.3001 3.3338| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 17.30 0.77 0.23 1274.61| | 2: 3.63 - 2.88 2711 122 0.83 23.63 1.32 0.23 1274.61| | 3: 2.88 - 2.52 2682 148 0.74 32.30 1.28 0.23 1274.61| | 4: 2.52 - 2.29 2661 139 0.93 11.22 1.29 0.26 132.95| | 5: 2.29 - 2.13 2678 122 0.92 13.30 1.33 0.26 132.95| | 6: 2.13 - 2.00 2692 117 0.90 16.15 1.33 0.26 132.95| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 132.95 max = 1274.61 mean = 710.14| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.97 mean = 18.99| |phase err.(test): min = 0.00 max = 89.87 mean = 19.16| |-----------------------------------------------------------------------------| ----------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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2785 r_free= 0.1820 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.410366 | | target function (ml) not normalized (work): 71637.581172 | | target function (ml) not normalized (free): 3262.673774 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3369 percent. r_work = 0.2919 r_free = 0.2002 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2867 0.2919 0.2002 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2867 0.2919 0.2002 n_refl.: 17050 remove outliers: r(all,work,free)=0.2155 0.2166 0.2002 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2127 0.2137 0.1980 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1606 0.1603 0.1683 n_refl.: 17045 remove outliers: r(all,work,free)=0.1604 0.1600 0.1683 n_refl.: 17043 ======================== 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 0.3816 399.184 374.538 0.673 1.005 0.395 11.894-9.307 99.02 97 4 0.1853 633.998 614.418 0.930 1.006 0.370 9.237-7.194 100.00 213 7 0.2187 518.547 508.123 0.961 1.006 0.355 7.162-5.571 100.00 427 22 0.2263 389.170 377.268 0.929 1.006 0.309 5.546-4.326 100.00 867 58 0.1369 534.268 530.380 0.966 1.005 0.235 4.315-3.360 100.00 1859 96 0.1288 508.094 504.040 1.021 1.003 0.202 3.356-2.611 100.00 3867 181 0.1647 333.789 328.996 1.013 1.001 0.034 2.608-2.000 99.99 8818 434 0.1639 217.573 213.762 1.025 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.5028 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1600 r_free=0.1683 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1600 r_free=0.1683 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.862155 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.847469 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1352 0.1632 0.0280 0.008 1.0 1.0 0.5 0.0 0 10.931 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.32 2.80 3.013 18.437 0.847 0.023 12.78 16.59 3.81 3.642 18.725 0.847 0.020 Individual atomic B min max mean iso aniso Overall: 6.27 113.88 20.01 4.08 1785 0 Protein: 6.27 112.62 17.26 4.08 1519 0 Water: 8.93 113.88 36.00 N/A 258 0 Other: 22.20 37.23 26.58 N/A 8 0 Chain A: 6.27 113.88 20.01 N/A 1785 0 Histogram: Values Number of atoms 6.27 - 17.04 1086 17.04 - 27.80 345 27.80 - 38.56 182 38.56 - 49.32 97 49.32 - 60.08 48 60.08 - 70.84 13 70.84 - 81.60 6 81.60 - 92.36 4 92.36 - 103.12 1 103.12 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1659 r_work=0.1281 r_free=0.1667 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1667 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1276 r_free = 0.1662 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1276 r_free= 0.1662 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019991 | | target function (ls_wunit_k1) not normalized (work): 324.568415 | | target function (ls_wunit_k1) not normalized (free): 27.357557 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1295 0.1276 0.1662 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1907 0.1905 0.1999 n_refl.: 17043 remove outliers: r(all,work,free)=0.1907 0.1905 0.1999 n_refl.: 17043 overall B=-0.39 to atoms: r(all,work,free)=0.1878 0.1876 0.1982 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1654 n_refl.: 17043 remove outliers: r(all,work,free)=0.1293 0.1275 0.1654 n_refl.: 17043 ======================== 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 0.3620 307.208 284.746 0.653 0.999 0.389 11.894-9.307 99.02 97 4 0.1712 487.920 476.083 0.927 0.999 0.380 9.237-7.194 100.00 213 7 0.1827 399.069 395.580 0.968 0.998 0.341 7.162-5.571 100.00 427 22 0.1871 299.502 294.091 0.944 0.996 0.301 5.546-4.326 100.00 867 58 0.1033 411.168 408.985 0.970 0.994 0.210 4.315-3.360 100.00 1859 96 0.0922 391.025 390.533 1.032 0.990 0.191 3.356-2.611 100.00 3867 181 0.1299 256.881 255.544 1.031 0.983 0.091 2.608-2.000 99.99 8818 434 0.1350 167.442 165.959 1.045 0.972 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3948 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1654 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1654 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1654 | n_water=258 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1286 r_free=0.1646 | n_water=251 | time (s): 19.380 (total time: 20.180) Filter (q & B) r_work=0.1285 r_free=0.1645 | n_water=249 | time (s): 1.870 (total time: 22.050) Compute maps r_work=0.1285 r_free=0.1645 | n_water=249 | time (s): 0.560 (total time: 22.610) Filter (map) r_work=0.1323 r_free=0.1644 | n_water=207 | time (s): 1.470 (total time: 24.080) Find peaks r_work=0.1323 r_free=0.1644 | n_water=207 | time (s): 0.480 (total time: 24.560) Add new water r_work=0.1550 r_free=0.1867 | n_water=357 | time (s): 1.730 (total time: 26.290) Refine new water occ: r_work=0.1338 r_free=0.1577 adp: r_work=0.1279 r_free=0.1562 occ: r_work=0.1284 r_free=0.1535 adp: r_work=0.1251 r_free=0.1536 occ: r_work=0.1253 r_free=0.1534 adp: r_work=0.1240 r_free=0.1537 ADP+occupancy (water only), MIN, final r_work=0.1240 r_free=0.1537 r_work=0.1240 r_free=0.1537 | n_water=357 | time (s): 14.320 (total time: 40.610) Filter (q & B) r_work=0.1241 r_free=0.1549 | n_water=351 | time (s): 1.600 (total time: 42.210) Filter (dist only) r_work=0.1242 r_free=0.1550 | n_water=350 | time (s): 27.480 (total time: 69.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.225278 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.969006 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1219 0.1602 0.0384 0.008 0.9 2.2 0.5 0.0 0 12.113 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.19 16.02 3.84 4.175 21.053 0.969 0.018 12.05 16.18 4.13 4.213 21.337 0.969 0.018 Individual atomic B min max mean iso aniso Overall: 6.99 107.23 21.31 4.28 1877 0 Protein: 6.99 107.23 17.83 4.27 1519 0 Water: 8.66 74.65 36.09 N/A 350 0 Other: 24.52 43.92 33.80 N/A 8 0 Chain A: 6.99 107.23 19.47 N/A 1734 0 Chain S: 17.04 61.81 43.59 N/A 143 0 Histogram: Values Number of atoms 6.99 - 17.02 1046 17.02 - 27.04 354 27.04 - 37.06 226 37.06 - 47.09 144 47.09 - 57.11 72 57.11 - 67.13 22 67.13 - 77.16 6 77.16 - 87.18 3 87.18 - 97.20 2 97.20 - 107.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1618 r_work=0.1206 r_free=0.1621 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1621 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1617 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1204 r_free= 0.1617 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017283 | | target function (ls_wunit_k1) not normalized (work): 280.603491 | | target function (ls_wunit_k1) not normalized (free): 25.325967 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1224 0.1204 0.1617 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1827 0.1822 0.1975 n_refl.: 17043 remove outliers: r(all,work,free)=0.1827 0.1822 0.1975 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1801 0.1795 0.1956 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1219 0.1199 0.1620 n_refl.: 17043 remove outliers: r(all,work,free)=0.1219 0.1199 0.1620 n_refl.: 17043 ======================== 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 0.3581 307.208 284.140 0.629 1.006 0.389 11.894-9.307 99.02 97 4 0.1523 487.920 482.154 0.916 1.006 0.380 9.237-7.194 100.00 213 7 0.1643 399.069 399.329 0.965 1.006 0.310 7.162-5.571 100.00 427 22 0.1558 299.502 295.664 0.936 1.005 0.244 5.546-4.326 100.00 867 58 0.0880 411.168 408.991 0.957 1.005 0.210 4.315-3.360 100.00 1859 96 0.0840 391.025 390.269 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1214 256.881 256.003 1.011 1.001 0.111 2.608-2.000 99.99 8818 434 0.1331 167.442 166.371 1.017 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3467 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1620 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1620 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1620 | n_water=350 | time (s): 0.750 (total time: 0.750) Filter (dist) r_work=0.1200 r_free=0.1627 | n_water=348 | time (s): 29.300 (total time: 30.050) Filter (q & B) r_work=0.1200 r_free=0.1627 | n_water=348 | time (s): 1.080 (total time: 31.130) Compute maps r_work=0.1200 r_free=0.1627 | n_water=348 | time (s): 0.640 (total time: 31.770) Filter (map) r_work=0.1276 r_free=0.1637 | n_water=249 | time (s): 1.770 (total time: 33.540) Find peaks r_work=0.1276 r_free=0.1637 | n_water=249 | time (s): 0.480 (total time: 34.020) Add new water r_work=0.1462 r_free=0.1836 | n_water=394 | time (s): 1.500 (total time: 35.520) Refine new water occ: r_work=0.1258 r_free=0.1612 adp: r_work=0.1253 r_free=0.1611 occ: r_work=0.1231 r_free=0.1586 adp: r_work=0.1222 r_free=0.1584 occ: r_work=0.1210 r_free=0.1569 adp: r_work=0.1202 r_free=0.1569 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1569 r_work=0.1202 r_free=0.1569 | n_water=394 | time (s): 23.860 (total time: 59.380) Filter (q & B) r_work=0.1205 r_free=0.1579 | n_water=385 | time (s): 1.940 (total time: 61.320) Filter (dist only) r_work=0.1205 r_free=0.1579 | n_water=385 | time (s): 28.700 (total time: 90.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.858063 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.165813 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1184 0.1561 0.0377 0.009 0.9 3.8 0.5 0.0 0 0.929 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.84 15.61 3.77 4.353 21.486 0.166 4.997 11.64 15.71 4.07 4.975 21.379 0.166 4.974 Individual atomic B min max mean iso aniso Overall: 6.43 105.76 20.65 4.67 1912 0 Protein: 6.43 105.76 17.08 4.66 1519 0 Water: 8.85 63.21 34.52 N/A 385 0 Other: 20.83 41.31 29.60 N/A 8 0 Chain A: 6.43 105.76 18.64 N/A 1727 0 Chain S: 20.05 63.21 39.33 N/A 185 0 Histogram: Values Number of atoms 6.43 - 16.36 1058 16.36 - 26.30 372 26.30 - 36.23 209 36.23 - 46.16 174 46.16 - 56.10 63 56.10 - 66.03 24 66.03 - 75.96 4 75.96 - 85.89 3 85.89 - 95.83 3 95.83 - 105.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.1164 r_free=0.1571 r_work=0.1164 r_free=0.1571 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1164 r_free = 0.1571 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1155 r_free = 0.1574 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1155 r_free= 0.1574 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.970218 | | target function (ml) not normalized (work): 80696.451804 | | target function (ml) not normalized (free): 4195.835400 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1175 0.1155 0.1574 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1748 0.1744 0.1898 n_refl.: 17043 remove outliers: r(all,work,free)=0.1748 0.1744 0.1898 n_refl.: 17043 overall B=-0.39 to atoms: r(all,work,free)=0.1718 0.1714 0.1884 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1172 0.1152 0.1571 n_refl.: 17043 remove outliers: r(all,work,free)=0.1171 0.1151 0.1571 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3720 309.241 276.772 0.589 1.007 0.358 11.894-9.307 99.02 97 4 0.1727 487.920 480.499 0.917 1.007 0.350 9.237-7.194 100.00 213 7 0.1808 399.069 398.619 0.972 1.007 0.300 7.162-5.571 100.00 427 22 0.1654 299.502 293.816 0.940 1.007 0.215 5.546-4.326 100.00 867 58 0.0939 411.168 407.767 0.962 1.006 0.201 4.315-3.360 100.00 1859 96 0.0905 391.025 388.680 1.011 1.004 0.191 3.356-2.611 100.00 3867 181 0.1290 256.881 254.689 1.012 1.001 0.152 2.608-2.000 99.99 8818 434 0.1083 167.442 166.122 1.019 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3820 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1151 r_free=0.1571 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1151 r_free=0.1571 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1151 r_free=0.1571 | n_water=385 | time (s): 0.760 (total time: 0.760) Filter (dist) r_work=0.1151 r_free=0.1571 | n_water=385 | time (s): 28.410 (total time: 29.170) Filter (q & B) r_work=0.1151 r_free=0.1571 | n_water=385 | time (s): 1.130 (total time: 30.300) Compute maps r_work=0.1151 r_free=0.1571 | n_water=385 | time (s): 0.690 (total time: 30.990) Filter (map) r_work=0.1211 r_free=0.1579 | n_water=293 | time (s): 1.480 (total time: 32.470) Find peaks r_work=0.1211 r_free=0.1579 | n_water=293 | time (s): 0.410 (total time: 32.880) Add new water r_work=0.1359 r_free=0.1722 | n_water=429 | time (s): 1.760 (total time: 34.640) Refine new water occ: r_work=0.1194 r_free=0.1561 adp: r_work=0.1187 r_free=0.1558 occ: r_work=0.1170 r_free=0.1541 adp: r_work=0.1161 r_free=0.1536 occ: r_work=0.1153 r_free=0.1524 adp: r_work=0.1145 r_free=0.1521 ADP+occupancy (water only), MIN, final r_work=0.1145 r_free=0.1521 r_work=0.1145 r_free=0.1521 | n_water=429 | time (s): 31.860 (total time: 66.500) Filter (q & B) r_work=0.1147 r_free=0.1531 | n_water=421 | time (s): 2.070 (total time: 68.570) Filter (dist only) r_work=0.1150 r_free=0.1530 | n_water=420 | time (s): 34.870 (total time: 103.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.923358 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.188868 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1140 0.1559 0.0419 0.009 1.0 2.6 0.5 0.0 0 0.962 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.40 15.59 4.19 4.489 21.004 0.189 4.964 11.29 15.56 4.27 4.672 21.060 0.189 4.957 Individual atomic B min max mean iso aniso Overall: 5.93 104.24 20.84 4.91 1947 0 Protein: 5.93 104.24 16.71 4.90 1519 0 Water: 8.83 67.04 35.65 N/A 420 0 Other: 19.24 38.61 26.80 N/A 8 0 Chain A: 5.93 104.24 18.25 N/A 1726 0 Chain S: 18.17 67.04 41.10 N/A 221 0 Histogram: Values Number of atoms 5.93 - 15.76 1051 15.76 - 25.59 371 25.59 - 35.42 207 35.42 - 45.25 182 45.25 - 55.08 92 55.08 - 64.91 27 64.91 - 74.74 9 74.74 - 84.58 4 84.58 - 94.41 2 94.41 - 104.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.1129 r_free=0.1556 r_work=0.1129 r_free=0.1557 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1129 r_free = 0.1557 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1120 r_free = 0.1560 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1120 r_free= 0.1560 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.952383 | | target function (ml) not normalized (work): 80401.937260 | | target function (ml) not normalized (free): 4186.754506 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1141 0.1120 0.1560 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1615 0.1605 0.1852 n_refl.: 17042 remove outliers: r(all,work,free)=0.1615 0.1605 0.1852 n_refl.: 17042 overall B=-0.33 to atoms: r(all,work,free)=0.1593 0.1582 0.1840 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1117 0.1551 n_refl.: 17042 remove outliers: r(all,work,free)=0.1136 0.1115 0.1551 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3698 303.153 281.820 0.572 1.001 0.340 11.894-9.307 99.02 97 4 0.1816 487.920 481.184 0.921 1.002 0.330 9.237-7.194 100.00 213 7 0.1806 399.069 397.342 0.979 1.002 0.244 7.162-5.571 100.00 427 22 0.1616 299.502 293.410 0.942 1.002 0.220 5.546-4.326 100.00 867 58 0.0920 411.168 407.833 0.965 1.003 0.181 4.315-3.360 100.00 1859 96 0.0882 391.025 388.737 1.010 1.002 0.171 3.356-2.611 100.00 3867 181 0.1256 256.881 254.605 1.008 1.002 0.141 2.608-2.000 99.99 8818 434 0.1031 167.442 166.257 1.006 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9584 b_overall=-1.1294 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1115 r_free=0.1551 After: r_work=0.1117 r_free=0.1550 ================================== NQH flips ================================== r_work=0.1117 r_free=0.1550 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1117 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1117 r_free=0.1550 | n_water=420 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1117 r_free=0.1550 | n_water=420 | time (s): 32.340 (total time: 33.000) Filter (q & B) r_work=0.1117 r_free=0.1550 | n_water=420 | time (s): 1.100 (total time: 34.100) Compute maps r_work=0.1117 r_free=0.1550 | n_water=420 | time (s): 0.830 (total time: 34.930) Filter (map) r_work=0.1184 r_free=0.1540 | n_water=326 | time (s): 2.030 (total time: 36.960) Find peaks r_work=0.1184 r_free=0.1540 | n_water=326 | time (s): 0.490 (total time: 37.450) Add new water r_work=0.1299 r_free=0.1649 | n_water=471 | time (s): 1.560 (total time: 39.010) Refine new water occ: r_work=0.1147 r_free=0.1526 adp: r_work=0.1140 r_free=0.1519 occ: r_work=0.1127 r_free=0.1510 adp: r_work=0.1118 r_free=0.1503 occ: r_work=0.1112 r_free=0.1497 adp: r_work=0.1106 r_free=0.1494 ADP+occupancy (water only), MIN, final r_work=0.1106 r_free=0.1494 r_work=0.1106 r_free=0.1494 | n_water=471 | time (s): 32.200 (total time: 71.210) Filter (q & B) r_work=0.1110 r_free=0.1507 | n_water=458 | time (s): 1.820 (total time: 73.030) Filter (dist only) r_work=0.1110 r_free=0.1507 | n_water=458 | time (s): 36.200 (total time: 109.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.920655 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.176469 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1126 0.1508 0.0381 0.009 1.1 7.0 0.5 0.0 0 0.960 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.08 3.81 4.588 20.926 0.176 4.943 11.17 15.02 3.85 4.627 20.976 0.176 4.937 Individual atomic B min max mean iso aniso Overall: 5.33 103.15 21.01 4.97 1985 0 Protein: 5.33 103.15 16.41 4.96 1519 0 Water: 8.39 63.33 36.17 N/A 458 0 Other: 19.38 36.52 25.97 N/A 8 0 Chain A: 5.33 103.15 17.96 N/A 1726 0 Chain S: 18.15 63.33 41.35 N/A 259 0 Histogram: Values Number of atoms 5.33 - 15.11 1022 15.11 - 24.90 392 24.90 - 34.68 206 34.68 - 44.46 208 44.46 - 54.24 109 54.24 - 64.02 31 64.02 - 73.81 8 73.81 - 83.59 3 83.59 - 93.37 2 93.37 - 103.15 4 =========================== Idealize ADP of riding H ========================== r_work=0.1117 r_free=0.1502 r_work=0.1117 r_free=0.1501 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1117 r_free = 0.1501 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1112 r_free = 0.1502 target_work(ml) = 4.933 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1112 r_free= 0.1502 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.932683 | | target function (ml) not normalized (work): 80072.248526 | | target function (ml) not normalized (free): 4162.929942 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1132 0.1397 5.4612 5.6734| | 2: 3.63 - 2.88 1.00 2711 122 0.1114 0.1517 5.2305 5.3612| | 3: 2.88 - 2.52 1.00 2681 148 0.1373 0.1629 5.134 5.1854| | 4: 2.52 - 2.29 1.00 2661 139 0.0910 0.1463 4.6107 4.9391| | 5: 2.29 - 2.13 1.00 2678 122 0.0950 0.1488 4.5685 4.8672| | 6: 2.13 - 2.00 1.00 2692 117 0.1106 0.1731 4.5612 4.7779| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2810 159 0.95 8.96 1.00 0.96 6405.18| | 2: 3.63 - 2.88 2711 122 0.92 12.88 1.01 0.96 6405.18| | 3: 2.88 - 2.52 2681 148 0.87 19.01 0.99 0.96 6405.18| | 4: 2.52 - 2.29 2661 139 0.93 11.96 1.01 0.98 2071.96| | 5: 2.29 - 2.13 2678 122 0.92 13.92 1.00 0.98 2071.96| | 6: 2.13 - 2.00 2692 117 0.90 16.67 0.99 0.98 2071.96| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2071.96 max = 6405.18 mean = 4261.39| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.96 mean = 13.86| |phase err.(test): min = 0.00 max = 88.53 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1131 0.1112 0.1502 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1570 0.1559 0.1819 n_refl.: 17040 remove outliers: r(all,work,free)=0.1570 0.1559 0.1819 n_refl.: 17040 overall B=-0.27 to atoms: r(all,work,free)=0.1554 0.1542 0.1808 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1113 0.1506 n_refl.: 17040 remove outliers: r(all,work,free)=0.1132 0.1113 0.1506 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3554 303.153 280.019 0.569 1.001 0.340 11.894-9.307 99.02 97 4 0.1795 487.920 479.424 0.921 1.002 0.320 9.237-7.194 100.00 213 7 0.1727 399.069 399.225 0.983 1.003 0.228 7.162-5.571 100.00 427 22 0.1572 299.502 294.470 0.940 1.003 0.207 5.546-4.326 100.00 867 58 0.0937 411.168 408.244 0.965 1.002 0.185 4.315-3.360 100.00 1859 96 0.0893 391.025 388.832 1.006 1.002 0.181 3.356-2.611 100.00 3867 181 0.1258 256.881 254.517 1.003 1.001 0.141 2.608-2.000 99.99 8818 434 0.1025 167.442 166.191 0.997 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9209 ================= 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 : 0.2785 0.1820 0.081 5.362 8.8 119.3 19.9 258 0.000 1_bss: 0.1600 0.1683 0.081 5.362 8.4 118.9 19.5 258 0.000 1_settarget: 0.1600 0.1683 0.081 5.362 8.4 118.9 19.5 258 0.000 1_nqh: 0.1600 0.1683 0.081 5.362 8.4 118.9 19.5 258 0.000 1_weight: 0.1600 0.1683 0.081 5.362 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1352 0.1632 0.008 0.960 8.4 118.9 19.5 258 0.155 1_adp: 0.1278 0.1659 0.008 0.960 6.3 113.9 20.0 258 0.155 1_regHadp: 0.1281 0.1667 0.008 0.960 6.3 113.9 20.0 258 0.155 1_occ: 0.1276 0.1662 0.008 0.960 6.3 113.9 20.0 258 0.155 2_bss: 0.1275 0.1654 0.008 0.960 5.9 113.5 19.6 258 0.155 2_settarget: 0.1275 0.1654 0.008 0.960 5.9 113.5 19.6 258 0.155 2_updatecdl: 0.1275 0.1654 0.008 0.981 5.9 113.5 19.6 258 0.155 2_nqh: 0.1275 0.1654 0.008 0.981 5.9 113.5 19.6 258 0.155 2_sol: 0.1242 0.1550 0.008 0.981 5.9 112.2 20.8 350 n/a 2_weight: 0.1242 0.1550 0.008 0.981 5.9 112.2 20.8 350 n/a 2_xyzrec: 0.1219 0.1602 0.008 0.925 5.9 112.2 20.8 350 n/a 2_adp: 0.1205 0.1618 0.008 0.925 7.0 107.2 21.3 350 n/a 2_regHadp: 0.1206 0.1621 0.008 0.925 7.0 107.2 21.3 350 n/a 2_occ: 0.1204 0.1617 0.008 0.925 7.0 107.2 21.3 350 n/a 3_bss: 0.1199 0.1620 0.008 0.925 6.6 106.9 20.9 350 n/a 3_settarget: 0.1199 0.1620 0.008 0.925 6.6 106.9 20.9 350 n/a 3_updatecdl: 0.1199 0.1620 0.008 0.925 6.6 106.9 20.9 350 n/a 3_nqh: 0.1199 0.1620 0.008 0.925 6.6 106.9 20.9 350 n/a 3_sol: 0.1205 0.1579 0.008 0.925 6.6 106.9 20.8 385 n/a 3_weight: 0.1205 0.1579 0.008 0.925 6.6 106.9 20.8 385 n/a 3_xyzrec: 0.1184 0.1561 0.009 0.945 6.6 106.9 20.8 385 n/a 3_adp: 0.1164 0.1571 0.009 0.945 6.4 105.8 20.6 385 n/a 3_regHadp: 0.1164 0.1571 0.009 0.945 6.4 105.8 20.6 385 n/a 3_occ: 0.1155 0.1574 0.009 0.945 6.4 105.8 20.6 385 n/a 4_bss: 0.1151 0.1571 0.009 0.945 6.0 105.4 20.3 385 n/a 4_settarget: 0.1151 0.1571 0.009 0.945 6.0 105.4 20.3 385 n/a 4_updatecdl: 0.1151 0.1571 0.009 0.945 6.0 105.4 20.3 385 n/a 4_nqh: 0.1151 0.1571 0.009 0.945 6.0 105.4 20.3 385 n/a 4_sol: 0.1150 0.1530 0.009 0.945 6.0 105.4 20.7 420 n/a 4_weight: 0.1150 0.1530 0.009 0.945 6.0 105.4 20.7 420 n/a 4_xyzrec: 0.1140 0.1559 0.009 0.965 6.0 105.4 20.7 420 n/a 4_adp: 0.1129 0.1556 0.009 0.965 5.9 104.2 20.8 420 n/a 4_regHadp: 0.1129 0.1557 0.009 0.965 5.9 104.2 20.8 420 n/a 4_occ: 0.1120 0.1560 0.009 0.965 5.9 104.2 20.8 420 n/a 5_bss: 0.1115 0.1551 0.009 0.965 5.6 103.9 20.5 420 n/a 5_settarget: 0.1115 0.1551 0.009 0.965 5.6 103.9 20.5 420 n/a 5_updatecdl: 0.1115 0.1551 0.009 0.965 5.6 103.9 20.5 420 n/a 5_setrh: 0.1117 0.1550 0.009 0.965 5.6 103.9 20.5 420 n/a 5_nqh: 0.1117 0.1550 0.009 0.965 5.6 103.9 20.5 420 n/a 5_sol: 0.1110 0.1507 0.009 0.965 5.6 103.9 20.9 458 n/a 5_weight: 0.1110 0.1507 0.009 0.965 5.6 103.9 20.9 458 n/a 5_xyzrec: 0.1126 0.1508 0.009 1.071 5.6 103.9 20.9 458 n/a 5_adp: 0.1117 0.1502 0.009 1.071 5.3 103.2 21.0 458 n/a 5_regHadp: 0.1117 0.1501 0.009 1.071 5.3 103.2 21.0 458 n/a 5_occ: 0.1112 0.1502 0.009 1.071 5.3 103.2 21.0 458 n/a end: 0.1113 0.1506 0.009 1.071 5.1 102.9 20.7 458 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4811713_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4811713_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1100 Refinement macro-cycles (run) : 894.6600 Write final files (write_after_run_outputs) : 22.8200 Total : 921.5900 Total CPU time: 15.71 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:43 PST -0800 (1735494043.55 s) Start R-work = 0.1600, R-free = 0.1683 Final R-work = 0.1113, R-free = 0.1506 =============================================================================== Job complete usr+sys time: 969.47 seconds wall clock time: 16 minutes 31.75 seconds (991.75 seconds total)