Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2780949.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2780949.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2780949.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 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: 1.31, 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: 0.38 Conformation dependent library (CDL) restraints added in 120.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 596 0.92 - 1.17: 1062 1.17 - 1.42: 635 1.42 - 1.67: 824 1.67 - 1.92: 36 Bond restraints: 3153 Sorted by residual: bond pdb=" N SER A 155 " pdb=" CA SER A 155 " ideal model delta sigma weight residual 1.456 1.697 -0.241 1.16e-02 7.43e+03 4.32e+02 bond pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 1.458 1.680 -0.222 1.18e-02 7.18e+03 3.55e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.237 1.025 0.211 1.17e-02 7.31e+03 3.26e+02 bond pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta sigma weight residual 1.459 1.231 0.227 1.28e-02 6.10e+03 3.15e+02 bond pdb=" CA VAL A 69 " pdb=" C VAL A 69 " ideal model delta sigma weight residual 1.522 1.308 0.214 1.26e-02 6.30e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 3141 4.52 - 9.04: 1848 9.04 - 13.56: 658 13.56 - 18.08: 115 18.08 - 22.61: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BLYS A 93 " pdb=" C BLYS A 93 " pdb=" N BGLU A 94 " ideal model delta sigma weight residual 122.03 106.01 16.02 1.04e+00 9.25e-01 2.37e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 105.70 13.50 9.00e-01 1.23e+00 2.25e+02 angle pdb=" O SER A 47 " pdb=" C SER A 47 " pdb=" N ARG A 48 " ideal model delta sigma weight residual 122.27 140.62 -18.35 1.23e+00 6.61e-01 2.23e+02 angle pdb=" CA ALA A 183 " pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 118.63 131.52 -12.89 9.20e-01 1.18e+00 1.96e+02 angle pdb=" CA VAL A 169 " pdb=" C VAL A 169 " pdb=" O VAL A 169 " ideal model delta sigma weight residual 121.41 106.99 14.42 1.04e+00 9.25e-01 1.92e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 16.93: 1296 16.93 - 33.83: 129 33.83 - 50.74: 39 50.74 - 67.64: 14 67.64 - 84.55: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 20 " pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" CB VAL A 20 " ideal model delta harmonic sigma weight residual -122.00 -146.70 24.70 0 2.50e+00 1.60e-01 9.76e+01 dihedral pdb=" C ALA A 39 " pdb=" N ALA A 39 " pdb=" CA ALA A 39 " pdb=" CB ALA A 39 " ideal model delta harmonic sigma weight residual -122.60 -144.65 22.05 0 2.50e+00 1.60e-01 7.78e+01 dihedral pdb=" N VAL A 20 " pdb=" C VAL A 20 " pdb=" CA VAL A 20 " pdb=" CB VAL A 20 " ideal model delta harmonic sigma weight residual 123.40 144.16 -20.76 0 2.50e+00 1.60e-01 6.90e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 126 0.270 - 0.541: 72 0.541 - 0.811: 33 0.811 - 1.081: 10 1.081 - 1.352: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 123 " pdb=" CA VAL A 123 " pdb=" CG1 VAL A 123 " pdb=" CG2 VAL A 123 " both_signs ideal model delta sigma weight residual False -2.63 -1.28 -1.35 2.00e-01 2.50e+01 4.57e+01 chirality pdb=" CA ALA A 39 " pdb=" N ALA A 39 " pdb=" C ALA A 39 " pdb=" CB ALA A 39 " both_signs ideal model delta sigma weight residual False 2.48 1.40 1.08 2.00e-01 2.50e+01 2.93e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.58 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.118 2.00e-02 2.50e+03 7.01e-02 1.48e+02 pdb=" CG PHE A 164 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.042 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.089 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.101 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.097 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.079 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.022 2.00e-02 2.50e+03 6.40e-02 1.23e+02 pdb=" CG BTYR A 67 " -0.079 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.045 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.048 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.096 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.019 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.053 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.082 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.201 9.50e-02 1.11e+02 9.12e-02 9.07e+01 pdb=" NE ARG A 48 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " 0.043 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " 0.073 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " -0.043 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.083 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.089 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 736 2.27 - 2.86: 7847 2.86 - 3.44: 10631 3.44 - 4.02: 15351 4.02 - 4.60: 22092 Nonbonded interactions: 56657 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.693 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.775 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.804 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.829 2.450 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.836 2.450 ... (remaining 56652 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_2780949_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= 0.2795 r_free= 0.1824 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.411232 | | target function (ml) not normalized (work): 71651.649086 | | target function (ml) not normalized (free): 3267.123101 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3212 0.2116 7.5473 5.0298| | 2: 3.63 - 2.88 1.00 2711 122 0.2636 0.1786 4.3304 4.3255| | 3: 2.88 - 2.52 1.00 2682 148 0.2555 0.1732 4.1822 4.1843| | 4: 2.52 - 2.29 1.00 2661 139 0.2576 0.1470 3.5047 3.5802| | 5: 2.29 - 2.13 1.00 2678 122 0.2653 0.1506 3.4123 3.4769| | 6: 2.13 - 2.00 1.00 2692 117 0.2749 0.1909 3.3266 3.4065| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.58 0.77 0.23 1293.70| | 2: 3.63 - 2.88 2711 122 0.83 23.76 1.31 0.23 1293.70| | 3: 2.88 - 2.52 2682 148 0.73 32.71 1.28 0.23 1293.70| | 4: 2.52 - 2.29 2661 139 0.93 11.46 1.30 0.26 135.77| | 5: 2.29 - 2.13 2678 122 0.92 13.64 1.31 0.26 135.77| | 6: 2.13 - 2.00 2692 117 0.90 16.38 1.33 0.26 135.77| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 135.77 max = 1293.70 mean = 721.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.90 mean = 19.26| |phase err.(test): min = 0.00 max = 89.22 mean = 19.57| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.241 1557 Z= 5.541 Angle : 5.357 19.115 2118 Z= 3.758 Chirality : 0.407 1.352 243 Planarity : 0.033 0.084 284 Dihedral : 14.093 84.545 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 3.11 % Allowed : 1.86 % Favored : 95.03 % Cbeta Deviations : 31.35 % 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: -2.57 (0.48), residues: 224 helix: -2.56 (0.41), residues: 102 sheet: -1.40 (0.82), residues: 28 loop : -0.45 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.106 0.021 ARG A 98 TYR 0.090 0.046 TYR A 141 PHE 0.105 0.036 PHE A 164 HIS 0.038 0.019 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2795 r_free= 0.1824 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.411232 | | target function (ml) not normalized (work): 71651.649086 | | target function (ml) not normalized (free): 3267.123101 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2947 percent. r_work = 0.2924 r_free = 0.1983 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2870 0.2924 0.1983 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2870 0.2924 0.1983 n_refl.: 17050 remove outliers: r(all,work,free)=0.2159 0.2170 0.1983 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2133 0.2143 0.1966 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1622 0.1620 0.1660 n_refl.: 17045 remove outliers: r(all,work,free)=0.1621 0.1619 0.1660 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 0.4074 391.297 358.356 0.635 1.013 0.380 11.894-9.307 99.02 97 4 0.1850 633.450 614.778 0.928 1.013 0.377 9.237-7.194 100.00 213 7 0.2158 518.098 510.408 0.960 1.013 0.355 7.162-5.571 100.00 427 22 0.2319 388.833 375.990 0.920 1.012 0.294 5.546-4.326 100.00 867 58 0.1363 533.806 528.393 0.967 1.010 0.251 4.315-3.360 100.00 1859 96 0.1301 507.655 503.813 1.015 1.006 0.181 3.356-2.611 100.00 3867 181 0.1657 333.500 329.291 1.011 1.000 0.039 2.608-2.000 99.99 8818 434 0.1666 217.385 212.953 1.028 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4162 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1619 r_free=0.1660 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1619 r_free=0.1660 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.288200 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.837806 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 0.1645 0.0293 0.009 1.0 1.0 0.5 0.0 0 11.144 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.45 2.93 3.013 18.461 0.838 0.023 12.77 16.74 3.97 3.614 18.707 0.838 0.020 Individual atomic B min max mean iso aniso Overall: 6.45 113.90 19.95 4.05 1785 0 Protein: 6.45 112.81 17.19 4.05 1519 0 Water: 8.84 113.90 36.00 N/A 258 0 Other: 21.98 37.35 26.58 N/A 8 0 Chain A: 6.45 113.90 19.95 N/A 1785 0 Histogram: Values Number of atoms 6.45 - 17.19 1099 17.19 - 27.94 331 27.94 - 38.69 182 38.69 - 49.43 101 49.43 - 60.18 45 60.18 - 70.92 14 70.92 - 81.67 5 81.67 - 92.41 5 92.41 - 103.16 0 103.16 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1674 r_work=0.1280 r_free=0.1680 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1680 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 = 0.1275 r_free = 0.1673 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1275 r_free= 0.1673 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020006 | | target function (ls_wunit_k1) not normalized (work): 324.819435 | | target function (ls_wunit_k1) not normalized (free): 27.395116 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1275 0.1673 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1900 0.1898 0.2004 n_refl.: 17043 remove outliers: r(all,work,free)=0.1900 0.1898 0.2004 n_refl.: 17043 overall B=-0.51 to atoms: r(all,work,free)=0.1864 0.1861 0.1982 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1291 0.1272 0.1666 n_refl.: 17043 remove outliers: r(all,work,free)=0.1290 0.1272 0.1666 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 0.3501 303.472 277.014 0.611 1.006 0.360 11.894-9.307 99.02 97 4 0.1718 488.087 476.805 0.917 1.007 0.354 9.237-7.194 100.00 213 7 0.1841 399.206 395.559 0.961 1.006 0.341 7.162-5.571 100.00 427 22 0.1833 299.605 294.387 0.932 1.006 0.267 5.546-4.326 100.00 867 58 0.1041 411.309 408.963 0.963 1.005 0.231 4.315-3.360 100.00 1859 96 0.0919 391.159 390.515 1.016 1.004 0.192 3.356-2.611 100.00 3867 181 0.1299 256.969 255.687 1.009 1.001 0.102 2.608-2.000 99.99 8818 434 0.1346 167.500 166.180 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1644 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1666 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1272 r_free=0.1666 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1666 | n_water=258 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1277 r_free=0.1657 | n_water=253 | time (s): 20.320 (total time: 21.090) Filter (q & B) r_work=0.1277 r_free=0.1656 | n_water=251 | time (s): 1.770 (total time: 22.860) Compute maps r_work=0.1277 r_free=0.1656 | n_water=251 | time (s): 0.540 (total time: 23.400) Filter (map) r_work=0.1310 r_free=0.1650 | n_water=213 | time (s): 1.520 (total time: 24.920) Find peaks r_work=0.1310 r_free=0.1650 | n_water=213 | time (s): 0.430 (total time: 25.350) Add new water r_work=0.1528 r_free=0.1890 | n_water=368 | time (s): 1.520 (total time: 26.870) Refine new water occ: r_work=0.1327 r_free=0.1613 adp: r_work=0.1270 r_free=0.1613 occ: r_work=0.1275 r_free=0.1567 adp: r_work=0.1243 r_free=0.1576 occ: r_work=0.1243 r_free=0.1565 adp: r_work=0.1231 r_free=0.1564 ADP+occupancy (water only), MIN, final r_work=0.1231 r_free=0.1564 r_work=0.1231 r_free=0.1564 | n_water=368 | time (s): 20.490 (total time: 47.360) Filter (q & B) r_work=0.1232 r_free=0.1570 | n_water=361 | time (s): 1.590 (total time: 48.950) Filter (dist only) r_work=0.1233 r_free=0.1572 | n_water=360 | time (s): 29.480 (total time: 78.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.428119 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.957698 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 0.1200 0.1599 0.0398 0.008 0.9 1.9 0.5 0.0 0 11.714 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 15.99 3.98 4.159 20.917 0.958 0.018 11.86 16.23 4.38 4.152 21.196 0.958 0.017 Individual atomic B min max mean iso aniso Overall: 6.17 107.30 21.21 4.23 1887 0 Protein: 6.17 107.30 17.60 4.22 1519 0 Water: 8.52 67.00 36.10 N/A 360 0 Other: 24.89 46.42 35.75 N/A 8 0 Chain A: 6.17 107.30 19.36 N/A 1740 0 Chain S: 17.09 67.00 43.08 N/A 147 0 Histogram: Values Number of atoms 6.17 - 16.28 994 16.28 - 26.40 401 26.40 - 36.51 217 36.51 - 46.62 161 46.62 - 56.73 77 56.73 - 66.85 26 66.85 - 76.96 4 76.96 - 87.07 5 87.07 - 97.18 0 97.18 - 107.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.1186 r_free=0.1623 r_work=0.1188 r_free=0.1624 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1624 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1181 r_free = 0.1635 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1181 r_free= 0.1635 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016748 | | target function (ls_wunit_k1) not normalized (work): 271.896931 | | target function (ls_wunit_k1) not normalized (free): 24.831946 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1181 0.1635 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1734 0.1723 0.1981 n_refl.: 17042 remove outliers: r(all,work,free)=0.1734 0.1723 0.1981 n_refl.: 17042 overall B=-0.42 to atoms: r(all,work,free)=0.1708 0.1696 0.1963 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1179 0.1629 n_refl.: 17042 remove outliers: r(all,work,free)=0.1199 0.1178 0.1629 n_refl.: 17041 ======================== 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 0.3219 300.309 284.649 0.590 1.005 0.340 11.894-9.307 99.02 97 4 0.1562 488.087 485.538 0.913 1.006 0.330 9.237-7.194 100.00 213 7 0.1614 399.206 401.030 0.980 1.006 0.300 7.162-5.571 100.00 427 22 0.1485 299.605 296.607 0.938 1.006 0.236 5.546-4.326 100.00 867 58 0.0872 411.309 409.048 0.962 1.005 0.215 4.315-3.360 100.00 1859 96 0.0817 391.159 390.321 1.015 1.003 0.202 3.356-2.611 100.00 3867 181 0.1191 256.969 256.241 1.010 1.000 0.132 2.608-2.000 99.99 8818 434 0.1320 167.500 166.430 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1646 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1178 r_free=0.1629 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1178 r_free=0.1629 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1629 | n_water=360 | time (s): 0.760 (total time: 0.760) Filter (dist) r_work=0.1178 r_free=0.1629 | n_water=360 | time (s): 29.260 (total time: 30.020) Filter (q & B) r_work=0.1178 r_free=0.1629 | n_water=360 | time (s): 1.210 (total time: 31.230) Compute maps r_work=0.1178 r_free=0.1629 | n_water=360 | time (s): 0.810 (total time: 32.040) Filter (map) r_work=0.1245 r_free=0.1642 | n_water=268 | time (s): 1.730 (total time: 33.770) Find peaks r_work=0.1245 r_free=0.1642 | n_water=268 | time (s): 0.430 (total time: 34.200) Add new water r_work=0.1422 r_free=0.1836 | n_water=417 | time (s): 1.390 (total time: 35.590) Refine new water occ: r_work=0.1232 r_free=0.1604 adp: r_work=0.1224 r_free=0.1612 occ: r_work=0.1208 r_free=0.1574 adp: r_work=0.1198 r_free=0.1582 occ: r_work=0.1192 r_free=0.1559 adp: r_work=0.1182 r_free=0.1564 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1564 r_work=0.1182 r_free=0.1564 | n_water=417 | time (s): 57.170 (total time: 92.760) Filter (q & B) r_work=0.1184 r_free=0.1568 | n_water=409 | time (s): 1.630 (total time: 94.390) Filter (dist only) r_work=0.1184 r_free=0.1568 | n_water=409 | time (s): 32.370 (total time: 126.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.955148 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.156775 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 0.1163 0.1599 0.0436 0.009 1.0 4.2 0.5 0.0 0 0.978 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 15.99 4.36 4.307 21.364 0.157 4.999 11.46 15.99 4.53 4.843 21.261 0.157 4.978 Individual atomic B min max mean iso aniso Overall: 6.12 105.00 20.69 4.57 1936 0 Protein: 6.12 105.00 16.79 4.56 1519 0 Water: 8.84 62.40 34.94 N/A 409 0 Other: 24.66 44.41 32.97 N/A 8 0 Chain A: 6.12 105.00 18.54 N/A 1736 0 Chain S: 20.30 62.40 39.37 N/A 200 0 Histogram: Values Number of atoms 6.12 - 16.01 1061 16.01 - 25.90 357 25.90 - 35.78 231 35.78 - 45.67 167 45.67 - 55.56 85 55.56 - 65.45 23 65.45 - 75.33 5 75.33 - 85.22 2 85.22 - 95.11 3 95.11 - 105.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1146 r_free=0.1599 r_work=0.1146 r_free=0.1601 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1146 r_free = 0.1601 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1606 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1140 r_free= 0.1606 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.973565 | | target function (ml) not normalized (work): 80740.855243 | | target function (ml) not normalized (free): 4204.978276 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1163 0.1140 0.1606 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1654 0.1643 0.1903 n_refl.: 17041 remove outliers: r(all,work,free)=0.1654 0.1643 0.1903 n_refl.: 17041 overall B=-0.34 to atoms: r(all,work,free)=0.1631 0.1619 0.1893 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1161 0.1139 0.1605 n_refl.: 17041 remove outliers: r(all,work,free)=0.1161 0.1139 0.1605 n_refl.: 17041 ======================== 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 0.3423 300.309 282.120 0.573 1.006 0.340 11.894-9.307 99.02 97 4 0.1710 488.087 482.719 0.912 1.007 0.330 9.237-7.194 100.00 213 7 0.1801 399.206 399.749 0.989 1.007 0.240 7.162-5.571 100.00 427 22 0.1575 299.605 293.898 0.942 1.006 0.220 5.546-4.326 100.00 867 58 0.0931 411.309 407.601 0.967 1.005 0.205 4.315-3.360 100.00 1859 96 0.0878 391.159 388.745 1.012 1.003 0.191 3.356-2.611 100.00 3867 181 0.1285 256.969 254.722 1.010 1.000 0.141 2.608-2.000 99.99 8818 434 0.1084 167.500 166.083 1.014 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1817 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1139 r_free=0.1605 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1139 r_free=0.1605 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1139 r_free=0.1605 | n_water=409 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.1139 r_free=0.1605 | n_water=409 | time (s): 32.090 (total time: 32.790) Filter (q & B) r_work=0.1139 r_free=0.1604 | n_water=408 | time (s): 2.300 (total time: 35.090) Compute maps r_work=0.1139 r_free=0.1604 | n_water=408 | time (s): 0.600 (total time: 35.690) Filter (map) r_work=0.1192 r_free=0.1627 | n_water=325 | time (s): 1.810 (total time: 37.500) Find peaks r_work=0.1192 r_free=0.1627 | n_water=325 | time (s): 0.590 (total time: 38.090) Add new water r_work=0.1319 r_free=0.1752 | n_water=468 | time (s): 1.790 (total time: 39.880) Refine new water occ: r_work=0.1165 r_free=0.1576 adp: r_work=0.1158 r_free=0.1584 occ: r_work=0.1145 r_free=0.1559 adp: r_work=0.1136 r_free=0.1562 occ: r_work=0.1131 r_free=0.1544 adp: r_work=0.1123 r_free=0.1548 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1548 r_work=0.1123 r_free=0.1548 | n_water=468 | time (s): 21.960 (total time: 61.840) Filter (q & B) r_work=0.1127 r_free=0.1551 | n_water=459 | time (s): 1.820 (total time: 63.660) Filter (dist only) r_work=0.1131 r_free=0.1555 | n_water=457 | time (s): 36.780 (total time: 100.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.105260 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.185286 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 0.1123 0.1580 0.0456 0.010 1.0 4.2 0.5 0.0 0 1.053 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.23 15.80 4.56 4.411 20.963 0.185 4.965 11.09 15.70 4.61 4.611 21.041 0.185 4.953 Individual atomic B min max mean iso aniso Overall: 5.78 102.38 21.04 4.85 1984 0 Protein: 5.78 102.38 16.42 4.84 1519 0 Water: 8.53 62.49 36.19 N/A 457 0 Other: 24.86 43.91 33.02 N/A 8 0 Chain A: 5.78 102.38 18.13 N/A 1735 0 Chain S: 17.65 62.49 41.30 N/A 249 0 Histogram: Values Number of atoms 5.78 - 15.44 1046 15.44 - 25.10 365 25.10 - 34.76 212 34.76 - 44.42 198 44.42 - 54.08 109 54.08 - 63.74 40 63.74 - 73.40 5 73.40 - 83.06 4 83.06 - 92.72 3 92.72 - 102.38 2 =========================== Idealize ADP of riding H ========================== r_work=0.1109 r_free=0.1570 r_work=0.1109 r_free=0.1569 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1109 r_free = 0.1569 target_work(ml) = 4.953 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1559 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1100 r_free= 0.1559 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.947992 | | target function (ml) not normalized (work): 80325.700215 | | target function (ml) not normalized (free): 4188.480650 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1100 0.1559 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1569 0.1555 0.1877 n_refl.: 17041 remove outliers: r(all,work,free)=0.1569 0.1555 0.1877 n_refl.: 17041 overall B=-0.27 to atoms: r(all,work,free)=0.1553 0.1538 0.1868 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1120 0.1098 0.1551 n_refl.: 17041 remove outliers: r(all,work,free)=0.1119 0.1097 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 0.3636 296.744 280.889 0.543 1.002 0.324 11.894-9.307 99.02 97 4 0.1817 488.087 481.506 0.914 1.003 0.320 9.237-7.194 100.00 213 7 0.1746 399.206 400.113 0.988 1.004 0.220 7.162-5.571 100.00 427 22 0.1518 299.605 293.531 0.940 1.003 0.200 5.546-4.326 100.00 867 58 0.0917 411.309 407.681 0.965 1.003 0.185 4.315-3.360 100.00 1859 96 0.0862 391.159 388.704 1.007 1.002 0.174 3.356-2.611 100.00 3867 181 0.1224 256.969 254.870 1.005 1.001 0.063 2.608-2.000 99.99 8818 434 0.1030 167.500 166.273 0.999 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.9469 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1097 r_free=0.1551 After: r_work=0.1099 r_free=0.1550 ================================== NQH flips ================================== r_work=0.1099 r_free=0.1550 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1099 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1099 r_free=0.1550 | n_water=457 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1099 r_free=0.1550 | n_water=457 | time (s): 37.970 (total time: 38.580) Filter (q & B) r_work=0.1099 r_free=0.1550 | n_water=456 | time (s): 1.590 (total time: 40.170) Compute maps r_work=0.1099 r_free=0.1550 | n_water=456 | time (s): 0.560 (total time: 40.730) Filter (map) r_work=0.1175 r_free=0.1586 | n_water=345 | time (s): 1.920 (total time: 42.650) Find peaks r_work=0.1175 r_free=0.1586 | n_water=345 | time (s): 0.620 (total time: 43.270) Add new water r_work=0.1282 r_free=0.1682 | n_water=478 | time (s): 2.160 (total time: 45.430) Refine new water occ: r_work=0.1136 r_free=0.1548 adp: r_work=0.1130 r_free=0.1550 occ: r_work=0.1115 r_free=0.1533 adp: r_work=0.1108 r_free=0.1533 occ: r_work=0.1100 r_free=0.1525 adp: r_work=0.1095 r_free=0.1524 ADP+occupancy (water only), MIN, final r_work=0.1095 r_free=0.1524 r_work=0.1095 r_free=0.1524 | n_water=478 | time (s): 41.920 (total time: 87.350) Filter (q & B) r_work=0.1098 r_free=0.1535 | n_water=469 | time (s): 1.580 (total time: 88.930) Filter (dist only) r_work=0.1098 r_free=0.1534 | n_water=467 | time (s): 39.800 (total time: 128.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.014122 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.182954 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 0.1117 0.1544 0.0427 0.010 1.1 6.4 0.5 0.0 0 1.007 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 15.44 4.27 4.532 20.743 0.183 4.949 11.07 15.34 4.27 4.597 20.848 0.183 4.943 Individual atomic B min max mean iso aniso Overall: 5.52 102.12 20.99 5.08 1994 0 Protein: 5.52 102.12 16.23 5.06 1519 0 Water: 8.28 66.68 36.28 N/A 467 0 Other: 24.51 40.31 32.18 N/A 8 0 Chain A: 5.52 102.12 17.93 N/A 1735 0 Chain S: 17.18 66.68 41.46 N/A 259 0 Histogram: Values Number of atoms 5.52 - 15.18 1047 15.18 - 24.84 361 24.84 - 34.50 218 34.50 - 44.16 189 44.16 - 53.82 127 53.82 - 63.48 30 63.48 - 73.14 12 73.14 - 82.80 3 82.80 - 92.46 3 92.46 - 102.12 4 =========================== Idealize ADP of riding H ========================== r_work=0.1107 r_free=0.1534 r_work=0.1107 r_free=0.1534 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1107 r_free = 0.1534 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1099 r_free = 0.1529 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1099 r_free= 0.1529 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.937461 | | target function (ml) not normalized (work): 80149.803859 | | target function (ml) not normalized (free): 4174.340015 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1110 0.1489 5.4476 5.7127| | 2: 3.63 - 2.88 1.00 2711 122 0.1088 0.1437 5.2236 5.3406| | 3: 2.88 - 2.52 1.00 2681 148 0.1356 0.1666 5.1397 5.2036| | 4: 2.52 - 2.29 1.00 2661 139 0.0923 0.1516 4.6281 4.9556| | 5: 2.29 - 2.13 1.00 2678 122 0.0942 0.1528 4.5817 4.901| | 6: 2.13 - 2.00 1.00 2692 117 0.1111 0.1646 4.5751 4.7657| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.94 9.24 1.00 0.96 6602.94| | 2: 3.63 - 2.88 2711 122 0.92 13.11 1.01 0.96 6602.94| | 3: 2.88 - 2.52 2681 148 0.87 19.23 0.99 0.96 6602.94| | 4: 2.52 - 2.29 2661 139 0.93 12.28 1.01 0.97 2164.05| | 5: 2.29 - 2.13 2678 122 0.91 14.28 1.00 0.97 2164.05| | 6: 2.13 - 2.00 2692 117 0.89 17.01 0.99 0.97 2164.05| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2164.05 max = 6602.94 mean = 4406.87| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.88 mean = 14.16| |phase err.(test): min = 0.00 max = 88.43 mean = 13.83| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1120 0.1099 0.1529 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1558 0.1546 0.1828 n_refl.: 17040 remove outliers: r(all,work,free)=0.1558 0.1546 0.1828 n_refl.: 17040 overall B=-0.21 to atoms: r(all,work,free)=0.1546 0.1533 0.1822 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1120 0.1100 0.1528 n_refl.: 17040 remove outliers: r(all,work,free)=0.1120 0.1100 0.1528 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 0.3580 296.744 278.536 0.542 1.005 0.330 11.894-9.307 99.02 97 4 0.1751 488.087 480.457 0.908 1.005 0.330 9.237-7.194 100.00 213 7 0.1761 399.206 399.478 0.986 1.005 0.220 7.162-5.571 100.00 427 22 0.1546 299.605 294.244 0.936 1.005 0.180 5.546-4.326 100.00 867 58 0.0917 411.309 408.015 0.962 1.004 0.177 4.315-3.360 100.00 1859 96 0.0868 391.159 388.682 1.003 1.003 0.161 3.356-2.611 100.00 3867 181 0.1237 256.969 254.818 1.000 1.000 0.063 2.608-2.000 99.99 8818 434 0.1025 167.500 166.299 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7429 ================= 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 : 0.2795 0.1824 0.083 5.357 8.8 119.3 19.9 258 0.000 1_bss: 0.1619 0.1660 0.083 5.357 8.4 118.9 19.5 258 0.000 1_settarget: 0.1619 0.1660 0.083 5.357 8.4 118.9 19.5 258 0.000 1_nqh: 0.1619 0.1660 0.083 5.357 8.4 118.9 19.5 258 0.000 1_weight: 0.1619 0.1660 0.083 5.357 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1352 0.1645 0.009 0.965 8.4 118.9 19.5 258 0.153 1_adp: 0.1277 0.1674 0.009 0.965 6.4 113.9 20.0 258 0.153 1_regHadp: 0.1280 0.1680 0.009 0.965 6.4 113.9 20.0 258 0.153 1_occ: 0.1275 0.1673 0.009 0.965 6.4 113.9 20.0 258 0.153 2_bss: 0.1272 0.1666 0.009 0.965 5.9 113.4 19.4 258 0.153 2_settarget: 0.1272 0.1666 0.009 0.965 5.9 113.4 19.4 258 0.153 2_updatecdl: 0.1272 0.1666 0.009 0.989 5.9 113.4 19.4 258 0.153 2_nqh: 0.1272 0.1666 0.009 0.989 5.9 113.4 19.4 258 0.153 2_sol: 0.1233 0.1572 0.009 0.989 5.9 112.3 20.7 360 n/a 2_weight: 0.1233 0.1572 0.009 0.989 5.9 112.3 20.7 360 n/a 2_xyzrec: 0.1200 0.1599 0.008 0.919 5.9 112.3 20.7 360 n/a 2_adp: 0.1186 0.1623 0.008 0.919 6.2 107.3 21.2 360 n/a 2_regHadp: 0.1188 0.1624 0.008 0.919 6.2 107.3 21.2 360 n/a 2_occ: 0.1181 0.1635 0.008 0.919 6.2 107.3 21.2 360 n/a 3_bss: 0.1178 0.1629 0.008 0.919 5.8 106.9 20.8 360 n/a 3_settarget: 0.1178 0.1629 0.008 0.919 5.8 106.9 20.8 360 n/a 3_updatecdl: 0.1178 0.1629 0.008 0.926 5.8 106.9 20.8 360 n/a 3_nqh: 0.1178 0.1629 0.008 0.926 5.8 106.9 20.8 360 n/a 3_sol: 0.1184 0.1568 0.008 0.926 5.8 106.9 20.9 409 n/a 3_weight: 0.1184 0.1568 0.008 0.926 5.8 106.9 20.9 409 n/a 3_xyzrec: 0.1163 0.1599 0.009 0.967 5.8 106.9 20.9 409 n/a 3_adp: 0.1146 0.1599 0.009 0.967 6.1 105.0 20.7 409 n/a 3_regHadp: 0.1146 0.1601 0.009 0.967 6.1 105.0 20.7 409 n/a 3_occ: 0.1140 0.1606 0.009 0.967 6.1 105.0 20.7 409 n/a 4_bss: 0.1139 0.1605 0.009 0.967 5.8 104.7 20.4 409 n/a 4_settarget: 0.1139 0.1605 0.009 0.967 5.8 104.7 20.4 409 n/a 4_updatecdl: 0.1139 0.1605 0.009 0.966 5.8 104.7 20.4 409 n/a 4_nqh: 0.1139 0.1605 0.009 0.966 5.8 104.7 20.4 409 n/a 4_sol: 0.1131 0.1555 0.009 0.966 5.8 104.7 20.9 457 n/a 4_weight: 0.1131 0.1555 0.009 0.966 5.8 104.7 20.9 457 n/a 4_xyzrec: 0.1123 0.1580 0.010 0.990 5.8 104.7 20.9 457 n/a 4_adp: 0.1109 0.1570 0.010 0.990 5.8 102.4 21.0 457 n/a 4_regHadp: 0.1109 0.1569 0.010 0.990 5.8 102.4 21.0 457 n/a 4_occ: 0.1100 0.1559 0.010 0.990 5.8 102.4 21.0 457 n/a 5_bss: 0.1097 0.1551 0.010 0.990 5.5 102.1 20.8 457 n/a 5_settarget: 0.1097 0.1551 0.010 0.990 5.5 102.1 20.8 457 n/a 5_updatecdl: 0.1097 0.1551 0.010 0.990 5.5 102.1 20.8 457 n/a 5_setrh: 0.1099 0.1550 0.010 0.990 5.5 102.1 20.8 457 n/a 5_nqh: 0.1099 0.1550 0.010 0.990 5.5 102.1 20.8 457 n/a 5_sol: 0.1098 0.1534 0.010 0.990 5.5 102.1 20.8 467 n/a 5_weight: 0.1098 0.1534 0.010 0.990 5.5 102.1 20.8 467 n/a 5_xyzrec: 0.1117 0.1544 0.010 1.106 5.5 102.1 20.8 467 n/a 5_adp: 0.1107 0.1534 0.010 1.106 5.5 102.1 21.0 467 n/a 5_regHadp: 0.1107 0.1534 0.010 1.106 5.5 102.1 21.0 467 n/a 5_occ: 0.1099 0.1529 0.010 1.106 5.5 102.1 21.0 467 n/a end: 0.1100 0.1528 0.010 1.106 5.3 101.9 20.8 467 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2780949_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2780949_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9800 Refinement macro-cycles (run) : 955.3200 Write final files (write_after_run_outputs) : 16.7500 Total : 976.0500 Total CPU time: 16.63 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:38 PST -0800 (1735494098.93 s) Start R-work = 0.1619, R-free = 0.1660 Final R-work = 0.1100, R-free = 0.1528 =============================================================================== Job complete usr+sys time: 1016.49 seconds wall clock time: 17 minutes 18.98 seconds (1038.98 seconds total)