Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6197065.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6197065.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6197065.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.45, per 1000 atoms: 0.43 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: 0.53 Conformation dependent library (CDL) restraints added in 213.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.92: 546 0.92 - 1.18: 1113 1.18 - 1.45: 756 1.45 - 1.72: 725 1.72 - 1.99: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 52 " pdb=" C ILE A 52 " ideal model delta sigma weight residual 1.522 1.303 0.219 1.19e-02 7.06e+03 3.38e+02 bond pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 1.237 1.439 -0.202 1.11e-02 8.12e+03 3.30e+02 bond pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 1.331 1.567 -0.236 1.38e-02 5.25e+03 2.93e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.150 0.171 1.00e-02 1.00e+04 2.92e+02 bond pdb=" C PRO A 184 " pdb=" O PRO A 184 " ideal model delta sigma weight residual 1.238 0.996 0.242 1.42e-02 4.96e+03 2.91e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 2838 4.18 - 8.35: 1931 8.35 - 12.52: 780 12.52 - 16.70: 196 16.70 - 20.87: 32 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 107.47 15.13 1.00e+00 1.00e+00 2.29e+02 angle pdb=" CA GLY A 120 " pdb=" C GLY A 120 " pdb=" O GLY A 120 " ideal model delta sigma weight residual 119.27 133.52 -14.25 1.01e+00 9.80e-01 1.99e+02 angle pdb=" O VAL A 51 " pdb=" C VAL A 51 " pdb=" N ILE A 52 " ideal model delta sigma weight residual 123.10 106.77 16.33 1.17e+00 7.31e-01 1.95e+02 angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.12 136.84 -14.72 1.06e+00 8.90e-01 1.93e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.91 108.45 13.46 9.80e-01 1.04e+00 1.89e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.81: 1316 17.81 - 35.60: 113 35.60 - 53.39: 40 53.39 - 71.18: 10 71.18 - 88.97: 2 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 -145.98 23.98 0 2.50e+00 1.60e-01 9.20e+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 123.40 143.84 -20.44 0 2.50e+00 1.60e-01 6.68e+01 dihedral pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual 122.80 140.54 -17.74 0 2.50e+00 1.60e-01 5.04e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.209: 97 0.209 - 0.415: 87 0.415 - 0.620: 36 0.620 - 0.826: 18 0.826 - 1.031: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 20 " pdb=" N VAL A 20 " pdb=" C VAL A 20 " pdb=" CB VAL A 20 " both_signs ideal model delta sigma weight residual False 2.44 1.41 1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" CA AASN A 76 " pdb=" N AASN A 76 " pdb=" C AASN A 76 " pdb=" CB AASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 3.48 -0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CG LEU A 101 " pdb=" CB LEU A 101 " pdb=" CD1 LEU A 101 " pdb=" CD2 LEU A 101 " both_signs ideal model delta sigma weight residual False -2.59 -1.66 -0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.050 2.00e-02 2.50e+03 7.04e-02 1.49e+02 pdb=" CG PHE A 162 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.101 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.119 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.081 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.034 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.049 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.076 2.00e-02 2.50e+03 6.09e-02 1.11e+02 pdb=" CG PHE A 119 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.080 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.096 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.070 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.046 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.096 2.00e-02 2.50e+03 5.59e-02 9.37e+01 pdb=" CG PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.083 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.011 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.100 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.023 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 588 2.24 - 2.83: 7474 2.83 - 3.42: 10735 3.42 - 4.01: 15411 4.01 - 4.60: 22349 Nonbonded interactions: 56557 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.647 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.732 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.800 2.100 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.851 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.864 2.450 ... (remaining 56552 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_6197065_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3615 r_free= 0.2033 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.465636 | | target function (ml) not normalized (work): 22015.583667 | | target function (ml) not normalized (free): 1150.006067 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3792 0.2223 4.8545 4.9109| | 2: 3.78 - 3.00 1.00 2430 110 0.3399 0.1712 4.0656 4.115| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.79 2500 142 0.50 48.77 0.83 0.13 6605.85| | 2: 3.78 - 3.00 2430 110 0.94 11.15 1.48 0.26 442.11| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 372.89 max = 12067.97 mean = 3567.74| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.23| |phase err.(test): min = 0.00 max = 90.00 mean = 33.06| |-----------------------------------------------------------------------------| ----------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 0.248 1557 Z= 5.480 Angle : 5.477 18.164 2118 Z= 3.848 Chirality : 0.364 1.031 243 Planarity : 0.029 0.081 284 Dihedral : 13.920 88.967 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 1.62 % Allowed : 1.62 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Cbeta Deviations : 26.49 % 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: -2.94 (0.46), residues: 224 helix: -2.72 (0.35), residues: 109 sheet: -1.48 (0.69), residues: 38 loop : -0.50 (0.67), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.076 0.019 ARG A 5 TYR 0.067 0.032 TYR A 139 PHE 0.122 0.051 PHE A 162 HIS 0.014 0.008 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3615 r_free= 0.2033 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.465636 | | target function (ml) not normalized (work): 22015.583667 | | target function (ml) not normalized (free): 1150.006067 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3572 0.3647 0.2134 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3572 0.3647 0.2134 n_refl.: 5182 remove outliers: r(all,work,free)=0.2517 0.2540 0.2134 n_refl.: 5178 overall B=-2.86 to atoms: r(all,work,free)=0.2407 0.2426 0.2086 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1552 0.1550 0.1587 n_refl.: 5178 remove outliers: r(all,work,free)=0.1548 0.1545 0.1587 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3777 449.882 411.175 0.671 1.057 0.407 11.894-9.307 99.02 97 4 0.1836 714.674 695.092 0.942 1.055 0.393 9.237-7.194 100.00 213 7 0.2191 584.461 575.300 0.978 1.049 0.348 7.162-5.571 100.00 427 22 0.2358 438.567 425.461 0.943 1.039 0.326 5.546-4.326 100.00 867 58 0.1382 602.091 595.613 0.985 1.021 0.268 4.315-3.360 100.00 1859 96 0.1287 572.595 566.460 1.052 0.992 0.200 3.356-3.002 100.00 1373 60 0.1571 441.037 433.299 1.059 0.962 0.054 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6612 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1545 r_free=0.1587 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1547 r_free=0.1592 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.125244 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.855826 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1166 0.1815 0.0649 0.010 1.0 3.5 0.5 0.0 0 9.563 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.66 18.15 6.49 3.013 15.996 1.856 0.018 10.24 18.11 7.87 4.908 16.193 1.856 0.015 Individual atomic B min max mean iso aniso Overall: 2.31 111.44 17.40 5.27 1785 0 Protein: 2.31 111.07 14.72 5.27 1519 0 Water: 4.00 111.44 32.97 N/A 258 0 Other: 17.70 35.37 24.12 N/A 8 0 Chain A: 2.31 111.44 17.40 N/A 1785 0 Histogram: Values Number of atoms 2.31 - 13.23 922 13.23 - 24.14 477 24.14 - 35.05 190 35.05 - 45.96 112 45.96 - 56.87 53 56.87 - 67.79 14 67.79 - 78.70 8 78.70 - 89.61 5 89.61 - 100.52 1 100.52 - 111.44 3 =========================== Idealize ADP of riding H ========================== r_work=0.1024 r_free=0.1811 r_work=0.1018 r_free=0.1818 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1018 r_free = 0.1818 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1013 r_free = 0.1802 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1013 r_free= 0.1802 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014037 | | target function (ls_wunit_k1) not normalized (work): 69.119741 | | target function (ls_wunit_k1) not normalized (free): 10.699149 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1053 0.1013 0.1802 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2102 0.2102 0.2206 n_refl.: 5176 remove outliers: r(all,work,free)=0.2102 0.2102 0.2206 n_refl.: 5176 overall B=-0.95 to atoms: r(all,work,free)=0.2063 0.2061 0.2195 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1052 0.1012 0.1791 n_refl.: 5176 remove outliers: r(all,work,free)=0.1052 0.1012 0.1791 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3354 329.981 312.362 0.670 1.020 0.388 11.894-9.307 99.02 97 4 0.1563 524.201 514.612 0.973 1.020 0.371 9.237-7.194 100.00 213 7 0.1691 428.692 428.585 1.010 1.018 0.321 7.162-5.571 100.00 427 22 0.1613 321.681 317.982 0.973 1.015 0.312 5.546-4.326 100.00 867 58 0.0908 441.623 438.321 0.994 1.008 0.232 4.315-3.360 100.00 1859 96 0.0761 419.988 420.066 1.044 0.997 0.200 3.356-3.002 100.00 1373 60 0.1000 323.493 322.155 1.023 0.986 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3990 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1012 r_free=0.1791 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1012 r_free=0.1790 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1012 r_free=0.1790 | n_water=258 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.1031 r_free=0.1769 | n_water=249 | time (s): 19.990 (total time: 20.500) Filter (q & B) r_work=0.1031 r_free=0.1770 | n_water=246 | time (s): 1.440 (total time: 21.940) Compute maps r_work=0.1031 r_free=0.1770 | n_water=246 | time (s): 0.430 (total time: 22.370) Filter (map) r_work=0.1338 r_free=0.1845 | n_water=140 | time (s): 1.330 (total time: 23.700) Find peaks r_work=0.1338 r_free=0.1845 | n_water=140 | time (s): 0.400 (total time: 24.100) Add new water r_work=0.1696 r_free=0.2168 | n_water=228 | time (s): 1.730 (total time: 25.830) Refine new water occ: r_work=0.1158 r_free=0.1711 adp: r_work=0.1136 r_free=0.1707 occ: r_work=0.1134 r_free=0.1686 adp: r_work=0.1123 r_free=0.1689 occ: r_work=0.1122 r_free=0.1677 adp: r_work=0.1119 r_free=0.1676 ADP+occupancy (water only), MIN, final r_work=0.1119 r_free=0.1676 r_work=0.1119 r_free=0.1676 | n_water=228 | time (s): 6.780 (total time: 32.610) Filter (q & B) r_work=0.1121 r_free=0.1687 | n_water=226 | time (s): 1.660 (total time: 34.270) Filter (dist only) r_work=0.1124 r_free=0.1683 | n_water=223 | time (s): 16.860 (total time: 51.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.152927 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.861197 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1017 0.1809 0.0792 0.009 1.0 5.4 0.5 0.6 0 11.576 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.17 18.09 7.92 4.649 16.753 2.861 0.014 9.48 18.38 8.90 5.494 17.128 2.861 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 107.92 16.48 6.50 1750 0 Protein: 0.00 107.92 14.98 6.49 1519 0 Water: 0.00 62.93 26.43 N/A 223 0 Other: 12.01 36.28 24.25 N/A 8 0 Chain A: 0.00 107.92 15.67 N/A 1665 0 Chain S: 2.97 59.74 32.37 N/A 85 0 Histogram: Values Number of atoms 0.00 - 10.79 690 10.79 - 21.58 659 21.58 - 32.38 211 32.38 - 43.17 108 43.17 - 53.96 41 53.96 - 64.75 28 64.75 - 75.55 5 75.55 - 86.34 3 86.34 - 97.13 4 97.13 - 107.92 1 =========================== Idealize ADP of riding H ========================== r_work=0.0948 r_free=0.1838 r_work=0.0946 r_free=0.1836 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0946 r_free = 0.1836 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0945 r_free = 0.1835 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0945 r_free= 0.1835 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012261 | | target function (ls_wunit_k1) not normalized (work): 60.371191 | | target function (ls_wunit_k1) not normalized (free): 9.971256 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0989 0.0945 0.1835 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2149 0.2154 0.2187 n_refl.: 5176 remove outliers: r(all,work,free)=0.2149 0.2154 0.2187 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2149 0.2154 0.2187 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0989 0.0944 0.1841 n_refl.: 5176 remove outliers: r(all,work,free)=0.0989 0.0944 0.1841 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3235 329.981 315.562 0.666 1.035 0.381 11.894-9.307 99.02 97 4 0.1512 524.201 518.922 0.955 1.035 0.360 9.237-7.194 100.00 213 7 0.1487 428.692 430.686 0.993 1.031 0.310 7.162-5.571 100.00 427 22 0.1458 321.681 319.152 0.972 1.025 0.310 5.546-4.326 100.00 867 58 0.0788 441.623 439.566 0.995 1.013 0.250 4.315-3.360 100.00 1859 96 0.0723 419.988 419.556 1.054 0.994 0.208 3.356-3.002 100.00 1373 60 0.0979 323.493 322.304 1.045 0.976 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.8628 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0944 r_free=0.1841 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0944 r_free=0.1841 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0944 r_free=0.1841 | n_water=223 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.0964 r_free=0.1826 | n_water=218 | time (s): 17.410 (total time: 18.100) Filter (q & B) r_work=0.1024 r_free=0.1833 | n_water=216 | time (s): 1.600 (total time: 19.700) Compute maps r_work=0.1024 r_free=0.1833 | n_water=216 | time (s): 0.470 (total time: 20.170) Filter (map) r_work=0.1296 r_free=0.1858 | n_water=140 | time (s): 1.400 (total time: 21.570) Find peaks r_work=0.1296 r_free=0.1858 | n_water=140 | time (s): 0.490 (total time: 22.060) Add new water r_work=0.1704 r_free=0.2261 | n_water=229 | time (s): 1.740 (total time: 23.800) Refine new water occ: r_work=0.1082 r_free=0.1812 adp: r_work=0.1077 r_free=0.1819 occ: r_work=0.1063 r_free=0.1802 adp: r_work=0.1064 r_free=0.1806 occ: r_work=0.1051 r_free=0.1786 adp: r_work=0.1052 r_free=0.1790 ADP+occupancy (water only), MIN, final r_work=0.1052 r_free=0.1790 r_work=0.1052 r_free=0.1790 | n_water=229 | time (s): 14.250 (total time: 38.050) Filter (q & B) r_work=0.1053 r_free=0.1795 | n_water=227 | time (s): 1.570 (total time: 39.620) Filter (dist only) r_work=0.1063 r_free=0.1812 | n_water=225 | time (s): 18.190 (total time: 57.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.160535 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.223001 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0961 0.1809 0.0847 0.011 1.1 4.2 0.5 0.6 0 0.580 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.61 18.09 8.47 5.419 17.736 0.223 5.175 9.20 18.14 8.94 7.307 17.721 0.223 5.080 Individual atomic B min max mean iso aniso Overall: 0.00 107.12 16.25 8.97 1752 0 Protein: 0.00 107.12 15.07 8.96 1519 0 Water: 0.00 60.53 23.80 N/A 225 0 Other: 11.30 44.79 26.55 N/A 8 0 Chain A: 0.00 107.12 15.67 N/A 1646 0 Chain S: 0.00 57.82 25.20 N/A 106 0 Histogram: Values Number of atoms 0.00 - 10.71 682 10.71 - 21.42 667 21.42 - 32.14 217 32.14 - 42.85 118 42.85 - 53.56 32 53.56 - 64.27 19 64.27 - 74.98 8 74.98 - 85.70 4 85.70 - 96.41 4 96.41 - 107.12 1 =========================== Idealize ADP of riding H ========================== r_work=0.0920 r_free=0.1814 r_work=0.0926 r_free=0.1822 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0926 r_free = 0.1822 target_work(ml) = 5.085 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0914 r_free = 0.1804 target_work(ml) = 5.077 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0914 r_free= 0.1804 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.077043 | | target function (ml) not normalized (work): 24999.360831 | | target function (ml) not normalized (free): 1870.821949 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0960 0.0914 0.1804 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2165 0.2179 0.2048 n_refl.: 5176 remove outliers: r(all,work,free)=0.2165 0.2179 0.2048 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2165 0.2179 0.2048 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0954 0.0908 0.1803 n_refl.: 5176 remove outliers: r(all,work,free)=0.0952 0.0906 0.1803 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3699 327.202 306.135 0.610 1.001 0.354 11.894-9.307 99.02 97 4 0.1860 524.201 508.207 0.941 1.005 0.350 9.237-7.194 100.00 213 7 0.1928 428.692 423.634 0.991 1.006 0.310 7.162-5.571 100.00 427 22 0.1948 321.681 312.131 0.975 1.005 0.310 5.546-4.326 100.00 867 58 0.0916 441.623 436.936 0.992 1.004 0.239 4.315-3.360 100.00 1859 96 0.0608 419.988 419.281 1.051 1.001 0.220 3.356-3.002 100.00 1373 60 0.0602 323.493 322.719 1.031 0.998 0.063 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.0872 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0906 r_free=0.1803 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.0906 r_free=0.1803 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0906 r_free=0.1803 | n_water=225 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.0917 r_free=0.1797 | n_water=222 | time (s): 18.080 (total time: 18.640) Filter (q & B) r_work=0.0970 r_free=0.1816 | n_water=219 | time (s): 1.210 (total time: 19.850) Compute maps r_work=0.0970 r_free=0.1816 | n_water=219 | time (s): 0.410 (total time: 20.260) Filter (map) r_work=0.1222 r_free=0.1909 | n_water=152 | time (s): 1.490 (total time: 21.750) Find peaks r_work=0.1222 r_free=0.1909 | n_water=152 | time (s): 0.430 (total time: 22.180) Add new water r_work=0.1579 r_free=0.2214 | n_water=232 | time (s): 1.740 (total time: 23.920) Refine new water occ: r_work=0.1014 r_free=0.1798 adp: r_work=0.1011 r_free=0.1818 occ: r_work=0.1000 r_free=0.1787 adp: r_work=0.1000 r_free=0.1801 occ: r_work=0.0990 r_free=0.1774 adp: r_work=0.0990 r_free=0.1789 ADP+occupancy (water only), MIN, final r_work=0.0990 r_free=0.1789 r_work=0.0990 r_free=0.1789 | n_water=232 | time (s): 8.990 (total time: 32.910) Filter (q & B) r_work=0.0991 r_free=0.1792 | n_water=231 | time (s): 1.450 (total time: 34.360) Filter (dist only) r_work=0.0996 r_free=0.1779 | n_water=230 | time (s): 19.400 (total time: 53.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.009399 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.209944 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0920 0.1799 0.0879 0.011 1.0 4.5 0.5 0.0 0 0.505 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.20 17.99 8.79 6.980 17.871 0.210 5.037 9.01 18.00 8.99 7.842 17.940 0.210 4.981 Individual atomic B min max mean iso aniso Overall: 0.00 107.76 16.52 10.21 1757 0 Protein: 0.00 107.76 15.40 10.18 1519 0 Water: 0.00 56.35 23.56 N/A 230 0 Other: 9.52 47.04 26.62 N/A 8 0 Chain A: 0.00 107.76 15.88 N/A 1639 0 Chain S: 0.84 55.22 25.45 N/A 118 0 Histogram: Values Number of atoms 0.00 - 10.78 672 10.78 - 21.55 648 21.55 - 32.33 250 32.33 - 43.10 121 43.10 - 53.88 29 53.88 - 64.66 19 64.66 - 75.43 8 75.43 - 86.21 5 86.21 - 96.99 4 96.99 - 107.76 1 =========================== Idealize ADP of riding H ========================== r_work=0.0901 r_free=0.1800 r_work=0.0903 r_free=0.1806 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0903 r_free = 0.1806 target_work(ml) = 4.984 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0889 r_free = 0.1785 target_work(ml) = 4.975 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0889 r_free= 0.1785 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.974846 | | target function (ml) not normalized (work): 24491.166231 | | target function (ml) not normalized (free): 2128.903726 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0935 0.0889 0.1785 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2185 0.2196 0.2107 n_refl.: 5175 remove outliers: r(all,work,free)=0.2185 0.2196 0.2107 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2185 0.2196 0.2107 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0935 0.0889 0.1780 n_refl.: 5175 remove outliers: r(all,work,free)=0.0933 0.0887 0.1780 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3809 329.378 294.070 0.591 0.989 0.338 11.894-9.307 99.02 97 4 0.1961 524.201 506.932 0.948 0.994 0.330 9.237-7.194 100.00 213 7 0.2154 428.692 420.492 1.008 0.997 0.289 7.162-5.571 100.00 427 22 0.2108 321.681 310.870 0.992 0.998 0.273 5.546-4.326 100.00 867 58 0.0974 441.623 436.677 1.011 1.000 0.230 4.315-3.360 100.00 1859 96 0.0558 419.988 419.746 1.078 1.002 0.220 3.356-3.002 100.00 1373 60 0.0446 323.493 323.615 1.057 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-7.4167 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0887 r_free=0.1780 After: r_work=0.0890 r_free=0.1780 ================================== NQH flips ================================== r_work=0.0890 r_free=0.1780 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0892 r_free=0.1778 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0892 r_free=0.1778 | n_water=230 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.0916 r_free=0.1787 | n_water=224 | time (s): 17.450 (total time: 18.170) Filter (q & B) r_work=0.1084 r_free=0.1843 | n_water=219 | time (s): 1.680 (total time: 19.850) Compute maps r_work=0.1084 r_free=0.1843 | n_water=219 | time (s): 0.660 (total time: 20.510) Filter (map) r_work=0.1303 r_free=0.1937 | n_water=156 | time (s): 1.940 (total time: 22.450) Find peaks r_work=0.1303 r_free=0.1937 | n_water=156 | time (s): 0.540 (total time: 22.990) Add new water r_work=0.1577 r_free=0.2209 | n_water=222 | time (s): 1.330 (total time: 24.320) Refine new water occ: r_work=0.1018 r_free=0.1776 adp: r_work=0.1004 r_free=0.1790 occ: r_work=0.0997 r_free=0.1776 adp: r_work=0.0997 r_free=0.1784 occ: r_work=0.0991 r_free=0.1773 adp: r_work=0.0990 r_free=0.1780 ADP+occupancy (water only), MIN, final r_work=0.0990 r_free=0.1780 r_work=0.0990 r_free=0.1780 | n_water=222 | time (s): 11.580 (total time: 35.900) Filter (q & B) r_work=0.0991 r_free=0.1779 | n_water=220 | time (s): 1.350 (total time: 37.250) Filter (dist only) r_work=0.0991 r_free=0.1779 | n_water=220 | time (s): 15.810 (total time: 53.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.935784 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.231194 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0928 0.1747 0.0819 0.010 1.1 6.7 0.5 0.0 0 0.468 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.28 17.47 8.19 7.799 18.115 0.231 5.038 9.06 17.54 8.48 8.968 18.247 0.231 4.981 Individual atomic B min max mean iso aniso Overall: 0.00 110.68 16.83 11.90 1747 0 Protein: 0.00 110.68 15.84 11.87 1519 0 Water: 0.44 58.72 23.21 N/A 220 0 Other: 13.26 53.10 29.45 N/A 8 0 Chain A: 0.00 110.68 16.26 N/A 1633 0 Chain S: 0.44 58.72 24.99 N/A 114 0 Histogram: Values Number of atoms 0.00 - 11.07 681 11.07 - 22.14 645 22.14 - 33.21 235 33.21 - 44.27 115 44.27 - 55.34 36 55.34 - 66.41 15 66.41 - 77.48 9 77.48 - 88.55 6 88.55 - 99.62 3 99.62 - 110.68 2 =========================== Idealize ADP of riding H ========================== r_work=0.0906 r_free=0.1754 r_work=0.0910 r_free=0.1754 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0910 r_free = 0.1754 target_work(ml) = 4.986 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0903 r_free = 0.1751 target_work(ml) = 4.981 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0903 r_free= 0.1751 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.981174 | | target function (ml) not normalized (work): 24517.337591 | | target function (ml) not normalized (free): 2117.364144 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1281 0.1730 5.553 6.1781| | 2: 3.78 - 3.00 1.00 2430 110 0.0443 0.1788 4.3947 11.273| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.91 12.27 1.00 0.98 13439.94| | 2: 3.78 - 3.00 2430 110 0.99 1.96 1.00 1.00 977.77| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 624.91 max = 22319.64 mean = 7287.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.80 mean = 7.18| |phase err.(test): min = 0.00 max = 78.32 mean = 6.91| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0946 0.0903 0.1751 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2162 0.2170 0.2147 n_refl.: 5174 remove outliers: r(all,work,free)=0.2162 0.2170 0.2147 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2162 0.2170 0.2147 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0945 0.0902 0.1760 n_refl.: 5174 remove outliers: r(all,work,free)=0.0945 0.0902 0.1760 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3807 329.378 291.955 0.585 0.985 0.330 11.894-9.307 99.02 97 4 0.1923 524.201 510.727 0.969 0.992 0.325 9.237-7.194 100.00 213 7 0.2170 428.692 420.990 1.008 0.996 0.320 7.162-5.571 100.00 427 22 0.2095 321.681 313.624 1.000 0.998 0.300 5.546-4.326 100.00 867 58 0.1012 441.623 434.688 1.012 1.000 0.240 4.315-3.360 100.00 1859 96 0.0588 419.988 420.519 1.089 1.003 0.230 3.356-3.002 100.00 1373 60 0.0428 323.493 323.119 1.070 1.005 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9688 ================= 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 : 0.3615 0.2033 0.083 5.477 8.8 119.3 19.9 258 0.000 1_bss: 0.1545 0.1587 0.083 5.477 6.0 116.4 17.0 258 0.000 1_settarget: 0.1545 0.1587 0.083 5.477 6.0 116.4 17.0 258 0.000 1_nqh: 0.1547 0.1592 0.083 5.477 6.0 116.4 17.0 258 0.006 1_weight: 0.1547 0.1592 0.083 5.477 6.0 116.4 17.0 258 0.006 1_xyzrec: 0.1166 0.1815 0.010 0.974 6.0 116.4 17.0 258 0.210 1_adp: 0.1024 0.1811 0.010 0.974 2.3 111.4 17.4 258 0.210 1_regHadp: 0.1018 0.1818 0.010 0.974 2.3 111.4 17.4 258 0.210 1_occ: 0.1013 0.1802 0.010 0.974 2.3 111.4 17.4 258 0.210 2_bss: 0.1012 0.1791 0.010 0.974 1.4 110.5 16.4 258 0.210 2_settarget: 0.1012 0.1791 0.010 0.974 1.4 110.5 16.4 258 0.210 2_updatecdl: 0.1012 0.1791 0.010 1.002 1.4 110.5 16.4 258 0.210 2_nqh: 0.1012 0.1790 0.010 1.002 1.4 110.5 16.4 258 0.207 2_sol: 0.1124 0.1683 0.010 1.002 1.0 110.1 15.8 223 n/a 2_weight: 0.1124 0.1683 0.010 1.002 1.0 110.1 15.8 223 n/a 2_xyzrec: 0.1017 0.1809 0.009 0.975 1.0 110.1 15.8 223 n/a 2_adp: 0.0948 0.1838 0.009 0.975 0.0 107.9 16.5 223 n/a 2_regHadp: 0.0946 0.1836 0.009 0.975 0.0 107.9 16.5 223 n/a 2_occ: 0.0945 0.1835 0.009 0.975 0.0 107.9 16.5 223 n/a 3_bss: 0.0944 0.1841 0.009 0.975 0.0 107.9 16.5 223 n/a 3_settarget: 0.0944 0.1841 0.009 0.975 0.0 107.9 16.5 223 n/a 3_updatecdl: 0.0944 0.1841 0.009 0.980 0.0 107.9 16.5 223 n/a 3_nqh: 0.0944 0.1841 0.009 0.980 0.0 107.9 16.5 223 n/a 3_sol: 0.1063 0.1812 0.009 0.980 0.0 107.9 16.3 225 n/a 3_weight: 0.1063 0.1812 0.009 0.980 0.0 107.9 16.3 225 n/a 3_xyzrec: 0.0961 0.1809 0.011 1.061 0.0 107.9 16.3 225 n/a 3_adp: 0.0920 0.1814 0.011 1.061 0.0 107.1 16.2 225 n/a 3_regHadp: 0.0926 0.1822 0.011 1.061 0.0 107.1 16.2 225 n/a 3_occ: 0.0914 0.1804 0.011 1.061 0.0 107.1 16.2 225 n/a 4_bss: 0.0906 0.1803 0.011 1.061 0.0 107.1 16.2 225 n/a 4_settarget: 0.0906 0.1803 0.011 1.061 0.0 107.1 16.2 225 n/a 4_updatecdl: 0.0906 0.1803 0.011 1.070 0.0 107.1 16.2 225 n/a 4_nqh: 0.0906 0.1803 0.011 1.070 0.0 107.1 16.2 225 n/a 4_sol: 0.0996 0.1779 0.011 1.070 0.0 107.1 16.4 230 n/a 4_weight: 0.0996 0.1779 0.011 1.070 0.0 107.1 16.4 230 n/a 4_xyzrec: 0.0920 0.1799 0.011 1.034 0.0 107.1 16.4 230 n/a 4_adp: 0.0901 0.1800 0.011 1.034 0.0 107.8 16.5 230 n/a 4_regHadp: 0.0903 0.1806 0.011 1.034 0.0 107.8 16.5 230 n/a 4_occ: 0.0889 0.1785 0.011 1.034 0.0 107.8 16.5 230 n/a 5_bss: 0.0887 0.1780 0.011 1.034 0.0 107.8 16.5 230 n/a 5_settarget: 0.0887 0.1780 0.011 1.034 0.0 107.8 16.5 230 n/a 5_updatecdl: 0.0887 0.1780 0.011 1.039 0.0 107.8 16.5 230 n/a 5_setrh: 0.0890 0.1780 0.011 1.039 0.0 107.8 16.5 230 n/a 5_nqh: 0.0892 0.1778 0.011 1.039 0.0 107.8 16.5 230 n/a 5_sol: 0.0991 0.1779 0.011 1.039 0.0 107.8 16.6 220 n/a 5_weight: 0.0991 0.1779 0.011 1.039 0.0 107.8 16.6 220 n/a 5_xyzrec: 0.0928 0.1747 0.010 1.077 0.0 107.8 16.6 220 n/a 5_adp: 0.0906 0.1754 0.010 1.077 0.0 110.7 16.8 220 n/a 5_regHadp: 0.0910 0.1754 0.010 1.077 0.0 110.7 16.8 220 n/a 5_occ: 0.0903 0.1751 0.010 1.077 0.0 110.7 16.8 220 n/a end: 0.0902 0.1760 0.010 1.077 0.0 110.7 16.8 220 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6197065_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6197065_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0800 Refinement macro-cycles (run) : 483.3400 Write final files (write_after_run_outputs) : 10.8700 Total : 497.2900 Total CPU time: 8.64 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:59 PST -0800 (1735492739.70 s) Start R-work = 0.1545, R-free = 0.1587 Final R-work = 0.0902, R-free = 0.1760 =============================================================================== Job complete usr+sys time: 526.54 seconds wall clock time: 9 minutes 8.21 seconds (548.21 seconds total)