Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5638674.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_5638674.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5638674.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: 1.43, per 1000 atoms: 0.42 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: 0.55 Conformation dependent library (CDL) restraints added in 156.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.91: 493 0.91 - 1.15: 1126 1.15 - 1.39: 584 1.39 - 1.64: 870 1.64 - 1.88: 80 Bond restraints: 3153 Sorted by residual: bond pdb=" N PHE A 162 " pdb=" CA PHE A 162 " ideal model delta sigma weight residual 1.459 1.699 -0.240 1.20e-02 6.94e+03 4.00e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.133 0.188 1.00e-02 1.00e+04 3.53e+02 bond pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 1.331 1.497 -0.167 8.90e-03 1.26e+04 3.50e+02 bond pdb=" C HIS A 138 " pdb=" O HIS A 138 " ideal model delta sigma weight residual 1.236 1.473 -0.237 1.32e-02 5.74e+03 3.24e+02 bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.496 -0.175 1.00e-02 1.00e+04 3.07e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.87: 3176 4.87 - 9.74: 1921 9.74 - 14.61: 576 14.61 - 19.48: 98 19.48 - 24.34: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 132.45 -13.25 9.00e-01 1.23e+00 2.17e+02 angle pdb=" O MET A 17 " pdb=" C MET A 17 " pdb=" N GLU A 18 " ideal model delta sigma weight residual 122.09 137.38 -15.29 1.04e+00 9.25e-01 2.16e+02 angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" O ILE A 21 " ideal model delta sigma weight residual 118.69 128.17 -9.48 6.70e-01 2.23e+00 2.00e+02 angle pdb=" CA MET A 17 " pdb=" C MET A 17 " pdb=" N GLU A 18 " ideal model delta sigma weight residual 116.97 100.54 16.43 1.20e+00 6.94e-01 1.88e+02 angle pdb=" N AASN A 76 " pdb=" CA AASN A 76 " pdb=" C AASN A 76 " ideal model delta sigma weight residual 111.33 127.20 -15.87 1.21e+00 6.83e-01 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 1287 17.16 - 34.33: 135 34.33 - 51.49: 44 51.49 - 68.65: 12 68.65 - 85.81: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N GLU A 16 " pdb=" C GLU A 16 " pdb=" CA GLU A 16 " pdb=" CB GLU A 16 " ideal model delta harmonic sigma weight residual 122.80 147.04 -24.24 0 2.50e+00 1.60e-01 9.40e+01 dihedral pdb=" C GLU A 16 " pdb=" N GLU A 16 " pdb=" CA GLU A 16 " pdb=" CB GLU A 16 " ideal model delta harmonic sigma weight residual -122.60 -146.15 23.55 0 2.50e+00 1.60e-01 8.87e+01 dihedral pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual 123.40 142.41 -19.01 0 2.50e+00 1.60e-01 5.78e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.220: 92 0.220 - 0.439: 82 0.439 - 0.658: 43 0.658 - 0.877: 22 0.877 - 1.095: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA GLU A 16 " pdb=" N GLU A 16 " pdb=" C GLU A 16 " pdb=" CB GLU A 16 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.10 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 3.41 -0.90 2.00e-01 2.50e+01 2.02e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 173 " 0.011 2.00e-02 2.50e+03 8.15e-02 9.95e+01 pdb=" CG ASN A 173 " -0.120 2.00e-02 2.50e+03 pdb=" OD1 ASN A 173 " 0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN A 173 " -0.077 2.00e-02 2.50e+03 pdb="HD21 ASN A 173 " -0.010 2.00e-02 2.50e+03 pdb="HD22 ASN A 173 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.120 9.50e-02 1.11e+02 7.64e-02 9.66e+01 pdb=" NE ARG A 48 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " 0.120 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.084 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.111 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.026 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " 0.025 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.050 2.00e-02 2.50e+03 5.39e-02 8.71e+01 pdb=" CG PHE A 162 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.068 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.039 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.014 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1076 2.33 - 2.89: 8139 2.89 - 3.46: 10488 3.46 - 4.03: 15238 4.03 - 4.60: 21760 Nonbonded interactions: 56701 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.757 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.803 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.815 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.816 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.844 2.450 x-y,-y,-z-4/3 ... (remaining 56696 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_5638674_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= 0.2791 r_free= 0.1837 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.383437 | | target function (ml) not normalized (work): 71200.162000 | | target function (ml) not normalized (free): 3270.688970 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3201 0.2188 7.4697 5.0394| | 2: 3.63 - 2.88 1.00 2711 122 0.2629 0.1732 4.33 4.341| | 3: 2.88 - 2.52 1.00 2682 148 0.2568 0.1675 4.1898 4.2019| | 4: 2.52 - 2.29 1.00 2661 139 0.2564 0.1551 3.4791 3.5737| | 5: 2.29 - 2.13 1.00 2678 122 0.2661 0.1564 3.3877 3.497| | 6: 2.13 - 2.00 1.00 2692 117 0.2745 0.1800 3.2829 3.3723| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.85 0.77 0.23 1335.82| | 2: 3.63 - 2.88 2711 122 0.82 24.14 1.31 0.23 1335.82| | 3: 2.88 - 2.52 2682 148 0.73 33.33 1.29 0.23 1335.82| | 4: 2.52 - 2.29 2661 139 0.94 10.89 1.30 0.26 129.54| | 5: 2.29 - 2.13 2678 122 0.92 13.10 1.32 0.26 129.54| | 6: 2.13 - 2.00 2692 117 0.90 15.91 1.34 0.26 129.54| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 129.54 max = 1335.82 mean = 739.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 19.21| |phase err.(test): min = 0.00 max = 89.60 mean = 19.25| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.260 1557 Z= 5.315 Angle : 5.304 19.146 2118 Z= 3.778 Chirality : 0.398 1.095 243 Planarity : 0.032 0.113 284 Dihedral : 14.211 85.809 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 32.43 % 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: -2.93 (0.45), residues: 224 helix: -2.98 (0.34), residues: 109 sheet: -0.98 (0.93), residues: 28 loop : -0.45 (0.55), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.139 0.024 ARG A 28 TYR 0.070 0.028 TYR A 139 PHE 0.074 0.039 PHE A 164 HIS 0.068 0.027 HIS A 115 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= 0.2791 r_free= 0.1837 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.383437 | | target function (ml) not normalized (work): 71200.162000 | | target function (ml) not normalized (free): 3270.688970 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2719 percent. r_work = 0.2918 r_free = 0.2015 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2867 0.2918 0.2015 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2867 0.2918 0.2015 n_refl.: 17050 remove outliers: r(all,work,free)=0.2156 0.2166 0.2015 n_refl.: 17045 overall B=-0.43 to atoms: r(all,work,free)=0.2128 0.2137 0.1998 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1614 0.1610 0.1686 n_refl.: 17045 remove outliers: r(all,work,free)=0.1612 0.1608 0.1686 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 0.4022 391.496 358.877 0.639 1.013 0.380 11.894-9.307 99.02 97 4 0.1834 633.773 616.844 0.930 1.013 0.380 9.237-7.194 100.00 213 7 0.2156 518.363 509.063 0.964 1.013 0.364 7.162-5.571 100.00 427 22 0.2336 389.032 376.221 0.923 1.012 0.289 5.546-4.326 100.00 867 58 0.1379 534.078 529.455 0.963 1.010 0.220 4.315-3.360 100.00 1859 96 0.1321 507.913 502.939 1.017 1.006 0.191 3.356-2.611 100.00 3867 181 0.1648 333.670 329.041 1.015 1.000 0.091 2.608-2.000 99.99 8818 434 0.1633 217.496 213.480 1.034 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.5189 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1608 r_free=0.1686 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1608 r_free=0.1686 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.742111 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.878463 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 0.1348 0.1630 0.0282 0.009 1.0 1.0 0.5 0.0 0 11.871 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.48 16.30 2.82 3.013 18.433 0.878 0.023 12.75 16.49 3.74 3.615 18.691 0.878 0.020 Individual atomic B min max mean iso aniso Overall: 6.11 113.87 19.95 4.09 1785 0 Protein: 6.11 113.13 17.19 4.09 1519 0 Water: 8.70 113.87 36.01 N/A 258 0 Other: 21.68 37.22 26.45 N/A 8 0 Chain A: 6.11 113.87 19.95 N/A 1785 0 Histogram: Values Number of atoms 6.11 - 16.89 1081 16.89 - 27.67 346 27.67 - 38.44 185 38.44 - 49.22 95 49.22 - 59.99 50 59.99 - 70.77 13 70.77 - 81.55 7 81.55 - 92.32 4 92.32 - 103.10 1 103.10 - 113.87 3 =========================== Idealize ADP of riding H ========================== r_work=0.1275 r_free=0.1649 r_work=0.1278 r_free=0.1655 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1278 r_free = 0.1655 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 = 0.1274 r_free = 0.1649 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.24 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= 0.1274 r_free= 0.1649 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020075 | | target function (ls_wunit_k1) not normalized (work): 325.944268 | | target function (ls_wunit_k1) not normalized (free): 26.872132 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1292 0.1274 0.1649 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1903 0.1901 0.1987 n_refl.: 17043 remove outliers: r(all,work,free)=0.1903 0.1901 0.1987 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1875 0.1873 0.1971 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1290 0.1272 0.1646 n_refl.: 17043 remove outliers: r(all,work,free)=0.1289 0.1271 0.1646 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 0.3493 304.207 278.469 0.620 1.006 0.368 11.894-9.307 99.02 97 4 0.1666 489.269 478.665 0.919 1.007 0.367 9.237-7.194 100.00 213 7 0.1850 400.172 396.147 0.959 1.007 0.351 7.162-5.571 100.00 427 22 0.1861 300.330 294.480 0.930 1.006 0.301 5.546-4.326 100.00 867 58 0.1046 412.305 409.683 0.958 1.005 0.210 4.315-3.360 100.00 1859 96 0.0931 392.106 391.433 1.015 1.004 0.191 3.356-2.611 100.00 3867 181 0.1290 257.591 256.283 1.012 1.001 0.101 2.608-2.000 99.99 8818 434 0.1343 167.905 166.609 1.018 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3532 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1271 r_free=0.1646 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1271 r_free=0.1646 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1271 r_free=0.1646 | n_water=258 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1280 r_free=0.1636 | n_water=252 | time (s): 19.840 (total time: 20.520) Filter (q & B) r_work=0.1281 r_free=0.1636 | n_water=250 | time (s): 1.420 (total time: 21.940) Compute maps r_work=0.1281 r_free=0.1636 | n_water=250 | time (s): 0.580 (total time: 22.520) Filter (map) r_work=0.1313 r_free=0.1629 | n_water=214 | time (s): 1.810 (total time: 24.330) Find peaks r_work=0.1313 r_free=0.1629 | n_water=214 | time (s): 0.470 (total time: 24.800) Add new water r_work=0.1524 r_free=0.1824 | n_water=366 | time (s): 1.490 (total time: 26.290) Refine new water occ: r_work=0.1339 r_free=0.1554 adp: r_work=0.1283 r_free=0.1559 occ: r_work=0.1288 r_free=0.1529 adp: r_work=0.1257 r_free=0.1537 occ: r_work=0.1259 r_free=0.1536 adp: r_work=0.1247 r_free=0.1533 ADP+occupancy (water only), MIN, final r_work=0.1247 r_free=0.1533 r_work=0.1247 r_free=0.1533 | n_water=366 | time (s): 19.150 (total time: 45.440) Filter (q & B) r_work=0.1248 r_free=0.1544 | n_water=354 | time (s): 1.910 (total time: 47.350) Filter (dist only) r_work=0.1249 r_free=0.1545 | n_water=353 | time (s): 28.560 (total time: 75.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.901823 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.995781 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 0.1217 0.1590 0.0373 0.009 1.0 2.6 0.5 0.0 0 12.951 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.17 15.90 3.73 4.174 21.030 0.996 0.018 12.01 16.04 4.03 4.186 21.286 0.996 0.018 Individual atomic B min max mean iso aniso Overall: 7.02 107.75 21.28 4.23 1880 0 Protein: 7.02 107.75 17.66 4.22 1519 0 Water: 8.93 65.78 36.58 N/A 353 0 Other: 23.84 43.77 33.92 N/A 8 0 Chain A: 7.02 107.75 19.47 N/A 1741 0 Chain S: 16.85 65.53 43.99 N/A 139 0 Histogram: Values Number of atoms 7.02 - 17.09 1057 17.09 - 27.17 356 27.17 - 37.24 213 37.24 - 47.31 139 47.31 - 57.39 72 57.39 - 67.46 33 67.46 - 77.53 3 77.53 - 87.61 4 87.61 - 97.68 1 97.68 - 107.75 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1604 r_work=0.1203 r_free=0.1604 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1604 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1609 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 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= 0.1200 r_free= 0.1609 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.017259 | | target function (ls_wunit_k1) not normalized (work): 280.196749 | | target function (ls_wunit_k1) not normalized (free): 24.711518 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1200 0.1609 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1761 0.1752 0.1965 n_refl.: 17042 remove outliers: r(all,work,free)=0.1761 0.1752 0.1965 n_refl.: 17042 overall B=-0.39 to atoms: r(all,work,free)=0.1736 0.1726 0.1947 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1197 0.1604 n_refl.: 17042 remove outliers: r(all,work,free)=0.1215 0.1196 0.1604 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 0.3204 301.036 285.674 0.601 1.005 0.350 11.894-9.307 99.02 97 4 0.1542 489.269 486.947 0.919 1.006 0.344 9.237-7.194 100.00 213 7 0.1686 400.172 400.497 0.971 1.006 0.300 7.162-5.571 100.00 427 22 0.1577 300.330 295.987 0.934 1.005 0.281 5.546-4.326 100.00 867 58 0.0907 412.305 409.404 0.958 1.005 0.205 4.315-3.360 100.00 1859 96 0.0825 392.106 391.248 1.016 1.003 0.191 3.356-2.611 100.00 3867 181 0.1216 257.591 256.820 1.013 1.001 0.101 2.608-2.000 99.99 8818 434 0.1326 167.905 166.872 1.019 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3789 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1604 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1196 r_free=0.1606 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1606 | n_water=353 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1196 r_free=0.1606 | n_water=353 | time (s): 25.930 (total time: 26.570) Filter (q & B) r_work=0.1196 r_free=0.1606 | n_water=353 | time (s): 0.910 (total time: 27.480) Compute maps r_work=0.1196 r_free=0.1606 | n_water=353 | time (s): 0.630 (total time: 28.110) Filter (map) r_work=0.1259 r_free=0.1593 | n_water=259 | time (s): 1.440 (total time: 29.550) Find peaks r_work=0.1259 r_free=0.1593 | n_water=259 | time (s): 0.540 (total time: 30.090) Add new water r_work=0.1441 r_free=0.1734 | n_water=399 | time (s): 1.720 (total time: 31.810) Refine new water occ: r_work=0.1248 r_free=0.1526 adp: r_work=0.1239 r_free=0.1527 occ: r_work=0.1224 r_free=0.1509 adp: r_work=0.1212 r_free=0.1507 occ: r_work=0.1205 r_free=0.1503 adp: r_work=0.1196 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1499 r_work=0.1196 r_free=0.1499 | n_water=399 | time (s): 39.170 (total time: 70.980) Filter (q & B) r_work=0.1198 r_free=0.1509 | n_water=393 | time (s): 1.750 (total time: 72.730) Filter (dist only) r_work=0.1198 r_free=0.1509 | n_water=393 | time (s): 29.950 (total time: 102.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.812989 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.186873 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 0.1183 0.1516 0.0333 0.009 1.0 3.2 0.5 0.0 0 0.906 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.83 15.16 3.33 4.310 21.414 0.187 4.999 11.60 15.38 3.78 4.944 21.336 0.187 4.980 Individual atomic B min max mean iso aniso Overall: 6.18 104.30 20.74 4.85 1920 0 Protein: 6.18 104.30 16.89 4.84 1519 0 Water: 8.62 62.28 35.36 N/A 393 0 Other: 25.02 46.26 33.59 N/A 8 0 Chain A: 6.18 104.30 18.72 N/A 1737 0 Chain S: 14.95 62.28 39.89 N/A 183 0 Histogram: Values Number of atoms 6.18 - 16.00 1061 16.00 - 25.81 344 25.81 - 35.62 219 35.62 - 45.43 169 45.43 - 55.24 82 55.24 - 65.05 31 65.05 - 74.86 5 74.86 - 84.68 4 84.68 - 94.49 3 94.49 - 104.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1538 r_work=0.1161 r_free=0.1540 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1161 r_free = 0.1540 target_work(ml) = 4.980 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1154 r_free = 0.1540 target_work(ml) = 4.975 | | occupancies: max = 1.00 min = 0.19 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= 0.1154 r_free= 0.1540 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ml) (work): 4.974671 | | target function (ml) not normalized (work): 80758.810692 | | target function (ml) not normalized (free): 4189.094350 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1173 0.1154 0.1540 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1678 0.1670 0.1866 n_refl.: 17041 remove outliers: r(all,work,free)=0.1678 0.1670 0.1866 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1653 0.1644 0.1853 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1172 0.1153 0.1534 n_refl.: 17041 remove outliers: r(all,work,free)=0.1171 0.1152 0.1534 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 0.3450 297.462 280.815 0.564 1.005 0.340 11.894-9.307 99.02 97 4 0.1877 489.269 481.813 0.913 1.007 0.312 9.237-7.194 100.00 213 7 0.1792 400.172 401.632 0.983 1.007 0.245 7.162-5.571 100.00 427 22 0.1628 300.330 295.108 0.940 1.006 0.241 5.546-4.326 100.00 867 58 0.0931 412.305 408.691 0.964 1.005 0.211 4.315-3.360 100.00 1859 96 0.0892 392.106 389.952 1.013 1.004 0.201 3.356-2.611 100.00 3867 181 0.1272 257.591 255.496 1.012 1.000 0.121 2.608-2.000 99.99 8818 434 0.1112 167.905 166.467 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1751 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1152 r_free=0.1534 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1152 r_free=0.1534 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1152 r_free=0.1534 | n_water=393 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1152 r_free=0.1534 | n_water=393 | time (s): 30.690 (total time: 31.590) Filter (q & B) r_work=0.1152 r_free=0.1534 | n_water=393 | time (s): 0.950 (total time: 32.540) Compute maps r_work=0.1152 r_free=0.1534 | n_water=393 | time (s): 0.660 (total time: 33.200) Filter (map) r_work=0.1199 r_free=0.1561 | n_water=310 | time (s): 1.550 (total time: 34.750) Find peaks r_work=0.1199 r_free=0.1561 | n_water=310 | time (s): 0.460 (total time: 35.210) Add new water r_work=0.1337 r_free=0.1651 | n_water=445 | time (s): 1.640 (total time: 36.850) Refine new water occ: r_work=0.1178 r_free=0.1503 adp: r_work=0.1168 r_free=0.1507 occ: r_work=0.1158 r_free=0.1490 adp: r_work=0.1147 r_free=0.1493 occ: r_work=0.1144 r_free=0.1486 adp: r_work=0.1135 r_free=0.1486 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1486 r_work=0.1135 r_free=0.1486 | n_water=445 | time (s): 30.070 (total time: 66.920) Filter (q & B) r_work=0.1138 r_free=0.1493 | n_water=434 | time (s): 1.760 (total time: 68.680) Filter (dist only) r_work=0.1138 r_free=0.1492 | n_water=433 | time (s): 33.710 (total time: 102.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.010301 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.157477 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 0.1125 0.1537 0.0411 0.010 1.0 3.5 0.5 0.0 0 1.005 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.25 15.37 4.11 4.580 20.978 0.157 4.961 11.15 15.24 4.09 4.685 20.954 0.157 4.952 Individual atomic B min max mean iso aniso Overall: 5.42 101.02 20.78 4.80 1960 0 Protein: 5.42 101.02 16.42 4.79 1519 0 Water: 8.10 63.60 35.86 N/A 433 0 Other: 24.67 44.66 31.99 N/A 8 0 Chain A: 5.42 101.02 18.18 N/A 1737 0 Chain S: 17.59 63.60 41.08 N/A 223 0 Histogram: Values Number of atoms 5.42 - 14.98 1009 14.98 - 24.54 390 24.54 - 34.10 202 34.10 - 43.66 199 43.66 - 53.22 103 53.22 - 62.78 39 62.78 - 72.34 7 72.34 - 81.90 6 81.90 - 91.46 2 91.46 - 101.02 3 =========================== Idealize ADP of riding H ========================== r_work=0.1115 r_free=0.1524 r_work=0.1115 r_free=0.1525 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1115 r_free = 0.1525 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1110 r_free = 0.1534 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1110 r_free= 0.1534 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.951611 | | target function (ml) not normalized (work): 80379.496907 | | target function (ml) not normalized (free): 4183.096471 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1110 0.1534 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1601 0.1588 0.1864 n_refl.: 17040 remove outliers: r(all,work,free)=0.1601 0.1588 0.1864 n_refl.: 17040 overall B=-0.26 to atoms: r(all,work,free)=0.1585 0.1572 0.1856 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1108 0.1532 n_refl.: 17040 remove outliers: r(all,work,free)=0.1129 0.1108 0.1532 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 0.3680 297.462 273.383 0.546 1.003 0.340 11.894-9.307 99.02 97 4 0.1765 489.269 483.993 0.914 1.004 0.320 9.237-7.194 100.00 213 7 0.1715 400.172 400.127 0.985 1.004 0.230 7.162-5.571 100.00 427 22 0.1575 300.330 295.614 0.941 1.004 0.220 5.546-4.326 100.00 867 58 0.0903 412.305 409.116 0.963 1.004 0.211 4.315-3.360 100.00 1859 96 0.0845 392.106 389.861 1.006 1.003 0.201 3.356-2.611 100.00 3867 181 0.1233 257.591 255.271 1.002 1.001 0.131 2.608-2.000 99.99 8818 434 0.1063 167.905 166.738 0.997 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8931 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1108 r_free=0.1532 After: r_work=0.1110 r_free=0.1529 ================================== NQH flips ================================== r_work=0.1110 r_free=0.1529 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1110 r_free=0.1529 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1110 r_free=0.1529 | n_water=433 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1114 r_free=0.1530 | n_water=431 | time (s): 34.280 (total time: 34.880) Filter (q & B) r_work=0.1114 r_free=0.1530 | n_water=431 | time (s): 1.110 (total time: 35.990) Compute maps r_work=0.1114 r_free=0.1530 | n_water=431 | time (s): 0.570 (total time: 36.560) Filter (map) r_work=0.1186 r_free=0.1543 | n_water=326 | time (s): 1.650 (total time: 38.210) Find peaks r_work=0.1186 r_free=0.1543 | n_water=326 | time (s): 0.470 (total time: 38.680) Add new water r_work=0.1310 r_free=0.1644 | n_water=454 | time (s): 1.500 (total time: 40.180) Refine new water occ: r_work=0.1153 r_free=0.1504 adp: r_work=0.1146 r_free=0.1501 occ: r_work=0.1132 r_free=0.1486 adp: r_work=0.1124 r_free=0.1484 occ: r_work=0.1118 r_free=0.1475 adp: r_work=0.1111 r_free=0.1473 ADP+occupancy (water only), MIN, final r_work=0.1111 r_free=0.1473 r_work=0.1111 r_free=0.1473 | n_water=454 | time (s): 32.230 (total time: 72.410) Filter (q & B) r_work=0.1114 r_free=0.1479 | n_water=446 | time (s): 1.630 (total time: 74.040) Filter (dist only) r_work=0.1114 r_free=0.1479 | n_water=445 | time (s): 35.450 (total time: 109.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.948015 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.177644 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 0.1129 0.1474 0.0345 0.010 1.0 4.5 0.5 0.0 0 0.974 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.29 14.74 3.45 4.517 20.669 0.178 4.947 11.19 14.70 3.51 4.630 20.713 0.178 4.942 Individual atomic B min max mean iso aniso Overall: 5.54 99.79 20.71 5.03 1972 0 Protein: 5.54 99.79 16.18 5.03 1519 0 Water: 7.83 65.08 35.98 N/A 445 0 Other: 24.46 43.51 31.37 N/A 8 0 Chain A: 5.54 99.79 17.89 N/A 1736 0 Chain S: 16.97 65.08 41.42 N/A 236 0 Histogram: Values Number of atoms 5.54 - 14.97 1035 14.97 - 24.39 358 24.39 - 33.82 207 33.82 - 43.24 197 43.24 - 52.67 119 52.67 - 62.09 33 62.09 - 71.52 13 71.52 - 80.94 2 80.94 - 90.37 4 90.37 - 99.79 4 =========================== Idealize ADP of riding H ========================== r_work=0.1119 r_free=0.1470 r_work=0.1118 r_free=0.1470 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1118 r_free = 0.1470 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1111 r_free = 0.1475 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1111 r_free= 0.1475 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.938726 | | target function (ml) not normalized (work): 80170.338160 | | target function (ml) not normalized (free): 4159.905418 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1115 0.1333 5.4618 5.6515| | 2: 3.63 - 2.88 1.00 2711 122 0.1085 0.1450 5.2182 5.3313| | 3: 2.88 - 2.52 1.00 2681 148 0.1369 0.1700 5.1263 5.2023| | 4: 2.52 - 2.29 1.00 2661 139 0.0954 0.1463 4.6361 4.9254| | 5: 2.29 - 2.13 1.00 2678 122 0.0979 0.1412 4.5891 4.8822| | 6: 2.13 - 2.00 1.00 2692 117 0.1118 0.1771 4.5715 4.7922| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.95 8.91 1.00 0.96 6190.31| | 2: 3.63 - 2.88 2711 122 0.93 12.60 1.01 0.96 6190.31| | 3: 2.88 - 2.52 2681 148 0.88 18.63 0.99 0.96 6190.31| | 4: 2.52 - 2.29 2661 139 0.93 11.99 1.01 0.98 2120.13| | 5: 2.29 - 2.13 2678 122 0.91 14.07 1.00 0.98 2120.13| | 6: 2.13 - 2.00 2692 117 0.89 16.81 0.99 0.98 2120.13| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2120.13 max = 6190.31 mean = 4176.66| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.95 mean = 13.80| |phase err.(test): min = 0.00 max = 89.72 mean = 13.30| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1128 0.1111 0.1475 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1583 0.1572 0.1823 n_refl.: 17040 remove outliers: r(all,work,free)=0.1583 0.1572 0.1823 n_refl.: 17040 overall B=-0.21 to atoms: r(all,work,free)=0.1571 0.1560 0.1816 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1111 0.1476 n_refl.: 17040 remove outliers: r(all,work,free)=0.1129 0.1111 0.1476 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 0.3730 297.462 274.007 0.543 1.002 0.330 11.894-9.307 99.02 97 4 0.1721 489.269 484.973 0.922 1.003 0.330 9.237-7.194 100.00 213 7 0.1720 400.172 401.001 0.992 1.003 0.230 7.162-5.571 100.00 427 22 0.1573 300.330 294.829 0.940 1.003 0.220 5.546-4.326 100.00 867 58 0.0919 412.305 409.510 0.965 1.003 0.190 4.315-3.360 100.00 1859 96 0.0872 392.106 389.757 1.003 1.002 0.191 3.356-2.611 100.00 3867 181 0.1238 257.591 255.126 0.998 1.001 0.121 2.608-2.000 99.99 8818 434 0.1051 167.905 166.577 0.987 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7261 ================= 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 : 0.2791 0.1837 0.080 5.304 8.8 119.3 19.9 258 0.000 1_bss: 0.1608 0.1686 0.080 5.304 8.4 118.9 19.5 258 0.000 1_settarget: 0.1608 0.1686 0.080 5.304 8.4 118.9 19.5 258 0.000 1_nqh: 0.1608 0.1686 0.080 5.304 8.4 118.9 19.5 258 0.000 1_weight: 0.1608 0.1686 0.080 5.304 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1348 0.1630 0.009 0.971 8.4 118.9 19.5 258 0.139 1_adp: 0.1275 0.1649 0.009 0.971 6.1 113.9 19.9 258 0.139 1_regHadp: 0.1278 0.1655 0.009 0.971 6.1 113.9 19.9 258 0.139 1_occ: 0.1274 0.1649 0.009 0.971 6.1 113.9 19.9 258 0.139 2_bss: 0.1271 0.1646 0.009 0.971 5.7 113.5 19.6 258 0.139 2_settarget: 0.1271 0.1646 0.009 0.971 5.7 113.5 19.6 258 0.139 2_updatecdl: 0.1271 0.1646 0.009 0.999 5.7 113.5 19.6 258 0.139 2_nqh: 0.1271 0.1646 0.009 0.999 5.7 113.5 19.6 258 0.139 2_sol: 0.1249 0.1545 0.009 0.999 5.7 112.8 20.8 353 n/a 2_weight: 0.1249 0.1545 0.009 0.999 5.7 112.8 20.8 353 n/a 2_xyzrec: 0.1217 0.1590 0.009 0.951 5.7 112.8 20.8 353 n/a 2_adp: 0.1201 0.1604 0.009 0.951 7.0 107.8 21.3 353 n/a 2_regHadp: 0.1203 0.1604 0.009 0.951 7.0 107.8 21.3 353 n/a 2_occ: 0.1200 0.1609 0.009 0.951 7.0 107.8 21.3 353 n/a 3_bss: 0.1196 0.1604 0.009 0.951 6.6 107.4 20.9 353 n/a 3_settarget: 0.1196 0.1604 0.009 0.951 6.6 107.4 20.9 353 n/a 3_updatecdl: 0.1196 0.1604 0.009 0.947 6.6 107.4 20.9 353 n/a 3_nqh: 0.1196 0.1606 0.009 0.947 6.6 107.4 20.9 353 n/a 3_sol: 0.1198 0.1509 0.009 0.947 6.6 107.4 20.9 393 n/a 3_weight: 0.1198 0.1509 0.009 0.947 6.6 107.4 20.9 393 n/a 3_xyzrec: 0.1183 0.1516 0.009 0.963 6.6 107.4 20.9 393 n/a 3_adp: 0.1160 0.1538 0.009 0.963 6.2 104.3 20.7 393 n/a 3_regHadp: 0.1161 0.1540 0.009 0.963 6.2 104.3 20.7 393 n/a 3_occ: 0.1154 0.1540 0.009 0.963 6.2 104.3 20.7 393 n/a 4_bss: 0.1152 0.1534 0.009 0.963 5.8 103.9 20.4 393 n/a 4_settarget: 0.1152 0.1534 0.009 0.963 5.8 103.9 20.4 393 n/a 4_updatecdl: 0.1152 0.1534 0.009 0.963 5.8 103.9 20.4 393 n/a 4_nqh: 0.1152 0.1534 0.009 0.963 5.8 103.9 20.4 393 n/a 4_sol: 0.1138 0.1492 0.009 0.963 5.8 103.9 20.8 433 n/a 4_weight: 0.1138 0.1492 0.009 0.963 5.8 103.9 20.8 433 n/a 4_xyzrec: 0.1125 0.1537 0.010 0.993 5.8 103.9 20.8 433 n/a 4_adp: 0.1115 0.1524 0.010 0.993 5.4 101.0 20.8 433 n/a 4_regHadp: 0.1115 0.1525 0.010 0.993 5.4 101.0 20.8 433 n/a 4_occ: 0.1110 0.1534 0.010 0.993 5.4 101.0 20.8 433 n/a 5_bss: 0.1108 0.1532 0.010 0.993 5.2 100.8 20.5 433 n/a 5_settarget: 0.1108 0.1532 0.010 0.993 5.2 100.8 20.5 433 n/a 5_updatecdl: 0.1108 0.1532 0.010 0.994 5.2 100.8 20.5 433 n/a 5_setrh: 0.1110 0.1529 0.010 0.994 5.2 100.8 20.5 433 n/a 5_nqh: 0.1110 0.1529 0.010 0.994 5.2 100.8 20.5 433 n/a 5_sol: 0.1114 0.1479 0.010 0.994 5.2 100.8 20.6 445 n/a 5_weight: 0.1114 0.1479 0.010 0.994 5.2 100.8 20.6 445 n/a 5_xyzrec: 0.1129 0.1474 0.010 1.042 5.2 100.8 20.6 445 n/a 5_adp: 0.1119 0.1470 0.010 1.042 5.5 99.8 20.7 445 n/a 5_regHadp: 0.1118 0.1470 0.010 1.042 5.5 99.8 20.7 445 n/a 5_occ: 0.1111 0.1475 0.010 1.042 5.5 99.8 20.7 445 n/a end: 0.1111 0.1476 0.010 1.042 5.3 99.6 20.5 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5638674_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5638674_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9100 Refinement macro-cycles (run) : 920.5000 Write final files (write_after_run_outputs) : 21.1400 Total : 945.5500 Total CPU time: 16.12 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:09 PST -0800 (1735494069.25 s) Start R-work = 0.1608, R-free = 0.1686 Final R-work = 0.1111, R-free = 0.1476 =============================================================================== Job complete usr+sys time: 990.46 seconds wall clock time: 16 minutes 53.93 seconds (1013.93 seconds total)