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_9255201.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9255201.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9255201.pdb" 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 = 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 3 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: 1.73, per 1000 atoms: 0.51 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: 0.57 Conformation dependent library (CDL) restraints added in 182.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.93: 647 0.93 - 1.19: 1037 1.19 - 1.46: 743 1.46 - 1.72: 709 1.72 - 1.98: 17 Bond restraints: 3153 Sorted by residual: bond pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 1.520 1.342 0.178 7.00e-03 2.04e+04 6.43e+02 bond pdb=" N BLEU A 153 " pdb=" CA BLEU A 153 " ideal model delta sigma weight residual 1.456 1.687 -0.230 1.21e-02 6.83e+03 3.62e+02 bond pdb=" C LEU A 7 " pdb=" O LEU A 7 " ideal model delta sigma weight residual 1.236 1.025 0.211 1.14e-02 7.69e+03 3.41e+02 bond pdb=" N VAL A 25 " pdb=" CA VAL A 25 " ideal model delta sigma weight residual 1.461 1.666 -0.206 1.19e-02 7.06e+03 2.99e+02 bond pdb=" N ARG A 28 " pdb=" CA ARG A 28 " ideal model delta sigma weight residual 1.459 1.676 -0.218 1.28e-02 6.10e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.16: 3405 5.16 - 10.31: 1802 10.31 - 15.47: 494 15.47 - 20.62: 69 20.62 - 25.78: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 121.38 105.91 15.47 8.20e-01 1.49e+00 3.56e+02 angle pdb=" CA HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 118.83 131.47 -12.64 8.70e-01 1.32e+00 2.11e+02 angle pdb=" O VAL A 23 " pdb=" C VAL A 23 " pdb=" N ASP A 24 " ideal model delta sigma weight residual 121.94 136.77 -14.83 1.03e+00 9.43e-01 2.07e+02 angle pdb=" OE1 GLN A 95 " pdb=" CD GLN A 95 " pdb=" NE2 GLN A 95 " ideal model delta sigma weight residual 122.60 136.83 -14.23 1.00e+00 1.00e+00 2.03e+02 angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 131.68 -12.48 9.00e-01 1.23e+00 1.92e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 1287 16.03 - 32.06: 127 32.06 - 48.09: 47 48.09 - 64.12: 17 64.12 - 80.15: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 69 " pdb=" N VAL A 69 " pdb=" CA VAL A 69 " pdb=" CB VAL A 69 " ideal model delta harmonic sigma weight residual -122.00 -141.43 19.43 0 2.50e+00 1.60e-01 6.04e+01 dihedral pdb=" C GLU A 59 " pdb=" N GLU A 59 " pdb=" CA GLU A 59 " pdb=" CB GLU A 59 " ideal model delta harmonic sigma weight residual -122.60 -141.77 19.17 0 2.50e+00 1.60e-01 5.88e+01 dihedral pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CA GLU A 59 " pdb=" CB GLU A 59 " ideal model delta harmonic sigma weight residual 122.80 141.11 -18.31 0 2.50e+00 1.60e-01 5.36e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 106 0.219 - 0.438: 72 0.438 - 0.657: 38 0.657 - 0.876: 19 0.876 - 1.095: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -3.72 1.09 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA ALA A 14 " pdb=" N ALA A 14 " pdb=" C ALA A 14 " pdb=" CB ALA A 14 " both_signs ideal model delta sigma weight residual False 2.48 3.53 -1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" CA BGLU A 64 " pdb=" N BGLU A 64 " pdb=" C BGLU A 64 " pdb=" CB BGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.072 2.00e-02 2.50e+03 7.07e-02 1.13e+02 pdb=" CG HIS A 115 " 0.112 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.096 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.098 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " -0.034 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.005 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG BTYR A 67 " -0.013 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.100 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.040 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.109 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.048 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.060 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " 0.201 9.50e-02 1.11e+02 8.74e-02 7.56e+01 pdb=" NE ARG A 145 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.082 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " -0.091 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " 0.016 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " 0.081 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.065 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " 0.018 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 760 2.28 - 2.86: 7840 2.86 - 3.44: 10641 3.44 - 4.02: 15227 4.02 - 4.60: 22108 Nonbonded interactions: 56576 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.696 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.736 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.763 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.837 2.100 nonbonded pdb=" H GLU A 147 " pdb=" O THR A 154 " model vdw 1.837 2.450 ... (remaining 56571 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_9255201_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= 0.3620 r_free= 0.1997 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468605 | | target function (ml) not normalized (work): 22030.223015 | | target function (ml) not normalized (free): 1141.167521 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3811 0.2233 4.8503 4.8923| | 2: 3.78 - 3.00 1.00 2430 110 0.3386 0.1598 4.0759 4.0587| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.76 0.83 0.13 6607.00| | 2: 3.78 - 3.00 2430 110 0.94 11.28 1.48 0.26 447.62| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 381.11 max = 12073.88 mean = 3571.04| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.28| |phase err.(test): min = 0.00 max = 89.97 mean = 33.41| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.303 1557 Z= 5.547 Angle : 5.376 15.872 2118 Z= 3.761 Chirality : 0.394 1.095 243 Planarity : 0.029 0.122 284 Dihedral : 13.828 80.154 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 31.35 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.48), residues: 224 helix: -2.71 (0.35), residues: 109 sheet: 0.13 (1.00), residues: 28 loop : -0.30 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.094 0.020 ARG A 27 TYR 0.049 0.023 TYR A 139 PHE 0.103 0.039 PHE A 119 HIS 0.056 0.029 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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3620 r_free= 0.1997 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468605 | | target function (ml) not normalized (work): 22030.223015 | | target function (ml) not normalized (free): 1141.167521 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3575 0.3652 0.2112 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3575 0.3652 0.2112 n_refl.: 5182 remove outliers: r(all,work,free)=0.2516 0.2541 0.2112 n_refl.: 5178 overall B=-2.51 to atoms: r(all,work,free)=0.2420 0.2441 0.2066 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1564 0.1566 0.1537 n_refl.: 5178 remove outliers: r(all,work,free)=0.1557 0.1559 0.1537 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 96.81 86 5 0.3849 447.606 400.048 0.628 1.061 0.381 11.894-9.307 99.02 97 4 0.1803 713.968 696.913 0.915 1.059 0.382 9.237-7.194 100.00 213 7 0.2191 583.884 575.385 0.941 1.053 0.363 7.162-5.571 100.00 427 22 0.2338 438.134 423.481 0.908 1.041 0.297 5.546-4.326 100.00 867 58 0.1390 601.496 592.914 0.952 1.022 0.218 4.315-3.360 100.00 1859 96 0.1313 572.029 566.460 1.024 0.990 0.196 3.356-3.002 100.00 1373 60 0.1589 440.601 432.400 1.040 0.958 0.064 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9180 b_overall=-4.3134 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1559 r_free=0.1537 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1562 r_free=0.1533 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.319434 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.713515 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 0.1147 0.1773 0.0626 0.010 1.0 1.9 0.5 0.0 0 9.660 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.47 17.73 6.26 3.012 16.352 1.714 0.017 10.07 17.62 7.56 4.836 16.590 1.714 0.014 Individual atomic B min max mean iso aniso Overall: 2.03 111.79 17.83 5.16 1785 0 Protein: 2.03 111.51 15.13 5.16 1519 0 Water: 4.36 111.79 33.50 N/A 258 0 Other: 17.63 35.29 24.30 N/A 8 0 Chain A: 2.03 111.79 17.83 N/A 1785 0 Histogram: Values Number of atoms 2.03 - 13.01 875 13.01 - 23.99 517 23.99 - 34.96 192 34.96 - 45.94 113 45.94 - 56.91 56 56.91 - 67.89 15 67.89 - 78.86 8 78.86 - 89.84 5 89.84 - 100.82 1 100.82 - 111.79 3 =========================== Idealize ADP of riding H ========================== r_work=0.1007 r_free=0.1762 r_work=0.1001 r_free=0.1766 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1001 r_free = 0.1766 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 = 0.0993 r_free = 0.1776 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0993 r_free= 0.1776 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.013514 | | target function (ls_wunit_k1) not normalized (work): 66.515329 | | target function (ls_wunit_k1) not normalized (free): 10.016640 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1032 0.0993 0.1776 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2012 0.2004 0.2248 n_refl.: 5174 remove outliers: r(all,work,free)=0.2012 0.2004 0.2248 n_refl.: 5174 overall B=-0.92 to atoms: r(all,work,free)=0.1975 0.1965 0.2237 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.1035 0.0996 0.1790 n_refl.: 5174 remove outliers: r(all,work,free)=0.1035 0.0996 0.1790 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 0.3207 316.962 297.854 0.638 0.999 0.360 11.894-9.307 99.02 97 4 0.1499 505.581 499.220 0.958 1.002 0.357 9.237-7.194 100.00 213 7 0.1606 413.465 414.422 0.997 1.002 0.315 7.162-5.571 100.00 427 22 0.1631 310.255 306.462 0.955 1.002 0.292 5.546-4.326 100.00 867 58 0.0889 425.936 422.883 0.966 1.001 0.202 4.315-3.360 100.00 1859 96 0.0754 405.070 405.168 1.011 0.999 0.193 3.356-3.002 100.00 1373 60 0.0992 312.002 310.493 0.988 0.998 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.1353 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0996 r_free=0.1790 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0996 r_free=0.1790 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0996 r_free=0.1790 | n_water=258 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1027 r_free=0.1785 | n_water=247 | time (s): 20.640 (total time: 21.300) Filter (q & B) r_work=0.1027 r_free=0.1786 | n_water=244 | time (s): 1.540 (total time: 22.840) Compute maps r_work=0.1027 r_free=0.1786 | n_water=244 | time (s): 0.450 (total time: 23.290) Filter (map) r_work=0.1307 r_free=0.1879 | n_water=148 | time (s): 1.380 (total time: 24.670) Find peaks r_work=0.1307 r_free=0.1879 | n_water=148 | time (s): 0.470 (total time: 25.140) Add new water r_work=0.1675 r_free=0.2149 | n_water=238 | time (s): 1.430 (total time: 26.570) Refine new water occ: r_work=0.1145 r_free=0.1680 adp: r_work=0.1118 r_free=0.1682 occ: r_work=0.1115 r_free=0.1669 adp: r_work=0.1104 r_free=0.1674 occ: r_work=0.1104 r_free=0.1662 adp: r_work=0.1104 r_free=0.1662 ADP+occupancy (water only), MIN, final r_work=0.1104 r_free=0.1662 r_work=0.1104 r_free=0.1662 | n_water=238 | time (s): 3.610 (total time: 30.180) Filter (q & B) r_work=0.1104 r_free=0.1662 | n_water=238 | time (s): 0.770 (total time: 30.950) Filter (dist only) r_work=0.1108 r_free=0.1658 | n_water=233 | time (s): 18.370 (total time: 49.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.537790 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.575787 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 0.0987 0.1803 0.0817 0.009 1.0 4.2 0.5 0.0 0 11.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.87 18.03 8.17 4.618 17.231 2.576 0.013 9.20 18.21 9.00 5.350 17.674 2.576 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.78 17.05 6.36 1760 0 Protein: 0.00 107.78 15.59 6.35 1519 0 Water: 0.00 63.68 26.36 N/A 233 0 Other: 11.96 33.53 23.59 N/A 8 0 Chain A: 0.00 107.78 16.27 N/A 1672 0 Chain S: 3.46 58.67 31.89 N/A 88 0 Histogram: Values Number of atoms 0.00 - 10.78 610 10.78 - 21.56 732 21.56 - 32.33 224 32.33 - 43.11 120 43.11 - 53.89 37 53.89 - 64.67 24 64.67 - 75.44 6 75.44 - 86.22 3 86.22 - 97.00 2 97.00 - 107.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.0920 r_free=0.1821 r_work=0.0917 r_free=0.1823 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0917 r_free = 0.1823 target_work(ls_wunit_k1) = 0.011 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0917 r_free = 0.1831 target_work(ls_wunit_k1) = 0.011 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0917 r_free= 0.1831 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011219 | | target function (ls_wunit_k1) not normalized (work): 55.220465 | | target function (ls_wunit_k1) not normalized (free): 9.962355 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0962 0.0917 0.1831 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2050 0.2047 0.2221 n_refl.: 5174 remove outliers: r(all,work,free)=0.2050 0.2047 0.2221 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2050 0.2047 0.2221 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0962 0.0916 0.1841 n_refl.: 5174 remove outliers: r(all,work,free)=0.0962 0.0916 0.1841 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 0.3172 316.962 302.983 0.677 1.003 0.360 11.894-9.307 99.02 97 4 0.1427 505.581 501.786 0.987 1.005 0.346 9.237-7.194 100.00 213 7 0.1388 413.465 414.486 1.027 1.006 0.300 7.162-5.571 100.00 427 22 0.1356 310.255 307.561 0.996 1.005 0.290 5.546-4.326 100.00 867 58 0.0785 425.936 423.364 1.012 1.003 0.240 4.315-3.360 100.00 1859 96 0.0710 405.070 404.988 1.061 0.999 0.200 3.356-3.002 100.00 1373 60 0.0955 312.002 311.395 1.042 0.996 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.5542 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0916 r_free=0.1841 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0917 r_free=0.1840 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0917 r_free=0.1840 | n_water=233 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.0938 r_free=0.1820 | n_water=227 | time (s): 20.150 (total time: 20.790) Filter (q & B) r_work=0.0997 r_free=0.1844 | n_water=225 | time (s): 1.980 (total time: 22.770) Compute maps r_work=0.0997 r_free=0.1844 | n_water=225 | time (s): 0.580 (total time: 23.350) Filter (map) r_work=0.1252 r_free=0.1834 | n_water=153 | time (s): 1.520 (total time: 24.870) Find peaks r_work=0.1252 r_free=0.1834 | n_water=153 | time (s): 0.590 (total time: 25.460) Add new water r_work=0.1627 r_free=0.2142 | n_water=233 | time (s): 1.790 (total time: 27.250) Refine new water r_work=0.1627 r_free=0.2142 | n_water=233 | time (s): 0.080 (total time: 27.330) Filter (q & B) r_work=0.1252 r_free=0.1834 | n_water=153 | time (s): 1.430 (total time: 28.760) Filter (dist only) r_work=0.1279 r_free=0.1845 | n_water=145 | time (s): 11.910 (total time: 40.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.365487 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.255632 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 0.1144 0.1964 0.0820 0.012 1.1 4.5 0.5 1.2 0 0.683 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.44 19.64 8.20 5.372 18.115 0.256 5.366 10.75 19.73 8.98 7.403 18.096 0.256 5.272 Individual atomic B min max mean iso aniso Overall: 0.00 105.87 16.27 8.73 1672 0 Protein: 0.00 105.87 15.56 8.73 1519 0 Water: 0.55 58.68 23.36 N/A 145 0 Other: 6.96 31.48 22.21 N/A 8 0 Chain A: 0.00 105.87 16.14 N/A 1655 0 Chain S: 0.55 46.73 28.86 N/A 17 0 Histogram: Values Number of atoms 0.00 - 10.59 606 10.59 - 21.17 679 21.17 - 31.76 220 31.76 - 42.35 94 42.35 - 52.94 39 52.94 - 63.52 15 63.52 - 74.11 11 74.11 - 84.70 3 84.70 - 95.28 3 95.28 - 105.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.1075 r_free=0.1973 r_work=0.1080 r_free=0.1987 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1080 r_free = 0.1987 target_work(ml) = 5.274 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1078 r_free = 0.1978 target_work(ml) = 5.273 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.1078 r_free= 0.1978 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ml) (work): 5.272544 | | target function (ml) not normalized (work): 25951.463195 | | target function (ml) not normalized (free): 1686.409173 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1078 0.1978 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2335 0.2337 0.2426 n_refl.: 5174 remove outliers: r(all,work,free)=0.2335 0.2337 0.2426 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2335 0.2337 0.2426 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.1106 0.1057 0.2014 n_refl.: 5174 remove outliers: r(all,work,free)=0.1106 0.1057 0.2014 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 0.3497 316.962 298.840 0.688 0.998 0.370 11.894-9.307 99.02 97 4 0.1701 505.581 494.851 0.966 1.002 0.350 9.237-7.194 100.00 213 7 0.1811 413.465 407.192 0.991 1.003 0.330 7.162-5.571 100.00 427 22 0.1749 310.255 304.921 0.978 1.003 0.330 5.546-4.326 100.00 867 58 0.1059 425.936 420.912 0.983 1.002 0.290 4.315-3.360 100.00 1859 96 0.0777 405.070 403.631 1.051 1.000 0.240 3.356-3.002 100.00 1373 60 0.0950 312.002 309.861 1.048 0.998 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.3655 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1057 r_free=0.2014 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1057 r_free=0.2015 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1057 r_free=0.2015 | n_water=145 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1060 r_free=0.2010 | n_water=144 | time (s): 11.750 (total time: 12.350) Filter (q & B) r_work=0.1066 r_free=0.2011 | n_water=143 | time (s): 1.820 (total time: 14.170) Compute maps r_work=0.1066 r_free=0.2011 | n_water=143 | time (s): 0.550 (total time: 14.720) Filter (map) r_work=0.1131 r_free=0.1968 | n_water=131 | time (s): 1.470 (total time: 16.190) Find peaks r_work=0.1131 r_free=0.1968 | n_water=131 | time (s): 0.470 (total time: 16.660) Add new water r_work=0.1438 r_free=0.2255 | n_water=190 | time (s): 1.150 (total time: 17.810) Refine new water occ: r_work=0.1114 r_free=0.2028 adp: r_work=0.1116 r_free=0.2043 occ: r_work=0.1100 r_free=0.2017 adp: r_work=0.1101 r_free=0.2032 occ: r_work=0.1085 r_free=0.2005 adp: r_work=0.1086 r_free=0.2018 ADP+occupancy (water only), MIN, final r_work=0.1086 r_free=0.2018 r_work=0.1086 r_free=0.2018 | n_water=190 | time (s): 10.610 (total time: 28.420) Filter (q & B) r_work=0.1086 r_free=0.2024 | n_water=187 | time (s): 1.260 (total time: 29.680) Filter (dist only) r_work=0.1087 r_free=0.2024 | n_water=186 | time (s): 14.530 (total time: 44.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.180230 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.215698 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 0.1018 0.2062 0.1044 0.012 1.1 4.2 0.5 1.2 0 0.590 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.18 20.62 10.44 6.845 18.325 0.216 5.166 9.92 20.45 10.53 8.081 18.335 0.216 5.108 Individual atomic B min max mean iso aniso Overall: 0.00 105.29 16.82 10.23 1713 0 Protein: 0.00 105.29 15.76 10.23 1519 0 Water: 0.00 59.97 25.23 N/A 186 0 Other: 3.77 31.96 22.21 N/A 8 0 Chain A: 0.00 105.29 16.23 N/A 1644 0 Chain S: 9.95 59.97 30.92 N/A 69 0 Histogram: Values Number of atoms 0.00 - 10.53 619 10.53 - 21.06 628 21.06 - 31.59 279 31.59 - 42.12 103 42.12 - 52.65 47 52.65 - 63.18 16 63.18 - 73.70 10 73.70 - 84.23 6 84.23 - 94.76 2 94.76 - 105.29 3 =========================== Idealize ADP of riding H ========================== r_work=0.0992 r_free=0.2045 r_work=0.0996 r_free=0.2049 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0996 r_free = 0.2049 target_work(ml) = 5.113 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0964 r_free = 0.2003 target_work(ml) = 5.090 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0964 r_free= 0.2003 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 5.089553 | | target function (ml) not normalized (work): 25050.781117 | | target function (ml) not normalized (free): 1880.440635 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1017 0.0964 0.2003 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2284 0.2282 0.2416 n_refl.: 5174 remove outliers: r(all,work,free)=0.2284 0.2282 0.2416 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2284 0.2282 0.2416 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.1013 0.0961 0.1991 n_refl.: 5174 remove outliers: r(all,work,free)=0.1013 0.0961 0.1991 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 0.3754 316.962 293.567 0.628 0.989 0.333 11.894-9.307 99.02 97 4 0.1796 505.581 492.642 0.978 0.994 0.336 9.237-7.194 100.00 213 7 0.2040 413.465 403.900 1.010 0.996 0.332 7.162-5.571 100.00 427 22 0.1946 310.255 302.759 0.994 0.998 0.330 5.546-4.326 100.00 867 58 0.1063 425.936 421.130 1.012 0.999 0.280 4.315-3.360 100.00 1859 96 0.0653 405.070 404.395 1.085 1.001 0.250 3.356-3.002 100.00 1373 60 0.0615 312.002 311.760 1.080 1.003 0.056 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.0287 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0961 r_free=0.1991 After: r_work=0.0964 r_free=0.1991 ================================== NQH flips ================================== r_work=0.0964 r_free=0.1991 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0964 r_free=0.1991 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0964 r_free=0.1991 | n_water=186 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.0970 r_free=0.1989 | n_water=184 | time (s): 14.480 (total time: 15.150) Filter (q & B) r_work=0.1003 r_free=0.1993 | n_water=183 | time (s): 1.730 (total time: 16.880) Compute maps r_work=0.1003 r_free=0.1993 | n_water=183 | time (s): 0.520 (total time: 17.400) Filter (map) r_work=0.1174 r_free=0.2015 | n_water=134 | time (s): 1.420 (total time: 18.820) Find peaks r_work=0.1174 r_free=0.2015 | n_water=134 | time (s): 0.480 (total time: 19.300) Add new water r_work=0.1437 r_free=0.2133 | n_water=188 | time (s): 1.320 (total time: 20.620) Refine new water occ: r_work=0.1043 r_free=0.2000 adp: r_work=0.1041 r_free=0.1999 occ: r_work=0.1031 r_free=0.1991 adp: r_work=0.1031 r_free=0.1996 occ: r_work=0.1022 r_free=0.1987 adp: r_work=0.1022 r_free=0.1991 ADP+occupancy (water only), MIN, final r_work=0.1022 r_free=0.1991 r_work=0.1022 r_free=0.1991 | n_water=188 | time (s): 11.810 (total time: 32.430) Filter (q & B) r_work=0.1024 r_free=0.1996 | n_water=184 | time (s): 1.220 (total time: 33.650) Filter (dist only) r_work=0.1027 r_free=0.1994 | n_water=182 | time (s): 14.300 (total time: 47.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.115244 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.214846 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 0.0994 0.1991 0.0997 0.011 1.2 8.3 0.5 1.2 0 0.558 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.94 19.91 9.97 7.808 18.327 0.215 5.103 9.74 19.93 10.20 8.604 18.436 0.215 5.057 Individual atomic B min max mean iso aniso Overall: 0.00 102.98 16.96 11.21 1709 0 Protein: 0.00 102.98 16.10 11.22 1519 0 Water: 0.02 58.56 23.90 N/A 182 0 Other: 6.34 32.33 21.91 N/A 8 0 Chain A: 0.00 102.98 16.46 N/A 1633 0 Chain S: 3.06 58.56 27.80 N/A 76 0 Histogram: Values Number of atoms 0.00 - 10.30 585 10.30 - 20.60 616 20.60 - 30.90 316 30.90 - 41.19 110 41.19 - 51.49 41 51.49 - 61.79 16 61.79 - 72.09 12 72.09 - 82.39 8 82.39 - 92.69 2 92.69 - 102.98 3 =========================== Idealize ADP of riding H ========================== r_work=0.0974 r_free=0.1993 r_work=0.0977 r_free=0.1999 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0977 r_free = 0.1999 target_work(ml) = 5.061 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0961 r_free = 0.1976 target_work(ml) = 5.053 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0961 r_free= 0.1976 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.052717 | | target function (ml) not normalized (work): 24869.473776 | | target function (ml) not normalized (free): 1980.657379 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1308 0.1911 5.5407 6.1066| | 2: 3.78 - 3.00 1.00 2430 110 0.0539 0.2087 4.5523 10.123| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.92 12.12 1.00 0.95 11891.91| | 2: 3.78 - 3.00 2430 110 0.98 2.84 1.00 0.97 1303.79| |alpha: min = 0.94 max = 0.97 mean = 0.96| |beta: min = 878.89 max = 18988.68 mean = 6664.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.97 mean = 7.54| |phase err.(test): min = 0.00 max = 83.93 mean = 7.54| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1013 0.0961 0.1976 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2340 0.2336 0.2497 n_refl.: 5174 remove outliers: r(all,work,free)=0.2340 0.2336 0.2497 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2340 0.2336 0.2497 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.1011 0.0959 0.1984 n_refl.: 5174 remove outliers: r(all,work,free)=0.1011 0.0959 0.1984 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 0.3795 316.962 289.299 0.648 0.987 0.330 11.894-9.307 99.02 97 4 0.1880 505.581 491.578 1.032 0.993 0.360 9.237-7.194 100.00 213 7 0.2053 413.465 402.764 1.056 0.996 0.344 7.162-5.571 100.00 427 22 0.2007 310.255 302.902 1.034 0.997 0.330 5.546-4.326 100.00 867 58 0.1107 425.936 421.178 1.064 0.999 0.290 4.315-3.360 100.00 1859 96 0.0652 405.070 404.151 1.149 1.002 0.250 3.356-3.002 100.00 1373 60 0.0536 312.002 311.776 1.146 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.8231 ================= 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 : 0.3620 0.1997 0.084 5.376 8.8 119.3 19.9 258 0.000 1_bss: 0.1559 0.1537 0.084 5.376 6.3 116.8 17.4 258 0.000 1_settarget: 0.1559 0.1537 0.084 5.376 6.3 116.8 17.4 258 0.000 1_nqh: 0.1562 0.1533 0.084 5.376 6.3 116.8 17.4 258 0.003 1_weight: 0.1562 0.1533 0.084 5.376 6.3 116.8 17.4 258 0.003 1_xyzrec: 0.1147 0.1773 0.010 0.964 6.3 116.8 17.4 258 0.201 1_adp: 0.1007 0.1762 0.010 0.964 2.0 111.8 17.8 258 0.201 1_regHadp: 0.1001 0.1766 0.010 0.964 2.0 111.8 17.8 258 0.201 1_occ: 0.0993 0.1776 0.010 0.964 2.0 111.8 17.8 258 0.201 2_bss: 0.0996 0.1790 0.010 0.964 1.1 110.9 16.9 258 0.201 2_settarget: 0.0996 0.1790 0.010 0.964 1.1 110.9 16.9 258 0.201 2_updatecdl: 0.0996 0.1790 0.010 0.987 1.1 110.9 16.9 258 0.201 2_nqh: 0.0996 0.1790 0.010 0.987 1.1 110.9 16.9 258 0.201 2_sol: 0.1108 0.1658 0.010 0.987 1.1 110.6 16.2 233 n/a 2_weight: 0.1108 0.1658 0.010 0.987 1.1 110.6 16.2 233 n/a 2_xyzrec: 0.0987 0.1803 0.009 0.980 1.1 110.6 16.2 233 n/a 2_adp: 0.0920 0.1821 0.009 0.980 0.0 107.8 17.0 233 n/a 2_regHadp: 0.0917 0.1823 0.009 0.980 0.0 107.8 17.0 233 n/a 2_occ: 0.0917 0.1831 0.009 0.980 0.0 107.8 17.0 233 n/a 3_bss: 0.0916 0.1841 0.009 0.980 0.0 107.8 17.0 233 n/a 3_settarget: 0.0916 0.1841 0.009 0.980 0.0 107.8 17.0 233 n/a 3_updatecdl: 0.0916 0.1841 0.009 0.983 0.0 107.8 17.0 233 n/a 3_nqh: 0.0917 0.1840 0.009 0.983 0.0 107.8 17.0 233 n/a 3_sol: 0.1279 0.1845 0.009 0.983 0.0 107.8 16.3 145 n/a 3_weight: 0.1279 0.1845 0.009 0.983 0.0 107.8 16.3 145 n/a 3_xyzrec: 0.1144 0.1964 0.012 1.086 0.0 107.8 16.3 145 n/a 3_adp: 0.1075 0.1973 0.012 1.086 0.0 105.9 16.3 145 n/a 3_regHadp: 0.1080 0.1987 0.012 1.086 0.0 105.9 16.3 145 n/a 3_occ: 0.1078 0.1978 0.012 1.086 0.0 105.9 16.3 145 n/a 4_bss: 0.1057 0.2014 0.012 1.086 0.0 105.9 16.3 145 n/a 4_settarget: 0.1057 0.2014 0.012 1.086 0.0 105.9 16.3 145 n/a 4_updatecdl: 0.1057 0.2014 0.012 1.109 0.0 105.9 16.3 145 n/a 4_nqh: 0.1057 0.2015 0.012 1.109 0.0 105.9 16.3 145 n/a 4_sol: 0.1087 0.2024 0.012 1.109 0.0 105.9 16.8 186 n/a 4_weight: 0.1087 0.2024 0.012 1.109 0.0 105.9 16.8 186 n/a 4_xyzrec: 0.1018 0.2062 0.012 1.110 0.0 105.9 16.8 186 n/a 4_adp: 0.0992 0.2045 0.012 1.110 0.0 105.3 16.8 186 n/a 4_regHadp: 0.0996 0.2049 0.012 1.110 0.0 105.3 16.8 186 n/a 4_occ: 0.0964 0.2003 0.012 1.110 0.0 105.3 16.8 186 n/a 5_bss: 0.0961 0.1991 0.012 1.110 0.0 105.3 16.8 186 n/a 5_settarget: 0.0961 0.1991 0.012 1.110 0.0 105.3 16.8 186 n/a 5_updatecdl: 0.0961 0.1991 0.012 1.116 0.0 105.3 16.8 186 n/a 5_setrh: 0.0964 0.1991 0.012 1.116 0.0 105.3 16.8 186 n/a 5_nqh: 0.0964 0.1991 0.012 1.116 0.0 105.3 16.8 186 n/a 5_sol: 0.1027 0.1994 0.012 1.116 0.0 105.3 16.8 182 n/a 5_weight: 0.1027 0.1994 0.012 1.116 0.0 105.3 16.8 182 n/a 5_xyzrec: 0.0994 0.1991 0.011 1.152 0.0 105.3 16.8 182 n/a 5_adp: 0.0974 0.1993 0.011 1.152 0.0 103.0 17.0 182 n/a 5_regHadp: 0.0977 0.1999 0.011 1.152 0.0 103.0 17.0 182 n/a 5_occ: 0.0961 0.1976 0.011 1.152 0.0 103.0 17.0 182 n/a end: 0.0959 0.1984 0.011 1.152 0.0 103.0 17.0 182 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_9255201_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_9255201_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8900 Refinement macro-cycles (run) : 447.9700 Write final files (write_after_run_outputs) : 11.2900 Total : 462.1500 Total CPU time: 8.09 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:27 PST -0800 (1735492707.32 s) Start R-work = 0.1559, R-free = 0.1537 Final R-work = 0.0959, R-free = 0.1984 =============================================================================== Job complete usr+sys time: 494.73 seconds wall clock time: 8 minutes 37.66 seconds (517.66 seconds total)