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_3941866.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 { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3941866.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3941866.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" } 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: 1.39, per 1000 atoms: 0.41 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: 0.28 Conformation dependent library (CDL) restraints added in 105.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 577 0.92 - 1.18: 1076 1.18 - 1.43: 652 1.43 - 1.68: 822 1.68 - 1.94: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.462 1.282 0.180 9.50e-03 1.11e+04 3.59e+02 bond pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.336 1.561 -0.225 1.25e-02 6.40e+03 3.25e+02 bond pdb=" CA ILE A 91 " pdb=" CB ILE A 91 " ideal model delta sigma weight residual 1.538 1.353 0.185 1.06e-02 8.90e+03 3.05e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.496 -0.175 1.00e-02 1.00e+04 3.05e+02 bond pdb=" C THR A 110 " pdb=" N ALA A 111 " ideal model delta sigma weight residual 1.335 1.560 -0.225 1.31e-02 5.83e+03 2.94e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 3369 5.06 - 10.13: 1881 10.13 - 15.19: 452 15.19 - 20.26: 64 20.26 - 25.32: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " ideal model delta sigma weight residual 123.46 109.43 14.03 9.90e-01 1.02e+00 2.01e+02 angle pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 121.10 136.58 -15.48 1.10e+00 8.26e-01 1.98e+02 angle pdb=" O GLU A 84 " pdb=" C GLU A 84 " pdb=" N SER A 85 " ideal model delta sigma weight residual 122.34 137.76 -15.42 1.25e+00 6.40e-01 1.52e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.82 108.08 12.74 1.05e+00 9.07e-01 1.47e+02 angle pdb=" O BASN A 76 " pdb=" C BASN A 76 " pdb=" N LEU A 77 " ideal model delta sigma weight residual 122.07 134.36 -12.29 1.03e+00 9.43e-01 1.42e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 15.87: 1273 15.87 - 31.71: 141 31.71 - 47.55: 42 47.55 - 63.39: 22 63.39 - 79.23: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -145.59 22.99 0 2.50e+00 1.60e-01 8.46e+01 dihedral pdb=" N ALYS A 99 " pdb=" C ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual 122.80 143.05 -20.25 0 2.50e+00 1.60e-01 6.56e+01 dihedral pdb=" N PRO A 158 " pdb=" C PRO A 158 " pdb=" CA PRO A 158 " pdb=" CB PRO A 158 " ideal model delta harmonic sigma weight residual 115.10 134.01 -18.91 0 2.50e+00 1.60e-01 5.72e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.254: 108 0.254 - 0.503: 80 0.503 - 0.753: 42 0.753 - 1.002: 10 1.002 - 1.251: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -3.88 1.25 2.00e-01 2.50e+01 3.91e+01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.62 -1.18 2.00e-01 2.50e+01 3.49e+01 chirality pdb=" CA MET A 133 " pdb=" N MET A 133 " pdb=" C MET A 133 " pdb=" CB MET A 133 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.71e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.039 2.00e-02 2.50e+03 5.81e-02 1.01e+02 pdb=" CG ATYR A 67 " 0.127 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.009 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.043 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.008 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.020 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.066 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.089 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.058 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.068 2.00e-02 2.50e+03 5.36e-02 8.62e+01 pdb=" CG BTYR A 67 " 0.042 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.052 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.041 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.115 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.036 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.029 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.013 2.00e-02 2.50e+03 5.28e-02 8.37e+01 pdb=" CG TYR A 139 " -0.097 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.086 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.058 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.053 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 598 2.24 - 2.83: 7500 2.83 - 3.42: 10849 3.42 - 4.01: 15322 4.01 - 4.60: 22313 Nonbonded interactions: 56582 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.652 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.749 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.794 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.811 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.827 2.100 ... (remaining 56577 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_3941866_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= 0.3624 r_free= 0.1996 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467898 | | target function (ml) not normalized (work): 22026.735132 | | target function (ml) not normalized (free): 1142.395605 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3813 0.2185 4.8487 4.8917| | 2: 3.78 - 3.00 1.00 2430 110 0.3394 0.1677 4.0761 4.0707| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.83 0.83 0.13 6609.92| | 2: 3.78 - 3.00 2430 110 0.94 11.17 1.48 0.26 447.85| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 380.33 max = 12073.68 mean = 3572.63| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.26| |phase err.(test): min = 0.00 max = 89.99 mean = 33.54| |-----------------------------------------------------------------------------| ----------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 : 0.079 0.225 1557 Z= 5.386 Angle : 5.321 17.827 2118 Z= 3.702 Chirality : 0.409 1.251 243 Planarity : 0.032 0.116 284 Dihedral : 13.882 79.230 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 1.08 % Allowed : 5.41 % Favored : 93.51 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 35.68 % 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: -2.87 (0.49), residues: 224 helix: -3.19 (0.32), residues: 103 sheet: -1.11 (0.77), residues: 38 loop : -0.05 (0.68), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.092 0.028 ARG A 5 TYR 0.072 0.032 TYR A 141 PHE 0.058 0.025 PHE A 164 HIS 0.050 0.017 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= 0.3624 r_free= 0.1996 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467898 | | target function (ml) not normalized (work): 22026.735132 | | target function (ml) not normalized (free): 1142.395605 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3579 0.3655 0.2102 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3579 0.3655 0.2102 n_refl.: 5182 remove outliers: r(all,work,free)=0.2531 0.2557 0.2102 n_refl.: 5178 overall B=-2.82 to atoms: r(all,work,free)=0.2422 0.2445 0.2055 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1565 0.1562 0.1620 n_refl.: 5178 remove outliers: r(all,work,free)=0.1560 0.1557 0.1620 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3853 449.455 410.947 0.681 1.047 0.407 11.894-9.307 99.02 97 4 0.1874 713.996 697.570 0.958 1.046 0.393 9.237-7.194 100.00 213 7 0.2171 583.907 574.785 0.993 1.041 0.354 7.162-5.571 100.00 427 22 0.2362 438.151 423.742 0.943 1.032 0.292 5.546-4.326 100.00 867 58 0.1392 601.519 593.841 0.987 1.018 0.221 4.315-3.360 100.00 1859 96 0.1301 572.051 565.452 1.051 0.993 0.210 3.356-3.002 100.00 1373 60 0.1588 440.618 433.214 1.050 0.969 0.097 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6112 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1557 r_free=0.1620 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1557 r_free=0.1620 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.782363 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.835786 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 0.1160 0.1810 0.0651 0.010 1.0 3.5 0.5 0.0 0 9.391 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.60 18.10 6.51 3.013 16.035 1.836 0.018 10.24 18.02 7.78 4.877 16.205 1.836 0.015 Individual atomic B min max mean iso aniso Overall: 1.79 111.48 17.38 5.26 1785 0 Protein: 1.79 111.25 14.67 5.25 1519 0 Water: 4.04 111.48 33.16 N/A 258 0 Other: 17.60 37.73 24.10 N/A 8 0 Chain A: 1.79 111.48 17.38 N/A 1785 0 Histogram: Values Number of atoms 1.79 - 12.76 899 12.76 - 23.72 495 23.72 - 34.69 194 34.69 - 45.66 108 45.66 - 56.63 57 56.63 - 67.60 14 67.60 - 78.57 8 78.57 - 89.54 6 89.54 - 100.51 1 100.51 - 111.48 3 =========================== Idealize ADP of riding H ========================== r_work=0.1024 r_free=0.1802 r_work=0.1018 r_free=0.1806 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1018 r_free = 0.1806 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 = 0.1012 r_free = 0.1810 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1012 r_free= 0.1810 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.014009 | | target function (ls_wunit_k1) not normalized (work): 68.982544 | | target function (ls_wunit_k1) not normalized (free): 10.878229 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1053 0.1012 0.1810 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2088 0.2087 0.2220 n_refl.: 5176 remove outliers: r(all,work,free)=0.2088 0.2087 0.2220 n_refl.: 5176 overall B=-0.95 to atoms: r(all,work,free)=0.2049 0.2046 0.2209 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1053 0.1012 0.1804 n_refl.: 5176 remove outliers: r(all,work,free)=0.1053 0.1012 0.1804 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3364 330.278 312.477 0.675 1.012 0.383 11.894-9.307 99.02 97 4 0.1500 524.673 515.047 0.982 1.013 0.352 9.237-7.194 100.00 213 7 0.1677 429.079 428.872 1.017 1.012 0.315 7.162-5.571 100.00 427 22 0.1645 321.971 318.109 0.976 1.010 0.292 5.546-4.326 100.00 867 58 0.0905 442.021 439.157 0.997 1.005 0.207 4.315-3.360 100.00 1859 96 0.0762 420.367 420.329 1.044 0.997 0.203 3.356-3.002 100.00 1373 60 0.1003 323.784 322.221 1.018 0.990 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4208 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1012 r_free=0.1804 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1012 r_free=0.1804 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1012 r_free=0.1804 | n_water=258 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1050 r_free=0.1823 | n_water=245 | time (s): 21.460 (total time: 22.110) Filter (q & B) r_work=0.1051 r_free=0.1821 | n_water=241 | time (s): 1.230 (total time: 23.340) Compute maps r_work=0.1051 r_free=0.1821 | n_water=241 | time (s): 0.430 (total time: 23.770) Filter (map) r_work=0.1335 r_free=0.1858 | n_water=144 | time (s): 1.580 (total time: 25.350) Find peaks r_work=0.1335 r_free=0.1858 | n_water=144 | time (s): 0.530 (total time: 25.880) Add new water r_work=0.1688 r_free=0.2173 | n_water=235 | time (s): 1.400 (total time: 27.280) Refine new water occ: r_work=0.1159 r_free=0.1714 adp: r_work=0.1133 r_free=0.1720 occ: r_work=0.1131 r_free=0.1702 adp: r_work=0.1119 r_free=0.1707 occ: r_work=0.1120 r_free=0.1702 adp: r_work=0.1116 r_free=0.1701 ADP+occupancy (water only), MIN, final r_work=0.1116 r_free=0.1701 r_work=0.1116 r_free=0.1701 | n_water=235 | time (s): 6.990 (total time: 34.270) Filter (q & B) r_work=0.1116 r_free=0.1701 | n_water=234 | time (s): 1.270 (total time: 35.540) Filter (dist only) r_work=0.1116 r_free=0.1696 | n_water=233 | time (s): 18.170 (total time: 53.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.092368 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.694956 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 0.1005 0.1818 0.0813 0.009 1.0 5.4 0.5 0.6 0 11.546 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.05 18.18 8.13 4.644 16.766 2.695 0.014 9.41 18.48 9.07 5.359 17.154 2.695 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.06 16.57 6.39 1760 0 Protein: 0.00 108.06 14.97 6.38 1519 0 Water: 0.00 63.59 26.74 N/A 233 0 Other: 12.67 34.97 24.08 N/A 8 0 Chain A: 0.00 108.06 15.68 N/A 1670 0 Chain S: 6.52 58.57 32.93 N/A 90 0 Histogram: Values Number of atoms 0.00 - 10.81 687 10.81 - 21.61 661 21.61 - 32.42 221 32.42 - 43.22 116 43.22 - 54.03 36 54.03 - 64.83 26 64.83 - 75.64 6 75.64 - 86.45 2 86.45 - 97.25 3 97.25 - 108.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.0941 r_free=0.1848 r_work=0.0939 r_free=0.1853 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0939 r_free = 0.1853 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0940 r_free = 0.1868 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0940 r_free= 0.1868 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.011955 | | target function (ls_wunit_k1) not normalized (work): 58.864681 | | target function (ls_wunit_k1) not normalized (free): 10.916119 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0987 0.0940 0.1868 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2114 0.2113 0.2266 n_refl.: 5176 remove outliers: r(all,work,free)=0.2114 0.2113 0.2266 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2114 0.2113 0.2266 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0987 0.0940 0.1877 n_refl.: 5176 remove outliers: r(all,work,free)=0.0987 0.0940 0.1877 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3166 330.278 317.091 0.684 1.009 0.379 11.894-9.307 99.02 97 4 0.1507 524.673 518.173 0.969 1.011 0.356 9.237-7.194 100.00 213 7 0.1487 429.079 430.935 1.016 1.011 0.305 7.162-5.571 100.00 427 22 0.1424 321.971 318.728 0.989 1.008 0.300 5.546-4.326 100.00 867 58 0.0812 442.021 438.856 1.002 1.004 0.220 4.315-3.360 100.00 1859 96 0.0717 420.367 420.077 1.052 0.997 0.210 3.356-3.002 100.00 1373 60 0.0964 323.784 322.753 1.027 0.990 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.8365 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0940 r_free=0.1877 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0940 r_free=0.1877 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0940 r_free=0.1877 | n_water=233 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0976 r_free=0.1848 | n_water=224 | time (s): 19.330 (total time: 19.880) Filter (q & B) r_work=0.1031 r_free=0.1864 | n_water=222 | time (s): 1.770 (total time: 21.650) Compute maps r_work=0.1031 r_free=0.1864 | n_water=222 | time (s): 0.480 (total time: 22.130) Filter (map) r_work=0.1291 r_free=0.1881 | n_water=145 | time (s): 1.300 (total time: 23.430) Find peaks r_work=0.1291 r_free=0.1881 | n_water=145 | time (s): 0.430 (total time: 23.860) Add new water r_work=0.1677 r_free=0.2224 | n_water=229 | time (s): 1.570 (total time: 25.430) Refine new water occ: r_work=0.1077 r_free=0.1827 adp: r_work=0.1071 r_free=0.1845 occ: r_work=0.1059 r_free=0.1829 adp: r_work=0.1058 r_free=0.1836 occ: r_work=0.1048 r_free=0.1822 adp: r_work=0.1048 r_free=0.1830 ADP+occupancy (water only), MIN, final r_work=0.1048 r_free=0.1830 r_work=0.1048 r_free=0.1830 | n_water=229 | time (s): 8.800 (total time: 34.230) Filter (q & B) r_work=0.1048 r_free=0.1830 | n_water=229 | time (s): 1.250 (total time: 35.480) Filter (dist only) r_work=0.1061 r_free=0.1825 | n_water=226 | time (s): 17.830 (total time: 53.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.083979 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.226832 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 0.0963 0.1858 0.0894 0.011 1.0 4.5 0.5 0.0 0 0.542 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.63 18.58 8.94 5.350 17.679 0.227 5.185 9.18 18.60 9.41 7.369 17.679 0.227 5.086 Individual atomic B min max mean iso aniso Overall: 0.00 108.64 16.21 9.05 1753 0 Protein: 0.00 108.64 15.11 9.04 1519 0 Water: 0.00 57.78 23.36 N/A 226 0 Other: 7.86 36.92 24.34 N/A 8 0 Chain A: 0.00 108.64 15.69 N/A 1652 0 Chain S: 0.00 57.78 24.83 N/A 101 0 Histogram: Values Number of atoms 0.00 - 10.86 693 10.86 - 21.73 660 21.73 - 32.59 222 32.59 - 43.45 109 43.45 - 54.32 39 54.32 - 65.18 15 65.18 - 76.04 8 76.04 - 86.91 2 86.91 - 97.77 4 97.77 - 108.64 1 =========================== Idealize ADP of riding H ========================== r_work=0.0918 r_free=0.1860 r_work=0.0924 r_free=0.1867 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0924 r_free = 0.1867 target_work(ml) = 5.091 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0914 r_free = 0.1858 target_work(ml) = 5.084 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0914 r_free= 0.1858 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.083976 | | target function (ml) not normalized (work): 25033.495790 | | target function (ml) not normalized (free): 1840.437889 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0962 0.0914 0.1858 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2157 0.2163 0.2220 n_refl.: 5176 remove outliers: r(all,work,free)=0.2157 0.2163 0.2220 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2157 0.2163 0.2220 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0958 0.0910 0.1853 n_refl.: 5176 remove outliers: r(all,work,free)=0.0954 0.0906 0.1853 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 0.3534 329.675 298.241 0.599 0.993 0.336 11.894-9.307 99.02 97 4 0.1808 524.673 509.305 0.943 0.997 0.333 9.237-7.194 100.00 213 7 0.1933 429.079 424.310 1.004 0.999 0.290 7.162-5.571 100.00 427 22 0.1853 321.971 311.920 0.981 0.999 0.280 5.546-4.326 100.00 867 58 0.0944 442.021 436.243 1.000 1.000 0.220 4.315-3.360 100.00 1859 96 0.0612 420.367 420.354 1.059 1.002 0.220 3.356-3.002 100.00 1373 60 0.0614 323.784 323.428 1.032 1.002 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9176 b_overall=-6.3774 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0906 r_free=0.1853 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0910 r_free=0.1857 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0910 r_free=0.1857 | n_water=226 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.0920 r_free=0.1849 | n_water=224 | time (s): 17.260 (total time: 17.940) Filter (q & B) r_work=0.0955 r_free=0.1863 | n_water=223 | time (s): 1.510 (total time: 19.450) Compute maps r_work=0.0955 r_free=0.1863 | n_water=223 | time (s): 0.520 (total time: 19.970) Filter (map) r_work=0.1219 r_free=0.1904 | n_water=154 | time (s): 1.380 (total time: 21.350) Find peaks r_work=0.1219 r_free=0.1904 | n_water=154 | time (s): 0.400 (total time: 21.750) Add new water r_work=0.1527 r_free=0.2153 | n_water=227 | time (s): 1.340 (total time: 23.090) Refine new water occ: r_work=0.1014 r_free=0.1837 adp: r_work=0.1008 r_free=0.1848 occ: r_work=0.0998 r_free=0.1833 adp: r_work=0.0997 r_free=0.1841 occ: r_work=0.0989 r_free=0.1826 adp: r_work=0.0989 r_free=0.1835 ADP+occupancy (water only), MIN, final r_work=0.0989 r_free=0.1835 r_work=0.0989 r_free=0.1835 | n_water=227 | time (s): 11.860 (total time: 34.950) Filter (q & B) r_work=0.0989 r_free=0.1837 | n_water=225 | time (s): 1.940 (total time: 36.890) Filter (dist only) r_work=0.0989 r_free=0.1840 | n_water=224 | time (s): 17.530 (total time: 54.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.034863 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.247093 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 0.0904 0.1921 0.1017 0.011 1.0 3.2 0.5 1.2 0 0.517 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.04 19.21 10.17 7.035 17.831 0.247 5.036 8.82 19.58 10.76 8.290 17.965 0.247 4.971 Individual atomic B min max mean iso aniso Overall: 0.00 112.12 16.54 10.85 1751 0 Protein: 0.00 112.12 15.54 10.84 1519 0 Water: 0.00 55.25 22.97 N/A 224 0 Other: 11.28 39.18 24.96 N/A 8 0 Chain A: 0.00 112.12 15.99 N/A 1643 0 Chain S: 0.00 55.25 24.89 N/A 108 0 Histogram: Values Number of atoms 0.00 - 11.21 708 11.21 - 22.42 642 22.42 - 33.64 240 33.64 - 44.85 95 44.85 - 56.06 39 56.06 - 67.27 8 67.27 - 78.48 11 78.48 - 89.69 3 89.69 - 100.91 4 100.91 - 112.12 1 =========================== Idealize ADP of riding H ========================== r_work=0.0882 r_free=0.1958 r_work=0.0885 r_free=0.1960 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0885 r_free = 0.1960 target_work(ml) = 4.975 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0874 r_free = 0.1956 target_work(ml) = 4.966 | | occupancies: max = 1.00 min = 0.19 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= 0.0874 r_free= 0.1956 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.966336 | | target function (ml) not normalized (work): 24444.307546 | | target function (ml) not normalized (free): 2182.777006 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0928 0.0874 0.1956 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2102 0.2094 0.2374 n_refl.: 5174 remove outliers: r(all,work,free)=0.2102 0.2094 0.2374 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2102 0.2094 0.2374 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0927 0.0873 0.1952 n_refl.: 5174 remove outliers: r(all,work,free)=0.0927 0.0873 0.1952 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 0.3621 329.675 300.479 0.600 0.987 0.328 11.894-9.307 99.02 97 4 0.1855 524.673 511.009 0.940 0.993 0.310 9.237-7.194 100.00 213 7 0.2137 429.079 420.084 1.007 0.996 0.300 7.162-5.571 100.00 427 22 0.1958 321.971 312.071 0.981 0.998 0.249 5.546-4.326 100.00 867 58 0.0979 442.021 435.880 1.012 1.000 0.225 4.315-3.360 100.00 1859 96 0.0568 420.367 420.268 1.078 1.002 0.220 3.356-3.002 100.00 1373 60 0.0436 323.784 323.530 1.050 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.2609 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0873 r_free=0.1952 After: r_work=0.0876 r_free=0.1951 ================================== NQH flips ================================== r_work=0.0876 r_free=0.1951 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0876 r_free=0.1954 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0876 r_free=0.1954 | n_water=224 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.0890 r_free=0.1963 | n_water=220 | time (s): 17.130 (total time: 17.600) Filter (q & B) r_work=0.1042 r_free=0.1971 | n_water=215 | time (s): 1.890 (total time: 19.490) Compute maps r_work=0.1042 r_free=0.1971 | n_water=215 | time (s): 0.610 (total time: 20.100) Filter (map) r_work=0.1251 r_free=0.1935 | n_water=162 | time (s): 1.900 (total time: 22.000) Find peaks r_work=0.1251 r_free=0.1935 | n_water=162 | time (s): 0.440 (total time: 22.440) Add new water r_work=0.1467 r_free=0.2092 | n_water=219 | time (s): 1.450 (total time: 23.890) Refine new water occ: r_work=0.0979 r_free=0.1915 adp: r_work=0.0965 r_free=0.1923 occ: r_work=0.0961 r_free=0.1918 adp: r_work=0.0960 r_free=0.1923 occ: r_work=0.0956 r_free=0.1916 adp: r_work=0.0955 r_free=0.1920 ADP+occupancy (water only), MIN, final r_work=0.0955 r_free=0.1920 r_work=0.0955 r_free=0.1920 | n_water=219 | time (s): 12.470 (total time: 36.360) Filter (q & B) r_work=0.0955 r_free=0.1922 | n_water=218 | time (s): 1.440 (total time: 37.800) Filter (dist only) r_work=0.0956 r_free=0.1898 | n_water=216 | time (s): 17.670 (total time: 55.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.959391 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.237270 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 0.0905 0.1927 0.1021 0.011 1.1 5.1 0.5 0.6 0 0.480 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.05 19.27 10.21 8.237 18.257 0.237 5.011 8.83 19.56 10.73 9.143 18.360 0.237 4.952 Individual atomic B min max mean iso aniso Overall: 0.00 112.33 16.78 12.09 1743 0 Protein: 0.00 112.33 15.91 12.09 1519 0 Water: 0.00 52.39 22.62 N/A 216 0 Other: 10.18 35.87 23.55 N/A 8 0 Chain A: 0.00 112.33 16.30 N/A 1637 0 Chain S: 0.00 52.39 24.20 N/A 106 0 Histogram: Values Number of atoms 0.00 - 11.23 703 11.23 - 22.47 627 22.47 - 33.70 237 33.70 - 44.93 108 44.93 - 56.16 37 56.16 - 67.40 12 67.40 - 78.63 8 78.63 - 89.86 6 89.86 - 101.09 4 101.09 - 112.33 1 =========================== Idealize ADP of riding H ========================== r_work=0.0883 r_free=0.1956 r_work=0.0886 r_free=0.1959 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0886 r_free = 0.1959 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0881 r_free = 0.1951 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0881 r_free= 0.1951 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.952096 | | target function (ml) not normalized (work): 24374.218729 | | target function (ml) not normalized (free): 2294.829943 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1253 0.1941 5.53 6.3184| | 2: 3.78 - 3.00 1.00 2430 110 0.0428 0.1968 4.3595 12.706| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 11.78 1.00 0.98 12525.03| | 2: 3.78 - 3.00 2430 110 0.99 1.88 1.00 1.00 916.92| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 581.51 max = 20674.31 mean = 6794.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.91 mean = 6.89| |phase err.(test): min = 0.00 max = 78.89 mean = 7.25| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0935 0.0881 0.1951 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2158 0.2146 0.2496 n_refl.: 5174 remove outliers: r(all,work,free)=0.2158 0.2146 0.2496 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2158 0.2146 0.2496 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0933 0.0879 0.1952 n_refl.: 5174 remove outliers: r(all,work,free)=0.0933 0.0879 0.1952 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 0.3606 329.675 302.693 0.616 0.988 0.338 11.894-9.307 99.02 97 4 0.1878 524.673 511.379 0.949 0.996 0.323 9.237-7.194 100.00 213 7 0.2082 429.079 420.756 1.003 0.999 0.302 7.162-5.571 100.00 427 22 0.2001 321.971 312.214 0.976 1.000 0.295 5.546-4.326 100.00 867 58 0.1029 442.021 436.553 1.013 1.001 0.235 4.315-3.360 100.00 1859 96 0.0580 420.367 420.256 1.089 1.001 0.230 3.356-3.002 100.00 1373 60 0.0396 323.784 323.326 1.066 1.001 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.7310 ================= 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 : 0.3624 0.1996 0.079 5.321 8.8 119.3 19.9 258 0.000 1_bss: 0.1557 0.1620 0.079 5.321 6.0 116.5 17.1 258 0.000 1_settarget: 0.1557 0.1620 0.079 5.321 6.0 116.5 17.1 258 0.000 1_nqh: 0.1557 0.1620 0.079 5.321 6.0 116.5 17.1 258 0.000 1_weight: 0.1557 0.1620 0.079 5.321 6.0 116.5 17.1 258 0.000 1_xyzrec: 0.1160 0.1810 0.010 0.965 6.0 116.5 17.1 258 0.214 1_adp: 0.1024 0.1802 0.010 0.965 1.8 111.5 17.4 258 0.214 1_regHadp: 0.1018 0.1806 0.010 0.965 1.8 111.5 17.4 258 0.214 1_occ: 0.1012 0.1810 0.010 0.965 1.8 111.5 17.4 258 0.214 2_bss: 0.1012 0.1804 0.010 0.965 0.8 110.5 16.4 258 0.214 2_settarget: 0.1012 0.1804 0.010 0.965 0.8 110.5 16.4 258 0.214 2_updatecdl: 0.1012 0.1804 0.010 1.001 0.8 110.5 16.4 258 0.214 2_nqh: 0.1012 0.1804 0.010 1.001 0.8 110.5 16.4 258 0.214 2_sol: 0.1116 0.1696 0.010 1.001 0.8 110.3 15.8 233 n/a 2_weight: 0.1116 0.1696 0.010 1.001 0.8 110.3 15.8 233 n/a 2_xyzrec: 0.1005 0.1818 0.009 0.981 0.8 110.3 15.8 233 n/a 2_adp: 0.0941 0.1848 0.009 0.981 0.0 108.1 16.6 233 n/a 2_regHadp: 0.0939 0.1853 0.009 0.981 0.0 108.1 16.6 233 n/a 2_occ: 0.0940 0.1868 0.009 0.981 0.0 108.1 16.6 233 n/a 3_bss: 0.0940 0.1877 0.009 0.981 0.0 108.1 16.6 233 n/a 3_settarget: 0.0940 0.1877 0.009 0.981 0.0 108.1 16.6 233 n/a 3_updatecdl: 0.0940 0.1877 0.009 0.981 0.0 108.1 16.6 233 n/a 3_nqh: 0.0940 0.1877 0.009 0.981 0.0 108.1 16.6 233 n/a 3_sol: 0.1061 0.1825 0.009 0.981 0.0 108.1 16.2 226 n/a 3_weight: 0.1061 0.1825 0.009 0.981 0.0 108.1 16.2 226 n/a 3_xyzrec: 0.0963 0.1858 0.011 1.041 0.0 108.1 16.2 226 n/a 3_adp: 0.0918 0.1860 0.011 1.041 0.0 108.6 16.2 226 n/a 3_regHadp: 0.0924 0.1867 0.011 1.041 0.0 108.6 16.2 226 n/a 3_occ: 0.0914 0.1858 0.011 1.041 0.0 108.6 16.2 226 n/a 4_bss: 0.0906 0.1853 0.011 1.041 0.0 108.6 16.2 226 n/a 4_settarget: 0.0906 0.1853 0.011 1.041 0.0 108.6 16.2 226 n/a 4_updatecdl: 0.0906 0.1853 0.011 1.053 0.0 108.6 16.2 226 n/a 4_nqh: 0.0910 0.1857 0.011 1.053 0.0 108.6 16.2 226 n/a 4_sol: 0.0989 0.1840 0.011 1.053 0.0 108.6 16.3 224 n/a 4_weight: 0.0989 0.1840 0.011 1.053 0.0 108.6 16.3 224 n/a 4_xyzrec: 0.0904 0.1921 0.011 1.050 0.0 108.6 16.3 224 n/a 4_adp: 0.0882 0.1958 0.011 1.050 0.0 112.1 16.5 224 n/a 4_regHadp: 0.0885 0.1960 0.011 1.050 0.0 112.1 16.5 224 n/a 4_occ: 0.0874 0.1956 0.011 1.050 0.0 112.1 16.5 224 n/a 5_bss: 0.0873 0.1952 0.011 1.050 0.0 112.1 16.5 224 n/a 5_settarget: 0.0873 0.1952 0.011 1.050 0.0 112.1 16.5 224 n/a 5_updatecdl: 0.0873 0.1952 0.011 1.056 0.0 112.1 16.5 224 n/a 5_setrh: 0.0876 0.1951 0.011 1.056 0.0 112.1 16.5 224 n/a 5_nqh: 0.0876 0.1954 0.011 1.056 0.0 112.1 16.5 224 n/a 5_sol: 0.0956 0.1898 0.011 1.056 0.0 112.1 16.6 216 n/a 5_weight: 0.0956 0.1898 0.011 1.056 0.0 112.1 16.6 216 n/a 5_xyzrec: 0.0905 0.1927 0.011 1.112 0.0 112.1 16.6 216 n/a 5_adp: 0.0883 0.1956 0.011 1.112 0.0 112.3 16.8 216 n/a 5_regHadp: 0.0886 0.1959 0.011 1.112 0.0 112.3 16.8 216 n/a 5_occ: 0.0881 0.1951 0.011 1.112 0.0 112.3 16.8 216 n/a end: 0.0879 0.1952 0.011 1.112 0.0 112.3 16.8 216 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3941866_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3941866_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5500 Refinement macro-cycles (run) : 483.9700 Write final files (write_after_run_outputs) : 10.6700 Total : 498.1900 Total CPU time: 8.64 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:59 PST -0800 (1735492739.95 s) Start R-work = 0.1557, R-free = 0.1620 Final R-work = 0.0879, R-free = 0.1952 =============================================================================== Job complete usr+sys time: 526.92 seconds wall clock time: 9 minutes 9.23 seconds (549.23 seconds total)