Starting phenix.refine on Fri Dec 27 17:58:26 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.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff 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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.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 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } 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: 1.55, per 1000 atoms: 0.46 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: 0.34 Conformation dependent library (CDL) restraints added in 153.6 milliseconds Time building geometry restraints manager: 0.48 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: 928 16.03 - 32.06: 116 32.06 - 48.09: 47 48.09 - 64.12: 17 64.12 - 80.15: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 152.30 27.70 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 1108 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 1.850 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 1.850 ... (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 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } 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: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2604 r_free= 0.1939 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.796906 | | target function (ml) not normalized (work): 232999.079967 | | target function (ml) not normalized (free): 11894.983064 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3031 0.2098 7.0895 4.9493| | 2: 3.57 - 2.84 1.00 2876 122 0.2433 0.1669 4.3463 4.3172| | 3: 2.84 - 2.48 1.00 2833 165 0.2358 0.1658 4.1287 4.1574| | 4: 2.47 - 2.25 1.00 2825 136 0.2343 0.1311 3.8281 3.8186| | 5: 2.25 - 2.09 1.00 2756 127 0.2443 0.1560 3.7921 3.8244| | 6: 2.09 - 1.97 1.00 2846 113 0.2508 0.1830 3.46 3.5537| | 7: 1.97 - 1.87 1.00 2787 165 0.2559 0.1976 3.1485 3.2617| | 8: 1.87 - 1.79 1.00 2789 144 0.2473 0.1927 3.078 3.1626| | 9: 1.79 - 1.72 1.00 2745 138 0.2455 0.1996 2.9136 2.9368| | 10: 1.72 - 1.66 1.00 2789 158 0.2414 0.2057 2.8172 2.9154| | 11: 1.66 - 1.61 1.00 2740 147 0.2497 0.1879 2.7709 2.8155| | 12: 1.61 - 1.56 1.00 2787 146 0.2528 0.1994 2.6396 2.6892| | 13: 1.56 - 1.52 1.00 2745 130 0.2560 0.2065 2.5814 2.6611| | 14: 1.52 - 1.48 1.00 2803 134 0.2542 0.1937 2.51 2.5505| | 15: 1.48 - 1.45 1.00 2738 128 0.2550 0.2168 2.4071 2.5712| | 16: 1.45 - 1.42 1.00 2756 161 0.2660 0.1944 2.4033 2.4236| | 17: 1.42 - 1.39 1.00 2785 139 0.2696 0.2056 2.3417 2.3455| | 18: 1.39 - 1.36 1.00 2741 179 0.2673 0.2347 2.2809 2.4595| | 19: 1.36 - 1.34 1.00 2807 134 0.2673 0.2277 2.2683 2.3361| | 20: 1.34 - 1.32 1.00 2696 147 0.2693 0.2030 2.1936 2.1413| | 21: 1.32 - 1.30 1.00 2785 112 0.2665 0.2074 2.1641 2.1347| | 22: 1.29 - 1.27 1.00 2704 152 0.2747 0.2590 2.1471 2.2057| | 23: 1.27 - 1.26 1.00 2802 156 0.2728 0.2172 2.0995 2.08| | 24: 1.26 - 1.24 1.00 2744 132 0.2758 0.2710 2.0751 2.219| | 25: 1.24 - 1.22 1.00 2734 148 0.2845 0.2748 2.047 2.1948| | 26: 1.22 - 1.21 1.00 2727 135 0.2864 0.2405 2.0258 2.087| | 27: 1.21 - 1.19 1.00 2814 148 0.2993 0.2598 2.0205 2.035| | 28: 1.19 - 1.18 1.00 2671 147 0.2987 0.2941 1.9825 2.0471| | 29: 1.18 - 1.16 1.00 2800 134 0.2932 0.2649 1.9567 2.0217| | 30: 1.16 - 1.15 1.00 2740 148 0.3089 0.2968 1.933 1.9661| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.58 2941 171 0.87 18.66 0.76 0.23 1459.12| | 2: 3.57 - 2.84 2876 122 0.81 25.96 1.27 0.23 1459.12| | 3: 2.84 - 2.48 2833 165 0.74 31.79 1.24 0.23 1211.50| | 4: 2.47 - 2.25 2825 136 0.81 25.60 1.26 0.25 568.85| | 5: 2.25 - 2.09 2756 127 0.77 29.41 1.28 0.25 568.85| | 6: 2.09 - 1.97 2846 113 0.83 23.01 1.29 0.25 314.74| | 7: 1.97 - 1.87 2787 165 0.89 17.40 1.28 0.26 98.01| | 8: 1.87 - 1.79 2789 144 0.85 21.89 1.25 0.26 98.01| | 9: 1.79 - 1.72 2745 138 0.87 19.46 1.24 0.26 59.96| | 10: 1.72 - 1.66 2789 158 0.86 21.07 1.23 0.26 52.34| | 11: 1.66 - 1.61 2740 147 0.85 22.09 1.24 0.25 50.55| | 12: 1.61 - 1.56 2787 146 0.87 19.51 1.24 0.25 32.38| | 13: 1.56 - 1.52 2745 130 0.86 21.44 1.25 0.25 32.38| | 14: 1.52 - 1.48 2803 134 0.86 21.56 1.23 0.25 28.68| | 15: 1.48 - 1.45 2738 128 0.86 21.03 1.23 0.25 21.89| | 16: 1.45 - 1.42 2756 161 0.85 22.43 1.24 0.25 21.89| | 17: 1.42 - 1.39 2785 139 0.86 21.57 1.23 0.24 18.35| | 18: 1.39 - 1.36 2741 179 0.86 21.62 1.22 0.24 16.30| | 19: 1.36 - 1.34 2807 134 0.85 22.33 1.21 0.24 16.30| | 20: 1.34 - 1.32 2696 147 0.86 21.20 1.21 0.24 13.05| | 21: 1.32 - 1.30 2785 112 0.86 21.72 1.20 0.24 12.82| | 22: 1.29 - 1.27 2704 152 0.85 22.38 1.21 0.24 12.56| | 23: 1.27 - 1.26 2802 156 0.86 22.13 1.21 0.24 11.20| | 24: 1.26 - 1.24 2744 132 0.85 22.93 1.19 0.24 11.20| | 25: 1.24 - 1.22 2734 148 0.84 24.08 1.20 0.24 10.79| | 26: 1.22 - 1.21 2727 135 0.84 24.48 1.19 0.23 10.33| | 27: 1.21 - 1.19 2814 148 0.83 25.25 1.20 0.23 10.33| | 28: 1.19 - 1.18 2671 147 0.82 26.36 1.19 0.23 9.91| | 29: 1.18 - 1.16 2800 134 0.81 26.78 1.16 0.22 9.75| | 30: 1.16 - 1.15 2740 148 0.79 28.55 1.15 0.22 9.75| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.75 max = 1459.12 mean = 214.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 23.12| |phase err.(test): min = 0.00 max = 89.64 mean = 22.86| |-----------------------------------------------------------------------------| ----------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 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 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: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2604 r_free= 0.1939 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.796906 | | target function (ml) not normalized (work): 232999.079967 | | target function (ml) not normalized (free): 11894.983064 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2562 0.2604 0.1940 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2562 0.2604 0.1940 n_refl.: 87602 remove outliers: r(all,work,free)=0.1977 0.1981 0.1940 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2003 0.2008 0.1955 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1650 0.1644 0.1762 n_refl.: 87594 remove outliers: r(all,work,free)=0.1650 0.1644 0.1762 n_refl.: 87593 ======================== 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 0.3963 386.280 358.245 0.684 1.001 0.410 11.894-9.307 99.02 97 4 0.1771 613.587 593.639 0.929 1.001 0.390 9.237-7.194 100.00 213 7 0.2157 501.839 488.918 0.950 1.002 0.357 7.162-5.571 100.00 427 22 0.2230 376.602 364.205 0.931 1.002 0.292 5.546-4.326 100.00 867 58 0.1291 516.982 510.203 0.964 1.002 0.224 4.315-3.360 100.00 1859 96 0.1146 491.653 488.652 1.004 1.002 0.147 3.356-2.611 100.00 3867 181 0.1444 322.991 319.530 0.999 1.001 0.048 2.608-2.026 99.99 8198 413 0.1363 214.113 211.650 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1654 104.562 103.780 1.011 1.001 0.000 1.573-1.221 100.00 36679 1900 0.2068 46.367 45.095 1.000 1.001 0.000 1.221-1.150 99.97 13689 708 0.2593 29.214 26.807 0.965 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0500 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1644 r_free=0.1762 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=0.1647 r_free=0.1764 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.104037 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2020.153657 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1749 0.1870 0.0121 0.002 0.4 4.8 0.0 0.0 0 0.125 0.1568 0.1714 0.0146 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1471 0.1644 0.0173 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1387 0.1583 0.0196 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1359 0.1565 0.0206 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1356 0.1564 0.0208 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1284 0.1501 0.0217 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1267 0.1498 0.0231 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1250 0.1485 0.0234 0.003 0.7 2.9 0.5 0.0 0 4.000 0.1249 0.1492 0.0243 0.004 0.7 2.9 0.5 0.0 0 5.000 0.1243 0.1485 0.0242 0.004 0.7 3.5 0.5 0.0 0 6.000 0.1238 0.1482 0.0244 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1229 0.1472 0.0243 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1229 0.1475 0.0246 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1230 0.1476 0.0247 0.006 0.9 3.2 0.5 0.0 0 10.000 0.1228 0.1480 0.0252 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1223 0.1475 0.0252 0.007 0.9 3.8 0.5 0.6 0 12.000 0.1222 0.1480 0.0257 0.008 1.0 3.8 0.5 0.6 0 13.552 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1472 0.0243 0.005 0.8 3.5 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.72 2.43 3.012 19.077 2020.154 0.017 12.29 14.72 2.43 3.012 19.077 60.605 0.017 12.36 14.68 2.32 2.668 19.076 252.519 0.017 12.74 15.42 2.68 2.834 19.310 1010.077 0.017 12.49 15.45 2.96 2.968 19.430 2020.154 0.016 12.49 15.57 3.07 3.377 19.685 3030.230 0.016 12.42 15.59 3.17 3.451 19.715 4040.307 0.015 12.20 15.38 3.17 3.097 19.507 5050.384 0.015 12.22 15.39 3.16 3.289 19.610 6060.461 0.015 12.32 15.65 3.33 3.514 19.719 7070.538 0.015 12.31 15.74 3.42 3.745 19.827 8080.615 0.015 12.30 15.74 3.44 3.778 19.831 9090.691 0.015 12.27 15.75 3.47 3.607 19.730 10100.768 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 252.519 Accepted refinement result: 12.36 14.68 2.32 2.668 19.076 252.519 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.46 20.10 3.31 0 1785 Protein: 9.08 115.02 17.01 3.32 0 1519 Water: 11.48 119.46 38.25 N/A 0 258 Other: 19.72 26.64 22.07 N/A 0 8 Chain A: 9.08 119.46 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.16 227 31.16 - 42.19 125 42.19 - 53.23 94 53.23 - 64.27 42 64.27 - 75.31 11 75.31 - 86.34 7 86.34 - 97.38 4 97.38 - 108.42 1 108.42 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1468 r_work=0.1237 r_free=0.1471 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1471 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1468 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1231 r_free= 0.1468 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016982 | | target function (ls_wunit_k1) not normalized (work): 1414.537820 | | target function (ls_wunit_k1) not normalized (free): 111.879853 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1243 0.1231 0.1468 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1675 0.1676 0.1692 n_refl.: 87593 remove outliers: r(all,work,free)=0.1675 0.1676 0.1692 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1680 0.1681 0.1695 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1458 n_refl.: 87593 remove outliers: r(all,work,free)=0.1239 0.1228 0.1458 n_refl.: 87593 ======================== 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 0.3558 303.722 280.026 0.661 1.002 0.388 11.894-9.307 99.02 97 4 0.1605 482.448 469.999 0.925 1.003 0.380 9.237-7.194 100.00 213 7 0.1886 394.583 389.186 0.964 1.003 0.350 7.162-5.571 100.00 427 22 0.1858 296.113 290.115 0.934 1.003 0.259 5.546-4.326 100.00 867 58 0.1015 406.490 403.390 0.963 1.002 0.199 4.315-3.360 100.00 1859 96 0.0883 386.574 385.416 1.008 1.002 0.170 3.356-2.611 100.00 3867 181 0.1176 253.959 252.793 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1021 168.352 167.623 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1110 82.214 82.409 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1446 36.457 35.967 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 22.971 21.459 0.983 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0405 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1458 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1229 r_free=0.1459 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1459 | n_water=258 | time (s): 1.770 (total time: 1.770) Filter (dist) r_work=0.1240 r_free=0.1456 | n_water=249 | time (s): 22.940 (total time: 24.710) Filter (q & B) r_work=0.1243 r_free=0.1456 | n_water=246 | time (s): 3.130 (total time: 27.840) Compute maps r_work=0.1243 r_free=0.1456 | n_water=246 | time (s): 1.180 (total time: 29.020) Filter (map) r_work=0.1262 r_free=0.1453 | n_water=223 | time (s): 3.290 (total time: 32.310) Find peaks r_work=0.1262 r_free=0.1453 | n_water=223 | time (s): 0.530 (total time: 32.840) Add new water r_work=0.1408 r_free=0.1624 | n_water=434 | time (s): 3.260 (total time: 36.100) Refine new water occ: r_work=0.1312 r_free=0.1486 adp: r_work=0.1226 r_free=0.1430 occ: r_work=0.1238 r_free=0.1416 adp: r_work=0.1206 r_free=0.1401 occ: r_work=0.1208 r_free=0.1390 adp: r_work=0.1200 r_free=0.1389 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1389 r_work=0.1200 r_free=0.1389 | n_water=434 | time (s): 51.990 (total time: 88.090) Filter (q & B) r_work=0.1204 r_free=0.1388 | n_water=420 | time (s): 2.870 (total time: 90.960) Filter (dist only) r_work=0.1204 r_free=0.1388 | n_water=419 | time (s): 35.500 (total time: 126.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.088171 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1493.841431 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1663 0.1768 0.0105 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1523 0.1646 0.0123 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1395 0.1540 0.0145 0.001 0.4 6.1 0.0 0.0 0 0.500 0.1344 0.1500 0.0156 0.001 0.5 6.1 0.0 0.0 0 0.750 0.1314 0.1480 0.0166 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1323 0.1491 0.0168 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1257 0.1454 0.0197 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1226 0.1423 0.0197 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1213 0.1417 0.0205 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1208 0.1418 0.0209 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1204 0.1417 0.0213 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1200 0.1416 0.0216 0.005 0.8 5.1 0.5 0.0 0 7.000 0.1198 0.1416 0.0219 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1195 0.1413 0.0218 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1192 0.1414 0.0222 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1192 0.1409 0.0218 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1190 0.1406 0.0217 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1189 0.1407 0.0218 0.008 0.9 5.1 0.5 0.0 0 13.000 0.1185 0.1414 0.0228 0.008 0.9 4.8 0.5 0.0 0 14.044 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1406 0.0217 0.007 0.9 5.1 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 14.06 2.17 3.777 21.798 1493.841 0.016 11.90 14.06 2.17 3.777 21.798 44.815 0.016 11.90 14.06 2.17 3.777 21.798 186.730 0.016 12.04 14.43 2.39 3.636 21.801 746.921 0.015 12.09 14.80 2.71 3.538 21.885 1493.841 0.015 11.96 14.70 2.74 3.449 22.105 2240.762 0.014 11.83 14.64 2.81 3.464 22.042 2987.683 0.014 11.77 14.69 2.92 3.511 21.972 3734.604 0.014 11.72 14.66 2.93 3.509 22.012 4481.524 0.014 11.77 14.71 2.94 3.544 22.200 5228.445 0.014 11.70 14.58 2.88 3.531 22.146 5975.366 0.014 11.67 14.61 2.94 3.551 22.169 6722.286 0.014 11.69 14.75 3.06 3.585 22.214 7469.207 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 186.730 Accepted refinement result: 11.90 14.06 2.17 3.777 21.798 186.730 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 22.21 3.31 196 1750 Protein: 9.11 115.04 17.04 3.32 0 1519 Water: 11.50 76.70 40.97 N/A 196 223 Other: 19.74 26.66 22.10 N/A 0 8 Chain A: 9.11 115.04 19.43 N/A 0 1750 Chain S: 15.52 60.00 47.05 N/A 196 0 Histogram: Values Number of atoms 9.11 - 19.70 1260 19.70 - 30.30 248 30.30 - 40.89 161 40.89 - 51.48 134 51.48 - 62.08 119 62.08 - 72.67 13 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1406 r_work=0.1190 r_free=0.1406 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1406 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1409 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1189 r_free= 0.1409 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015022 | | target function (ls_wunit_k1) not normalized (work): 1251.253992 | | target function (ls_wunit_k1) not normalized (free): 101.104648 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1189 0.1409 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1592 0.1591 0.1643 n_refl.: 87593 remove outliers: r(all,work,free)=0.1592 0.1591 0.1643 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1593 0.1592 0.1644 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1186 0.1405 n_refl.: 87593 remove outliers: r(all,work,free)=0.1196 0.1185 0.1405 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3260 300.593 279.912 0.611 1.002 0.360 11.894-9.307 99.02 97 4 0.1556 482.448 476.994 0.923 1.003 0.347 9.237-7.194 100.00 213 7 0.1748 394.583 393.254 0.977 1.003 0.300 7.162-5.571 100.00 427 22 0.1594 296.113 291.436 0.938 1.003 0.219 5.546-4.326 100.00 867 58 0.0865 406.490 403.579 0.959 1.003 0.200 4.315-3.360 100.00 1859 96 0.0795 386.574 385.702 1.004 1.003 0.180 3.356-2.611 100.00 3867 181 0.1081 253.959 252.962 1.011 1.002 0.120 2.608-2.026 99.99 8198 413 0.1020 168.352 167.792 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1103 82.214 82.429 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1436 36.457 36.002 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2246 22.971 21.491 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0090 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1405 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1185 r_free=0.1405 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1405 | n_water=419 | time (s): 1.960 (total time: 1.960) Filter (dist) r_work=0.1185 r_free=0.1402 | n_water=414 | time (s): 34.120 (total time: 36.080) Filter (q & B) r_work=0.1185 r_free=0.1402 | n_water=414 | time (s): 0.980 (total time: 37.060) Compute maps r_work=0.1185 r_free=0.1402 | n_water=414 | time (s): 1.340 (total time: 38.400) Filter (map) r_work=0.1226 r_free=0.1398 | n_water=285 | time (s): 2.550 (total time: 40.950) Find peaks r_work=0.1226 r_free=0.1398 | n_water=285 | time (s): 0.560 (total time: 41.510) Add new water r_work=0.1349 r_free=0.1520 | n_water=482 | time (s): 3.280 (total time: 44.790) Refine new water occ: r_work=0.1255 r_free=0.1449 adp: r_work=0.1257 r_free=0.1450 occ: r_work=0.1231 r_free=0.1426 adp: r_work=0.1231 r_free=0.1427 occ: r_work=0.1212 r_free=0.1408 adp: r_work=0.1207 r_free=0.1405 ADP+occupancy (water only), MIN, final r_work=0.1207 r_free=0.1405 r_work=0.1207 r_free=0.1405 | n_water=482 | time (s): 175.520 (total time: 220.310) Filter (q & B) r_work=0.1211 r_free=0.1404 | n_water=452 | time (s): 3.110 (total time: 223.420) Filter (dist only) r_work=0.1211 r_free=0.1404 | n_water=451 | time (s): 37.490 (total time: 260.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.753145 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.999403 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1241 0.1373 0.0132 0.002 0.6 4.8 0.5 0.0 0 0.088 0.1197 0.1332 0.0135 0.003 0.7 3.8 0.5 0.0 0 0.263 0.1179 0.1317 0.0138 0.004 0.8 3.5 0.5 0.0 0 0.526 0.1171 0.1313 0.0142 0.005 0.9 3.2 0.5 0.0 0 0.789 0.1168 0.1310 0.0141 0.006 1.0 3.2 0.5 0.0 0 1.052 0.1165 0.1308 0.0143 0.007 1.0 3.8 0.5 0.0 0 1.315 0.1163 0.1309 0.0146 0.007 1.1 3.8 0.5 0.0 0 1.578 0.1161 0.1308 0.0146 0.008 1.1 4.2 0.5 0.0 0 1.841 0.1171 0.1312 0.0141 0.005 0.9 3.2 0.5 0.0 0 0.877 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1161 0.1308 0.0146 0.008 1.1 4.2 0.5 0.0 0 1.841 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.61 13.08 1.46 3.780 21.307 45.999 3.619 11.61 13.08 1.46 3.780 21.307 1.380 3.619 11.62 13.08 1.46 3.777 21.307 5.750 3.619 11.70 13.20 1.51 3.713 21.289 23.000 3.616 11.66 13.24 1.58 3.741 21.270 45.999 3.613 11.63 13.27 1.63 3.757 21.247 68.999 3.609 11.57 13.23 1.66 3.773 21.244 91.999 3.604 11.54 13.21 1.67 3.783 21.242 114.999 3.601 11.53 13.20 1.67 3.796 21.225 137.998 3.599 11.52 13.20 1.68 3.813 21.213 160.998 3.598 11.51 13.18 1.68 3.823 21.207 183.998 3.597 11.50 13.17 1.67 3.831 21.201 206.997 3.596 11.48 13.16 1.68 3.835 21.206 229.997 3.595 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.380 Accepted refinement result: 11.61 13.08 1.46 3.780 21.307 1.380 3.619 Individual atomic B min max mean iso aniso Overall: 9.11 115.05 21.31 3.31 232 1746 Protein: 9.11 115.05 17.04 3.32 0 1519 Water: 11.51 76.71 35.66 N/A 232 219 Other: 19.75 26.67 22.11 N/A 0 8 Chain A: 9.11 115.05 19.35 N/A 0 1746 Chain S: 15.52 60.01 36.07 N/A 232 0 Histogram: Values Number of atoms 9.11 - 19.71 1263 19.71 - 30.30 294 30.30 - 40.89 217 40.89 - 51.49 126 51.49 - 62.08 55 62.08 - 72.67 12 72.67 - 83.27 5 83.27 - 93.86 4 93.86 - 104.45 0 104.45 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1161 r_free=0.1308 r_work=0.1161 r_free=0.1308 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1161 r_free = 0.1308 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1153 r_free = 0.1305 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1153 r_free= 0.1305 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.612470 | | target function (ml) not normalized (work): 300897.048391 | | target function (ml) not normalized (free): 15848.587522 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1161 0.1153 0.1305 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1491 0.1490 0.1539 n_refl.: 87590 remove outliers: r(all,work,free)=0.1491 0.1490 0.1539 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1489 0.1488 0.1537 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1155 0.1147 0.1304 n_refl.: 87590 remove outliers: r(all,work,free)=0.1152 0.1144 0.1304 n_refl.: 87582 ======================== 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 90.62 82 5 0.3891 287.006 266.595 0.486 1.000 0.307 11.894-9.307 96.08 94 4 0.2279 475.818 462.886 0.865 1.002 0.290 9.237-7.194 99.09 211 7 0.2332 389.084 384.669 0.947 1.002 0.200 7.162-5.571 100.00 427 22 0.2085 296.113 285.778 0.915 1.002 0.180 5.546-4.326 100.00 867 58 0.1102 406.490 401.587 0.957 1.002 0.170 4.315-3.360 100.00 1859 96 0.0950 386.574 384.101 0.993 1.002 0.124 3.356-2.611 100.00 3867 181 0.1157 253.959 251.599 0.996 1.002 0.043 2.608-2.026 99.99 8198 413 0.0933 168.352 167.563 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.214 82.489 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.457 36.044 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2161 22.971 21.517 0.981 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0239 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1144 r_free=0.1304 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1149 r_free=0.1307 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1149 r_free=0.1307 | n_water=451 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1148 r_free=0.1304 | n_water=448 | time (s): 45.830 (total time: 48.240) Filter (q & B) r_work=0.1149 r_free=0.1306 | n_water=445 | time (s): 3.750 (total time: 51.990) Compute maps r_work=0.1149 r_free=0.1306 | n_water=445 | time (s): 1.790 (total time: 53.780) Filter (map) r_work=0.1176 r_free=0.1298 | n_water=335 | time (s): 3.740 (total time: 57.520) Find peaks r_work=0.1176 r_free=0.1298 | n_water=335 | time (s): 0.690 (total time: 58.210) Add new water r_work=0.1243 r_free=0.1382 | n_water=496 | time (s): 3.510 (total time: 61.720) Refine new water occ: r_work=0.1169 r_free=0.1322 adp: r_work=0.1169 r_free=0.1323 occ: r_work=0.1153 r_free=0.1311 adp: r_work=0.1152 r_free=0.1309 occ: r_work=0.1143 r_free=0.1300 adp: r_work=0.1139 r_free=0.1297 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1297 r_work=0.1139 r_free=0.1297 | n_water=496 | time (s): 301.250 (total time: 362.970) Filter (q & B) r_work=0.1146 r_free=0.1306 | n_water=458 | time (s): 3.970 (total time: 366.940) Filter (dist only) r_work=0.1146 r_free=0.1305 | n_water=457 | time (s): 47.460 (total time: 414.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.774339 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.334398 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1204 0.1347 0.0143 0.002 0.6 3.8 0.5 0.0 0 0.089 0.1166 0.1315 0.0149 0.003 0.8 2.9 0.5 0.0 0 0.266 0.1153 0.1306 0.0153 0.005 0.9 3.2 0.5 0.0 0 0.532 0.1147 0.1304 0.0157 0.006 0.9 3.2 0.5 0.0 0 0.798 0.1143 0.1303 0.0160 0.006 1.0 3.2 0.5 0.0 0 1.065 0.1141 0.1302 0.0161 0.007 1.0 3.2 0.5 0.0 0 1.331 0.1139 0.1302 0.0164 0.008 1.1 3.5 0.5 0.0 0 1.597 0.1137 0.1302 0.0165 0.009 1.1 3.2 0.5 0.0 0 1.863 0.1146 0.1304 0.0158 0.006 1.0 3.2 0.5 0.0 0 0.887 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1137 0.1302 0.0165 0.009 1.1 3.2 0.5 0.0 0 1.863 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.37 13.02 1.65 3.780 21.274 46.334 3.604 11.37 13.02 1.65 3.780 21.274 1.390 3.604 11.37 13.02 1.65 3.780 21.274 5.792 3.604 11.40 13.09 1.69 3.717 21.264 23.167 3.599 11.42 13.18 1.76 3.742 21.239 46.334 3.600 11.38 13.21 1.83 3.762 21.224 69.502 3.596 11.33 13.17 1.84 3.775 21.220 92.669 3.592 11.32 13.19 1.87 3.786 21.215 115.836 3.591 11.28 13.15 1.86 3.795 21.215 139.003 3.588 11.30 13.20 1.90 3.815 21.200 162.170 3.589 11.27 13.16 1.89 3.822 21.198 185.338 3.586 11.26 13.16 1.90 3.829 21.197 208.505 3.585 11.24 13.14 1.90 3.836 21.197 231.672 3.584 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.390 Accepted refinement result: 11.37 13.02 1.65 3.780 21.274 1.390 3.604 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.26 3.31 241 1743 Protein: 9.11 115.04 17.03 3.32 0 1519 Water: 11.50 76.70 35.28 N/A 241 216 Other: 19.74 26.66 22.10 N/A 0 8 Chain A: 9.11 115.04 19.31 N/A 0 1743 Chain S: 15.51 60.00 35.32 N/A 241 0 Histogram: Values Number of atoms 9.11 - 19.70 1264 19.70 - 30.29 301 30.29 - 40.89 221 40.89 - 51.48 126 51.48 - 62.07 49 62.07 - 72.66 12 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1137 r_free=0.1302 r_work=0.1137 r_free=0.1302 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1137 r_free = 0.1302 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1130 r_free = 0.1300 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1130 r_free= 0.1300 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600866 | | target function (ml) not normalized (work): 299901.727097 | | target function (ml) not normalized (free): 15808.348843 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1138 0.1130 0.1300 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1467 0.1466 0.1517 n_refl.: 87582 remove outliers: r(all,work,free)=0.1467 0.1466 0.1517 n_refl.: 87582 overall B=-0.01 to atoms: r(all,work,free)=0.1466 0.1465 0.1517 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1129 0.1302 n_refl.: 87582 remove outliers: r(all,work,free)=0.1136 0.1128 0.1302 n_refl.: 87578 ======================== 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 89.58 81 5 0.4128 283.548 249.411 0.432 0.999 0.298 11.894-9.307 95.10 93 4 0.2412 469.598 455.917 0.860 1.001 0.239 9.237-7.194 98.18 209 7 0.2320 386.064 381.768 0.936 1.002 0.190 7.162-5.571 100.00 427 22 0.2094 296.113 285.649 0.916 1.002 0.155 5.546-4.326 100.00 867 58 0.1132 406.490 401.383 0.966 1.002 0.140 4.315-3.360 100.00 1859 96 0.0894 386.574 384.623 1.005 1.002 0.130 3.356-2.611 100.00 3867 181 0.1116 253.959 251.800 1.008 1.002 0.029 2.608-2.026 99.99 8198 413 0.0913 168.352 167.612 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0883 82.214 82.510 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1242 36.457 36.049 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.971 21.508 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0161 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1128 r_free=0.1302 After: r_work=0.1129 r_free=0.1302 ================================== NQH flips ================================== r_work=0.1129 r_free=0.1302 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1129 r_free=0.1302 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1129 r_free=0.1302 | n_water=457 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1129 r_free=0.1304 | n_water=456 | time (s): 50.510 (total time: 53.010) Filter (q & B) r_work=0.1129 r_free=0.1304 | n_water=456 | time (s): 1.400 (total time: 54.410) Compute maps r_work=0.1129 r_free=0.1304 | n_water=456 | time (s): 1.890 (total time: 56.300) Filter (map) r_work=0.1153 r_free=0.1289 | n_water=362 | time (s): 3.940 (total time: 60.240) Find peaks r_work=0.1153 r_free=0.1289 | n_water=362 | time (s): 0.720 (total time: 60.960) Add new water r_work=0.1200 r_free=0.1339 | n_water=494 | time (s): 3.970 (total time: 64.930) Refine new water occ: r_work=0.1148 r_free=0.1292 adp: r_work=0.1148 r_free=0.1294 occ: r_work=0.1137 r_free=0.1281 adp: r_work=0.1136 r_free=0.1281 occ: r_work=0.1129 r_free=0.1274 adp: r_work=0.1126 r_free=0.1271 ADP+occupancy (water only), MIN, final r_work=0.1126 r_free=0.1271 r_work=0.1126 r_free=0.1271 | n_water=494 | time (s): 305.780 (total time: 370.710) Filter (q & B) r_work=0.1131 r_free=0.1276 | n_water=462 | time (s): 3.930 (total time: 374.640) Filter (dist only) r_work=0.1131 r_free=0.1275 | n_water=461 | time (s): 49.000 (total time: 423.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.818309 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.018035 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1225 0.1335 0.0111 0.004 0.7 8.0 0.0 0.0 0 0.091 0.1175 0.1302 0.0127 0.004 0.8 8.3 0.0 0.0 0 0.273 0.1153 0.1288 0.0135 0.005 0.9 7.7 0.5 0.0 0 0.545 0.1142 0.1280 0.0138 0.006 1.0 8.0 0.5 0.0 0 0.818 0.1138 0.1278 0.0140 0.006 1.1 8.0 0.5 0.0 0 1.091 0.1134 0.1275 0.0142 0.008 1.1 7.7 0.5 0.0 0 1.364 0.1132 0.1275 0.0143 0.008 1.1 7.7 0.5 0.0 0 1.636 0.1131 0.1275 0.0144 0.009 1.1 7.7 0.5 0.0 0 1.909 0.1140 0.1279 0.0139 0.006 1.0 8.0 0.5 0.0 0 0.909 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1131 0.1275 0.0144 0.009 1.1 7.7 0.5 0.0 0 1.909 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 12.75 1.44 3.779 21.253 48.018 3.599 11.31 12.75 1.44 3.779 21.253 1.441 3.599 11.31 12.75 1.44 3.773 21.253 6.002 3.599 11.39 12.86 1.48 3.715 21.235 24.009 3.597 11.33 12.88 1.55 3.743 21.218 48.018 3.593 11.32 12.94 1.62 3.761 21.202 72.027 3.591 11.28 12.89 1.61 3.775 21.201 96.036 3.587 11.23 12.86 1.63 3.786 21.201 120.045 3.583 11.21 12.86 1.65 3.797 21.198 144.054 3.582 11.22 12.90 1.68 3.817 21.184 168.063 3.582 11.19 12.87 1.67 3.822 21.186 192.072 3.580 11.19 12.88 1.68 3.834 21.183 216.081 3.580 11.19 12.89 1.70 3.844 21.183 240.090 3.580 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.441 Accepted refinement result: 11.31 12.75 1.44 3.779 21.253 1.441 3.599 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 21.22 3.31 247 1741 Protein: 9.10 115.03 17.03 3.32 0 1519 Water: 11.49 76.69 35.03 N/A 247 214 Other: 19.74 26.65 22.09 N/A 0 8 Chain A: 9.10 115.03 19.26 N/A 0 1741 Chain S: 15.36 60.00 35.04 N/A 247 0 Histogram: Values Number of atoms 9.10 - 19.69 1266 19.69 - 30.29 301 30.29 - 40.88 222 40.88 - 51.47 129 51.47 - 62.07 48 62.07 - 72.66 11 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1275 r_work=0.1131 r_free=0.1275 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1275 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1128 r_free = 0.1274 target_work(ml) = 3.597 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1128 r_free= 0.1274 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.597326 | | target function (ml) not normalized (work): 299592.462779 | | target function (ml) not normalized (free): 15780.084194 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1334 0.1291 5.6669 5.5377| | 2: 3.57 - 2.84 1.00 2888 124 0.1045 0.1365 5.1362 5.2113| | 3: 2.83 - 2.48 1.00 2820 163 0.1109 0.1184 4.9206 4.9469| | 4: 2.47 - 2.25 1.00 2825 136 0.0893 0.0975 4.6052 4.637| | 5: 2.25 - 2.09 1.00 2756 127 0.0861 0.0996 4.5497 4.6221| | 6: 2.09 - 1.97 1.00 2846 113 0.0852 0.0981 4.2501 4.3504| | 7: 1.97 - 1.87 1.00 2787 165 0.0881 0.1145 3.9726 4.0912| | 8: 1.87 - 1.79 1.00 2789 144 0.0909 0.1065 3.8828 3.9699| | 9: 1.79 - 1.72 1.00 2745 138 0.0869 0.1202 3.6386 3.8353| | 10: 1.72 - 1.66 1.00 2831 160 0.0912 0.1211 3.5575 3.7131| | 11: 1.66 - 1.61 1.00 2712 147 0.0862 0.1003 3.4897 3.5613| | 12: 1.61 - 1.56 1.00 2773 144 0.0896 0.1140 3.3229 3.455| | 13: 1.56 - 1.52 1.00 2745 130 0.0936 0.1035 3.2988 3.3988| | 14: 1.52 - 1.48 1.00 2803 134 0.0973 0.1064 3.2327 3.325| | 15: 1.48 - 1.45 1.00 2738 128 0.0994 0.1241 3.1483 3.2737| | 16: 1.45 - 1.42 1.00 2756 161 0.1050 0.1241 3.1306 3.2333| | 17: 1.42 - 1.39 1.00 2785 139 0.1136 0.1314 3.1148 3.2362| | 18: 1.39 - 1.36 1.00 2741 179 0.1194 0.1325 3.1015 3.2328| | 19: 1.36 - 1.34 1.00 2807 134 0.1254 0.1545 3.1083 3.2578| | 20: 1.34 - 1.32 1.00 2696 147 0.1365 0.1455 3.1097 3.1509| | 21: 1.32 - 1.30 1.00 2785 112 0.1462 0.1516 3.1097 3.1069| | 22: 1.29 - 1.27 1.00 2704 152 0.1553 0.2006 3.119 3.3033| | 23: 1.27 - 1.26 1.00 2802 156 0.1643 0.1774 3.1311 3.1964| | 24: 1.26 - 1.24 1.00 2744 132 0.1709 0.1825 3.1259 3.2307| | 25: 1.24 - 1.22 1.00 2733 148 0.1876 0.2155 3.1403 3.2616| | 26: 1.22 - 1.21 1.00 2727 135 0.1906 0.1751 3.1479 3.195| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2160 3.1704 3.1591| | 28: 1.19 - 1.18 1.00 2671 147 0.2199 0.2306 3.1648 3.1777| | 29: 1.18 - 1.16 1.00 2800 134 0.2263 0.2390 3.1461 3.2279| | 30: 1.16 - 1.15 1.00 2739 148 0.2448 0.2447 3.1426 3.1662| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.58 2920 171 0.95 8.09 1.00 0.97 5263.56| | 2: 3.57 - 2.84 2888 124 0.93 11.89 1.01 0.97 5263.56| | 3: 2.83 - 2.48 2820 163 0.90 15.80 0.99 0.97 4406.63| | 4: 2.47 - 2.25 2825 136 0.92 12.90 1.00 0.98 2196.88| | 5: 2.25 - 2.09 2756 127 0.91 15.02 1.01 0.98 2196.88| | 6: 2.09 - 1.97 2846 113 0.93 12.04 1.02 0.98 1285.59| | 7: 1.97 - 1.87 2787 165 0.95 9.23 1.02 0.97 508.38| | 8: 1.87 - 1.79 2789 144 0.93 12.63 1.00 0.97 508.38| | 9: 1.79 - 1.72 2745 138 0.94 10.01 0.98 0.97 287.30| | 10: 1.72 - 1.66 2831 160 0.94 11.13 0.98 0.97 243.03| | 11: 1.66 - 1.61 2712 147 0.94 11.70 0.98 0.97 232.87| | 12: 1.61 - 1.56 2773 144 0.95 8.90 0.99 0.97 137.08| | 13: 1.56 - 1.52 2745 130 0.95 10.38 1.03 0.97 137.08| | 14: 1.52 - 1.48 2803 134 0.94 10.76 1.02 0.98 123.14| | 15: 1.48 - 1.45 2738 128 0.95 9.95 1.02 0.98 97.61| | 16: 1.45 - 1.42 2756 161 0.94 11.10 1.02 0.98 97.61| | 17: 1.42 - 1.39 2785 139 0.95 10.91 1.01 0.98 88.92| | 18: 1.39 - 1.36 2741 179 0.94 11.53 1.01 0.98 83.88| | 19: 1.36 - 1.34 2807 134 0.94 11.88 1.00 0.98 83.88| | 20: 1.34 - 1.32 2696 147 0.94 12.14 0.98 0.96 79.89| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.96 79.61| | 22: 1.29 - 1.27 2704 152 0.93 13.68 0.98 0.96 80.02| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.94 82.10| | 24: 1.26 - 1.24 2744 132 0.92 14.87 0.96 0.94 82.10| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 84.14| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.03 0.93 86.39| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.93 86.39| | 28: 1.19 - 1.18 2671 147 0.88 20.44 1.01 0.92 90.22| | 29: 1.18 - 1.16 2800 134 0.88 20.59 0.99 0.92 91.66| | 30: 1.16 - 1.15 2739 148 0.86 22.10 0.98 0.92 91.66| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.61 max = 5263.56 mean = 825.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.95 mean = 13.34| |phase err.(test): min = 0.00 max = 88.42 mean = 13.34| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1128 0.1274 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1464 0.1463 0.1499 n_refl.: 87578 remove outliers: r(all,work,free)=0.1464 0.1463 0.1499 n_refl.: 87578 overall B=-0.00 to atoms: r(all,work,free)=0.1463 0.1462 0.1499 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1135 0.1128 0.1274 n_refl.: 87578 remove outliers: r(all,work,free)=0.1132 0.1124 0.1274 n_refl.: 87570 ======================== 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 86.46 78 5 0.4057 278.070 238.185 0.412 0.999 0.290 11.894-9.307 91.18 89 4 0.2308 478.576 453.561 0.847 1.001 0.224 9.237-7.194 97.73 208 7 0.2311 387.147 377.668 0.920 1.002 0.176 7.162-5.571 100.00 427 22 0.2112 296.113 285.046 0.908 1.002 0.150 5.546-4.326 100.00 867 58 0.1136 406.490 401.559 0.964 1.002 0.120 4.315-3.360 100.00 1859 96 0.0903 386.574 384.977 1.006 1.002 0.120 3.356-2.611 100.00 3867 181 0.1097 253.959 252.184 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0908 168.352 167.767 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0883 82.214 82.583 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1245 36.457 36.071 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2169 22.971 21.519 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0114 ================= 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 : 0.2604 0.1939 0.084 5.376 8.8 119.3 19.9 258 0.000 1_bss: 0.1644 0.1762 0.084 5.376 9.1 119.5 20.1 258 0.000 1_settarget: 0.1644 0.1762 0.084 5.376 9.1 119.5 20.1 258 0.000 1_nqh: 0.1647 0.1764 0.084 5.376 9.1 119.5 20.1 258 0.003 1_weight: 0.1647 0.1764 0.084 5.376 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1229 0.1472 0.005 0.821 9.1 119.5 20.1 258 0.131 1_adp: 0.1236 0.1468 0.005 0.821 9.1 119.5 20.1 258 0.131 1_regHadp: 0.1237 0.1471 0.005 0.821 9.1 119.5 20.1 258 0.131 1_occ: 0.1231 0.1468 0.005 0.821 9.1 119.5 20.1 258 0.131 2_bss: 0.1228 0.1458 0.005 0.821 9.1 119.5 20.1 258 0.131 2_settarget: 0.1228 0.1458 0.005 0.821 9.1 119.5 20.1 258 0.131 2_updatecdl: 0.1228 0.1458 0.005 0.837 9.1 119.5 20.1 258 0.131 2_nqh: 0.1229 0.1459 0.005 0.837 9.1 119.5 20.1 258 0.134 2_sol: 0.1204 0.1388 0.005 0.837 9.1 115.0 22.2 419 n/a 2_weight: 0.1204 0.1388 0.005 0.837 9.1 115.0 22.2 419 n/a 2_xyzrec: 0.1190 0.1406 0.007 0.901 9.1 115.0 22.2 419 n/a 2_adp: 0.1190 0.1406 0.007 0.901 9.1 115.0 22.2 419 n/a 2_regHadp: 0.1190 0.1406 0.007 0.901 9.1 115.0 22.2 419 n/a 2_occ: 0.1189 0.1409 0.007 0.901 9.1 115.0 22.2 419 n/a 3_bss: 0.1185 0.1405 0.007 0.901 9.1 115.0 22.2 419 n/a 3_settarget: 0.1185 0.1405 0.007 0.901 9.1 115.0 22.2 419 n/a 3_updatecdl: 0.1185 0.1405 0.007 0.902 9.1 115.0 22.2 419 n/a 3_nqh: 0.1185 0.1405 0.007 0.902 9.1 115.0 22.2 419 n/a 3_sol: 0.1211 0.1404 0.007 0.902 9.1 115.0 21.3 451 n/a 3_weight: 0.1211 0.1404 0.007 0.902 9.1 115.0 21.3 451 n/a 3_xyzrec: 0.1161 0.1308 0.008 1.085 9.1 115.0 21.3 451 n/a 3_adp: 0.1161 0.1308 0.008 1.085 9.1 115.0 21.3 451 n/a 3_regHadp: 0.1161 0.1308 0.008 1.085 9.1 115.0 21.3 451 n/a 3_occ: 0.1153 0.1305 0.008 1.085 9.1 115.0 21.3 451 n/a 4_bss: 0.1144 0.1304 0.008 1.085 9.1 115.0 21.3 451 n/a 4_settarget: 0.1144 0.1304 0.008 1.085 9.1 115.0 21.3 451 n/a 4_updatecdl: 0.1144 0.1304 0.008 1.084 9.1 115.0 21.3 451 n/a 4_nqh: 0.1149 0.1307 0.008 1.084 9.1 115.0 21.3 451 n/a 4_sol: 0.1146 0.1305 0.008 1.084 9.1 115.0 21.3 457 n/a 4_weight: 0.1146 0.1305 0.008 1.084 9.1 115.0 21.3 457 n/a 4_xyzrec: 0.1137 0.1302 0.009 1.124 9.1 115.0 21.3 457 n/a 4_adp: 0.1137 0.1302 0.009 1.124 9.1 115.0 21.3 457 n/a 4_regHadp: 0.1137 0.1302 0.009 1.124 9.1 115.0 21.3 457 n/a 4_occ: 0.1130 0.1300 0.009 1.124 9.1 115.0 21.3 457 n/a 5_bss: 0.1128 0.1302 0.009 1.124 9.1 115.0 21.3 457 n/a 5_settarget: 0.1128 0.1302 0.009 1.124 9.1 115.0 21.3 457 n/a 5_updatecdl: 0.1128 0.1302 0.009 1.126 9.1 115.0 21.3 457 n/a 5_setrh: 0.1129 0.1302 0.009 1.126 9.1 115.0 21.3 457 n/a 5_nqh: 0.1129 0.1302 0.009 1.126 9.1 115.0 21.3 457 n/a 5_sol: 0.1131 0.1275 0.009 1.126 9.1 115.0 21.2 461 n/a 5_weight: 0.1131 0.1275 0.009 1.126 9.1 115.0 21.2 461 n/a 5_xyzrec: 0.1131 0.1275 0.009 1.137 9.1 115.0 21.2 461 n/a 5_adp: 0.1131 0.1275 0.009 1.137 9.1 115.0 21.2 461 n/a 5_regHadp: 0.1131 0.1275 0.009 1.137 9.1 115.0 21.2 461 n/a 5_occ: 0.1128 0.1274 0.009 1.137 9.1 115.0 21.2 461 n/a end: 0.1124 0.1274 0.009 1.137 9.1 115.0 21.2 461 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_9255201_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_9255201_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4500 Refinement macro-cycles (run) : 13576.8600 Write final files (write_after_run_outputs) : 100.0600 Total : 13680.3700 Total CPU time: 3.81 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:07:58 PST -0800 (1735366078.12 s) Start R-work = 0.1644, R-free = 0.1762 Final R-work = 0.1124, R-free = 0.1274 =============================================================================== Job complete usr+sys time: 13872.06 seconds wall clock time: 252 minutes 19.54 seconds (15139.54 seconds total)