Starting phenix.refine on Mon May 20 17:17:05 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/3fm7.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=True secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/3fm7.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/3fm7.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1598 Classifications: {'peptide': 103} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1609 Classifications: {'peptide': 104} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 23} Chain: "D" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 24} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1381 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "F" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1380 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Time building chain proxies: 2.43, per 1000 atoms: 0.36 Number of scatterers: 6838 At special positions: 0 Unit cell: (115.79, 115.79, 90.5004, 90, 90, 120) Space group: P 62 (No. 171) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 666 8.00 N 569 7.00 C 2187 6.00 H 3394 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 - 3.50 Amino acid : False - 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: 4.73 Conformation dependent library (CDL) restraints added in 549.5 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 3382 1.15 - 1.31: 591 1.31 - 1.48: 1393 1.48 - 1.64: 1508 1.64 - 1.81: 32 Bond restraints: 6906 Sorted by residual: bond pdb=" NE2 GLN A 33 " pdb="HE21 GLN A 33 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N ALA E 82 " pdb=" H ALA E 82 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NE2 GLN F 27 " pdb="HE21 GLN F 27 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN D 116 " pdb="HE21 GLN D 116 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N PHE F 86 " pdb=" H PHE F 86 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6901 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.50: 230 107.50 - 114.12: 8500 114.12 - 120.73: 1545 120.73 - 127.35: 2144 127.35 - 133.97: 26 Bond angle restraints: 12445 Sorted by residual: angle pdb=" C ASN F 51 " pdb=" N PRO F 52 " pdb=" CA PRO F 52 " ideal model delta sigma weight residual 119.89 122.75 -2.86 1.02e+00 9.61e-01 7.84e+00 angle pdb=" N VAL E 7 " pdb=" CA VAL E 7 " pdb=" C VAL E 7 " ideal model delta sigma weight residual 106.72 111.14 -4.42 1.59e+00 3.96e-01 7.74e+00 angle pdb=" N ASN C 119 " pdb=" CA ASN C 119 " pdb=" C ASN C 119 " ideal model delta sigma weight residual 107.61 112.16 -4.55 1.74e+00 3.30e-01 6.84e+00 angle pdb=" N ASN E 10 " pdb=" CA ASN E 10 " pdb=" C ASN E 10 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.71e+00 angle pdb=" CA GLY A 72 " pdb=" C GLY A 72 " pdb=" N ALA A 73 " ideal model delta sigma weight residual 118.67 116.19 2.48 9.80e-01 1.04e+00 6.40e+00 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.78: 2904 26.78 - 53.56: 289 53.56 - 80.34: 53 80.34 - 107.12: 5 107.12 - 133.91: 2 Dihedral angle restraints: 3253 sinusoidal: 1731 harmonic: 1522 Sorted by residual: dihedral pdb=" CA MET F 13 " pdb=" C MET F 13 " pdb=" N SER F 14 " pdb=" CA SER F 14 " ideal model delta harmonic sigma weight residual 180.00 46.09 133.91 0 5.00e+00 4.00e-02 7.17e+02 dihedral pdb=" CA ASN C 114 " pdb=" C ASN C 114 " pdb=" N VAL C 115 " pdb=" CA VAL C 115 " ideal model delta harmonic sigma weight residual 180.00 52.83 127.17 0 5.00e+00 4.00e-02 6.47e+02 dihedral pdb=" CA MET E 13 " pdb=" C MET E 13 " pdb=" N SER E 14 " pdb=" CA SER E 14 " ideal model delta harmonic sigma weight residual -180.00 -75.18 -104.82 0 5.00e+00 4.00e-02 4.39e+02 ... (remaining 3250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 437 0.022 - 0.043: 11 0.043 - 0.065: 19 0.065 - 0.087: 59 0.087 - 0.108: 13 Chirality restraints: 539 Sorted by residual: chirality pdb=" CA ASN D 114 " pdb=" N ASN D 114 " pdb=" C ASN D 114 " pdb=" CB ASN D 114 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.93e-01 chirality pdb=" CA ILE B 103 " pdb=" N ILE B 103 " pdb=" C ILE B 103 " pdb=" CB ILE B 103 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.09 2.00e-01 2.50e+01 2.10e-01 chirality pdb=" CA ILE B 23 " pdb=" N ILE B 23 " pdb=" C ILE B 23 " pdb=" CB ILE B 23 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 2.04e-01 ... (remaining 536 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 40 " -0.000 2.00e-02 2.50e+03 7.01e-04 1.97e-02 pdb=" CG TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP B 40 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 40 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP B 40 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 46 " 0.000 2.00e-02 2.50e+03 7.99e-04 1.91e-02 pdb=" CG PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE F 46 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 46 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE F 46 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE F 46 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE F 46 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 54 " -0.000 2.00e-02 2.50e+03 6.55e-04 1.72e-02 pdb=" CG TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP E 54 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP E 54 " 0.000 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 0.75 - 1.52: 48 1.52 - 2.29: 1738 2.29 - 3.06: 20457 3.06 - 3.83: 30156 3.83 - 4.60: 47763 Warning: very small nonbonded interaction distances. Nonbonded interactions: 100162 Sorted by model distance: nonbonded pdb=" HA ASN C 114 " pdb="HG23 VAL C 115 " model vdw 0.746 2.440 nonbonded pdb=" HG3 GLN C 133 " pdb=" HB3 LYS F 36 " model vdw 0.848 2.440 nonbonded pdb=" HA GLN C 116 " pdb=" HB2 ALA C 117 " model vdw 0.871 2.440 nonbonded pdb=" HG2 ARG B 94 " pdb="HH11 ARG B 94 " model vdw 0.985 2.270 nonbonded pdb=" HA MET F 13 " pdb=" HB2 SER F 14 " model vdw 1.040 2.440 ... (remaining 100157 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: 5 Type Number sf(0) Gaussians S 22 15.91 1 O 666 7.97 1 N 569 6.97 1 C 2187 5.97 1 H 3394 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 ===================== Setting occupancies to: 1.000: selected atoms: 3394 of 6838 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 6838 n_use_u_iso = 6838 n_use_u_aniso = 0 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 = 6838 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6838 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 6838 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 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 } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "3fm7_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3394 occupancy sum: 3394.00 (% of total atoms 49.68) Rotatable: count: 1005 occupancy sum: 1005.00 (% of total atoms 14.71) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 35.65 A, n_refl.=8745 (all), 9.95 % free)-------------| | | | r_work= 0.3573 r_free= 0.3825 coordinate error (max.-lik. estimate): 0.14 A | | | | normalized target function (ml) (work): 6.431057 | | target function (ml) not normalized (work): 50644.571594 | | target function (ml) not normalized (free): 5712.019596 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 35.65 - 6.35 1.00 1358 142 0.4105 0.4302 7.4385 7.4058| | 2: 6.35 - 5.05 1.00 1326 136 0.3185 0.3402 6.6863 6.7637| | 3: 5.04 - 4.41 1.00 1320 143 0.3188 0.3218 6.3284 6.4613| | 4: 4.41 - 4.01 0.99 1291 153 0.3401 0.3699 6.1277 6.4141| | 5: 4.01 - 3.72 0.99 1285 148 0.3360 0.4071 5.9732 6.2399| | 6: 3.72 - 3.50 0.99 1295 148 0.3851 0.4177 5.9746 6.1601| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 35.65 - 6.35 1358 142 0.52 50.23 0.82 0.72 437329.23| | 2: 6.35 - 5.05 1326 136 0.56 47.21 1.23 0.89 198795.77| | 3: 5.04 - 4.41 1320 143 0.78 29.03 1.38 1.01 71014.34| | 4: 4.41 - 4.01 1291 153 0.71 34.61 1.41 1.00 52577.48| | 5: 4.01 - 3.72 1285 148 0.62 42.28 1.34 0.96 45018.50| | 6: 3.72 - 3.50 1295 148 0.64 41.10 1.46 0.94 40633.46| |alpha: min = 0.72 max = 1.01 mean = 0.92| |beta: min = 40633.46 max = 437329.23 mean = 143438.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.64| |phase err.(work): min = 0.00 max = 89.98 mean = 40.81| |phase err.(test): min = 0.00 max = 89.61 mean = 40.40| |-----------------------------------------------------------------------------| ----------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 : 0.003 0.016 3512 Z= 0.224 Angle : 0.846 4.753 4762 Z= 0.586 Chirality : 0.032 0.108 539 Planarity : 0.000 0.001 601 Dihedral : 23.554 133.906 1264 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 44.73 Ramachandran Plot: Outliers : 4.77 % Allowed : 13.60 % Favored : 81.62 % Rotamer: Outliers : 25.33 % Allowed : 17.15 % Favored : 57.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 2.64 % 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: -5.75 (0.30), residues: 419 helix: -4.63 (0.19), residues: 131 sheet: -1.47 (0.57), residues: 92 loop : -4.46 (0.27), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 60 TYR 0.001 0.000 TYR F 65 PHE 0.001 0.000 PHE F 46 TRP 0.001 0.000 TRP B 40 HIS 0.000 0.000 HIS A 76 Individual atomic B min max mean iso aniso Overall: 2.00 500.00 94.66 89.80 3444 0 Protein: 2.00 500.00 94.66 89.80 3444 0 Chain A: 2.00 500.00 114.65 N/A 807 0 Chain B: 2.00 458.88 97.81 N/A 813 0 Chain C: 2.00 495.15 104.99 N/A 215 0 Chain D: 2.00 500.00 119.77 N/A 215 0 Chain E: 2.00 478.28 71.82 N/A 697 0 Chain F: 2.00 403.25 79.76 N/A 697 0 Histogram: Values Number of atoms 2.00 - 51.80 934 51.80 - 101.60 1312 101.60 - 151.40 657 151.40 - 201.20 310 201.20 - 251.00 111 251.00 - 300.80 57 300.80 - 350.60 34 350.60 - 400.40 17 400.40 - 450.20 6 450.20 - 500.00 6 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.50 - 35.65 A, n_refl.=8745 (all), 9.95 % free)-------------| | | | r_work= 0.3573 r_free= 0.3825 coordinate error (max.-lik. estimate): 0.14 A | | | | normalized target function (ml) (work): 6.431057 | | target function (ml) not normalized (work): 50644.571594 | | target function (ml) not normalized (free): 5712.019596 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3589 0.3573 0.3825 n_refl.: 8745 re-set all scales: r(all,work,free)=0.3589 0.3573 0.3825 n_refl.: 8745 remove outliers: r(all,work,free)=0.3585 0.3571 0.3811 n_refl.: 8739 overall B=17.64 to atoms: r(all,work,free)=0.4218 0.4229 0.4187 n_refl.: 8739 bulk-solvent and scaling: r(all,work,free)=0.2240 0.2141 0.3139 n_refl.: 8739 remove outliers: r(all,work,free)=0.2235 0.2135 0.3139 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3558 1472.375 1342.545 1.239 0.973 0.325 15.490-12.512 99.01 89 11 0.2187 1306.036 1261.365 1.106 0.974 0.283 12.419-9.967 99.48 175 15 0.1814 1476.037 1437.608 1.169 0.977 0.280 9.933-7.985 99.73 337 34 0.1928 1108.226 1073.275 1.178 0.978 0.264 7.976-6.403 100.00 631 64 0.2456 609.809 575.118 1.094 0.979 0.229 6.399-5.132 99.93 1234 135 0.2161 578.066 550.281 0.973 0.981 0.174 5.129-4.115 99.81 2357 259 0.1739 559.520 545.409 0.991 0.984 0.113 4.114-3.501 98.83 2959 341 0.2478 337.971 323.299 1.036 0.987 0.037 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0046 b_overall=-0.2819 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.683200 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.127326 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2266 0.3213 0.0947 0.003 0.7 7.5 1.9 15.6 0 0.125 0.2205 0.3200 0.0995 0.003 0.6 8.8 1.9 17.2 0 0.250 0.2167 0.3213 0.1046 0.003 0.7 8.9 1.9 17.7 0 0.500 0.2112 0.3209 0.1097 0.004 0.7 10.1 1.9 18.2 0 1.000 0.2041 0.3198 0.1157 0.005 0.8 12.6 1.9 20.3 0 2.000 0.2008 0.3218 0.1211 0.006 0.8 15.7 1.9 20.3 0 3.000 0.1970 0.3215 0.1245 0.008 0.9 17.6 1.9 21.6 0 4.000 0.1954 0.3232 0.1279 0.009 1.0 21.1 1.9 23.0 0 5.000 0.1929 0.3231 0.1302 0.010 1.0 22.7 1.9 23.5 0 6.000 0.1912 0.3235 0.1323 0.011 1.1 23.2 1.9 23.7 0 7.000 0.1906 0.3248 0.1341 0.012 1.2 25.4 1.9 23.7 0 8.000 0.1891 0.3238 0.1347 0.013 1.2 26.1 1.9 23.7 0 9.000 0.1876 0.3233 0.1357 0.014 1.3 27.3 1.9 24.0 0 10.000 0.1893 0.3236 0.1343 0.013 1.2 25.7 1.9 24.0 0 8.842 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2041 0.3198 0.1157 0.005 0.8 12.6 1.9 20.3 0 2.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.41 31.98 11.57 64.040 110.958 0.127 0.050 25.50 31.79 6.30 46.617 120.211 0.004 0.072 25.18 31.66 6.48 46.704 120.043 0.016 0.071 24.09 31.25 7.16 47.097 119.457 0.064 0.065 23.03 30.87 7.84 47.623 118.928 0.127 0.061 22.30 30.59 8.29 48.061 118.674 0.191 0.057 21.73 30.39 8.66 48.544 118.386 0.255 0.055 21.24 30.24 9.00 49.074 118.026 0.318 0.053 20.84 30.13 9.29 49.560 117.750 0.382 0.051 20.53 30.04 9.50 49.981 117.579 0.446 0.050 20.26 29.95 9.69 50.403 117.392 0.509 0.049 20.48 29.96 9.48 50.417 118.756 0.573 0.050 20.23 29.85 9.62 50.843 118.404 0.637 0.049 max suggested for this run: 22.19 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.004 Accepted refinement result: 25.50 31.79 6.30 46.617 120.211 0.004 0.072 Individual atomic B min max mean iso aniso Overall: 65.29 512.64 130.67 57.55 3444 0 Protein: 65.29 512.64 130.67 57.55 3444 0 Chain A: 79.38 512.64 152.14 N/A 807 0 Chain B: 80.42 471.52 133.60 N/A 813 0 Chain C: 75.53 507.79 144.30 N/A 215 0 Chain D: 80.63 512.64 155.04 N/A 215 0 Chain E: 65.29 490.92 106.55 N/A 697 0 Chain F: 72.76 415.89 114.81 N/A 697 0 Histogram: Values Number of atoms 65.29 - 110.02 1507 110.02 - 154.76 1248 154.76 - 199.49 399 199.49 - 244.23 144 244.23 - 288.96 61 288.96 - 333.70 36 333.70 - 378.44 26 378.44 - 423.17 14 423.17 - 467.91 3 467.91 - 512.64 6 =========================== Idealize ADP of riding H ========================== r_work=0.2550 r_free=0.3179 r_work=0.2620 r_free=0.3157 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2620 r_free= 0.3157 coordinate error (max.-lik. estimate): 0.14 A | | | | normalized target function (ls_wunit_k1) (work): 0.075686 | | target function (ls_wunit_k1) not normalized (work): 595.576819 | | target function (ls_wunit_k1) not normalized (free): 104.158958 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2672 0.2620 0.3157 n_refl.: 8738 re-set all scales: r(all,work,free)=0.5180 0.5209 0.4920 n_refl.: 8738 remove outliers: r(all,work,free)=0.5180 0.5209 0.4920 n_refl.: 8738 overall B=-34.56 to atoms: r(all,work,free)=0.3968 0.3980 0.3912 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2371 0.2302 0.3004 n_refl.: 8738 remove outliers: r(all,work,free)=0.2371 0.2302 0.3004 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3146 653.329 614.132 1.287 1.010 0.326 15.490-12.512 99.01 89 11 0.1796 579.521 561.934 1.137 1.011 0.288 12.419-9.967 99.48 175 15 0.1414 654.954 644.514 1.230 1.014 0.285 9.933-7.985 99.73 337 34 0.1539 491.747 481.398 1.246 1.015 0.291 7.976-6.403 100.00 631 64 0.2338 270.588 258.355 1.090 1.018 0.238 6.399-5.132 99.93 1234 135 0.2231 256.502 244.781 0.960 1.021 0.197 5.129-4.115 99.81 2357 259 0.2099 248.273 242.035 0.949 1.026 0.138 4.114-3.501 98.83 2959 341 0.3063 149.966 142.202 0.945 1.032 0.074 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=7.4061 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 5.518727 wxc_scale = 0.030 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.038310 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2459 0.3034 0.0574 0.003 0.6 8.7 1.4 14.8 0 0.016 0.2422 0.3015 0.0593 0.003 0.6 9.2 1.4 14.5 0 0.049 0.2373 0.3004 0.0632 0.003 0.6 9.1 1.4 15.3 0 0.099 0.2346 0.3000 0.0654 0.003 0.6 9.4 1.7 15.0 0 0.148 0.2327 0.3010 0.0682 0.003 0.6 9.1 1.4 15.6 0 0.198 0.2305 0.3005 0.0700 0.003 0.6 9.7 1.4 16.4 0 0.247 0.2285 0.3002 0.0718 0.003 0.6 9.7 1.4 16.6 0 0.296 0.2274 0.3007 0.0732 0.004 0.7 10.0 1.4 16.6 0 0.346 0.2346 0.3006 0.0660 0.003 0.6 9.4 1.4 15.3 0 0.165 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2346 0.3000 0.0654 0.003 0.6 9.4 1.7 15.0 0 0.148 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.46 30.00 6.54 45.468 107.778 0.038 5.662 29.37 31.24 1.87 33.414 123.223 0.001 5.712 28.10 30.42 2.31 33.149 122.164 0.005 5.701 25.30 28.78 3.47 34.126 119.069 0.019 5.672 23.33 28.00 4.67 36.662 116.369 0.038 5.625 22.30 27.94 5.64 38.891 114.328 0.057 5.599 21.83 28.03 6.20 40.383 113.167 0.077 5.589 21.56 28.14 6.57 41.208 111.900 0.096 5.587 21.44 28.19 6.75 41.905 111.409 0.115 5.585 21.37 28.25 6.88 42.405 111.141 0.134 5.584 21.33 28.32 7.00 42.801 110.915 0.153 5.584 21.29 28.37 7.08 43.111 110.805 0.172 5.583 21.26 28.41 7.15 43.370 110.708 0.192 5.583 max suggested for this run: 21.56 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.019 Accepted refinement result: 25.30 28.78 3.47 34.126 119.069 0.019 5.672 Individual atomic B min max mean iso aniso Overall: 30.79 473.08 118.53 38.00 3444 0 Protein: 30.79 473.08 118.53 38.00 3444 0 Chain A: 71.98 473.08 147.83 N/A 807 0 Chain B: 51.10 431.96 123.60 N/A 813 0 Chain C: 37.98 468.23 134.04 N/A 215 0 Chain D: 54.72 473.08 147.48 N/A 215 0 Chain E: 30.79 451.36 86.60 N/A 697 0 Chain F: 35.26 376.33 96.92 N/A 697 0 Histogram: Values Number of atoms 30.79 - 75.01 567 75.01 - 119.24 1424 119.24 - 163.47 1003 163.47 - 207.70 290 207.70 - 251.93 76 251.93 - 296.16 35 296.16 - 340.39 26 340.39 - 384.62 14 384.62 - 428.85 3 428.85 - 473.08 6 =========================== Idealize ADP of riding H ========================== r_work=0.2530 r_free=0.2878 r_work=0.2566 r_free=0.2873 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2566 r_free= 0.2873 coordinate error (max.-lik. estimate): 0.36 A | | | | normalized target function (ml) (work): 5.680253 | | target function (ml) not normalized (work): 44697.908092 | | target function (ml) not normalized (free): 5009.113554 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2596 0.2566 0.2873 n_refl.: 8738 re-set all scales: r(all,work,free)=0.4596 0.4632 0.4282 n_refl.: 8738 remove outliers: r(all,work,free)=0.4596 0.4632 0.4282 n_refl.: 8738 overall B=-8.89 to atoms: r(all,work,free)=0.4279 0.4311 0.4014 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2515 0.2471 0.2922 n_refl.: 8738 remove outliers: r(all,work,free)=0.2515 0.2471 0.2922 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3401 753.263 692.418 1.205 0.961 0.322 15.490-12.512 99.01 89 11 0.1937 668.165 645.387 1.170 0.964 0.293 12.419-9.967 99.48 175 15 0.1567 755.137 740.069 1.236 0.969 0.285 9.933-7.985 99.73 337 34 0.1719 566.966 550.367 1.250 0.972 0.268 7.976-6.403 100.00 631 64 0.2642 311.977 293.324 1.129 0.976 0.220 6.399-5.132 99.93 1234 135 0.2495 295.737 279.119 1.005 0.982 0.172 5.129-4.115 99.81 2357 259 0.2188 286.249 277.560 0.985 0.991 0.089 4.114-3.501 98.83 2959 341 0.3215 172.905 162.534 0.997 1.001 0.059 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=4.0147 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2471 r_free=0.2922 After: r_work=0.2471 r_free=0.2922 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 5.820937 wxc_scale = 0.029 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.033493 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2475 0.2922 0.0447 0.003 0.6 10.3 1.4 14.8 0 0.017 0.2473 0.2922 0.0448 0.003 0.6 10.3 1.4 14.8 0 0.051 0.2471 0.2923 0.0452 0.003 0.6 10.3 1.4 14.8 0 0.102 0.2469 0.2923 0.0455 0.003 0.6 10.1 1.4 14.8 0 0.153 0.2466 0.2922 0.0456 0.003 0.6 10.3 1.4 14.8 0 0.204 0.2462 0.2922 0.0460 0.004 0.6 10.3 1.4 14.8 0 0.255 0.2458 0.2922 0.0463 0.004 0.6 10.3 1.4 14.8 0 0.306 0.2455 0.2922 0.0466 0.004 0.6 10.3 1.4 14.8 0 0.358 0.2468 0.2922 0.0454 0.003 0.6 10.3 1.4 14.8 0 0.170 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2469 0.2923 0.0455 0.003 0.6 10.1 1.4 14.8 0 0.153 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.69 29.23 4.55 32.630 121.604 0.033 5.823 29.82 30.93 1.11 27.525 130.437 0.001 5.885 28.99 30.39 1.39 26.939 130.512 0.004 5.865 26.09 28.84 2.75 28.957 127.352 0.017 5.806 23.69 28.16 4.47 31.469 123.408 0.033 5.773 23.29 28.26 4.98 32.082 122.658 0.050 5.769 23.26 28.36 5.10 32.327 122.127 0.067 5.772 23.20 28.40 5.19 32.487 122.027 0.084 5.772 23.17 28.43 5.26 32.601 121.984 0.100 5.771 23.14 28.45 5.31 32.691 121.969 0.117 5.771 23.11 28.45 5.34 32.761 121.967 0.134 5.770 23.10 28.46 5.37 32.820 121.976 0.151 5.770 23.08 28.46 5.39 32.871 121.988 0.167 5.769 max suggested for this run: 24.32 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.017 Accepted refinement result: 26.09 28.84 2.75 28.957 127.352 0.017 5.806 Individual atomic B min max mean iso aniso Overall: 48.29 459.19 121.06 33.41 3444 0 Protein: 48.29 459.19 121.06 33.41 3444 0 Chain A: 83.75 459.19 149.50 N/A 807 0 Chain B: 64.55 418.07 125.47 N/A 813 0 Chain C: 58.75 454.34 134.55 N/A 215 0 Chain D: 70.02 459.19 149.06 N/A 215 0 Chain E: 48.29 437.47 91.95 N/A 697 0 Chain F: 51.97 362.44 99.28 N/A 697 0 Histogram: Values Number of atoms 48.29 - 89.38 922 89.38 - 130.47 1368 130.47 - 171.56 797 171.56 - 212.65 220 212.65 - 253.74 68 253.74 - 294.83 29 294.83 - 335.92 19 335.92 - 377.01 13 377.01 - 418.10 4 418.10 - 459.19 4 =========================== Idealize ADP of riding H ========================== r_work=0.2609 r_free=0.2884 r_work=0.2617 r_free=0.2887 ----------X-ray data---------- |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2617 r_free= 0.2887 coordinate error (max.-lik. estimate): 0.17 A | | | | normalized target function (ml) (work): 5.809751 | | target function (ml) not normalized (work): 45716.931395 | | target function (ml) not normalized (free): 5122.191300 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 35.65 - 6.35 1.00 1354 141 0.2318 0.2632 6.3386 6.5317| | 2: 6.35 - 5.05 1.00 1326 136 0.2409 0.2789 5.9478 6.0683| | 3: 5.04 - 4.41 1.00 1320 143 0.2263 0.2467 5.7893 5.8143| | 4: 4.41 - 4.01 0.99 1291 153 0.2768 0.3066 5.6649 5.8204| | 5: 4.01 - 3.72 0.99 1285 148 0.3237 0.3323 5.5178 5.5808| | 6: 3.72 - 3.50 0.99 1293 148 0.3733 0.3800 5.5702 5.5946| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 35.65 - 6.35 1354 141 0.73 31.99 0.92 0.98 67526.82| | 2: 6.35 - 5.05 1326 136 0.72 34.42 1.02 1.03 36507.77| | 3: 5.04 - 4.41 1320 143 0.83 24.17 1.12 1.08 18480.06| | 4: 4.41 - 4.01 1291 153 0.77 29.32 1.14 1.11 14590.64| | 5: 4.01 - 3.72 1285 148 0.68 37.56 1.19 1.08 13064.10| | 6: 3.72 - 3.50 1293 148 0.67 38.98 1.24 1.04 13216.63| |alpha: min = 0.98 max = 1.11 mean = 1.05| |beta: min = 13064.10 max = 67526.82 mean = 27569.87| |figures of merit: min = 0.00 max = 1.00 mean = 0.73| |phase err.(work): min = 0.00 max = 89.94 mean = 32.71| |phase err.(test): min = 0.00 max = 90.00 mean = 32.58| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2644 0.2617 0.2887 n_refl.: 8738 re-set all scales: r(all,work,free)=0.4913 0.4954 0.4556 n_refl.: 8738 remove outliers: r(all,work,free)=0.4913 0.4954 0.4556 n_refl.: 8738 overall B=-17.38 to atoms: r(all,work,free)=0.4296 0.4329 0.4023 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2485 0.2442 0.2882 n_refl.: 8738 remove outliers: r(all,work,free)=0.2485 0.2442 0.2882 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3388 753.263 692.279 1.160 0.975 0.324 15.490-12.512 99.01 89 11 0.1913 668.165 645.393 1.126 0.976 0.297 12.419-9.967 99.48 175 15 0.1610 755.137 740.806 1.154 0.980 0.275 9.933-7.985 99.73 337 34 0.1722 566.966 549.036 1.197 0.981 0.275 7.976-6.403 100.00 631 64 0.2607 311.977 292.311 1.076 0.983 0.229 6.399-5.132 99.93 1234 135 0.2473 295.737 279.358 0.984 0.986 0.195 5.129-4.115 99.81 2357 259 0.2163 286.249 279.059 0.990 0.989 0.111 4.114-3.501 98.83 2959 341 0.3143 172.905 163.369 1.003 0.992 0.054 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=1.8221 ================= 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) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3573 0.3825 0.003 0.846 2.0 500.0 94.7 0 0.000 1_bss: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_settarget: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_updatephipsi: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_weight: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_xyzrec: 0.2041 0.3198 0.005 0.758 19.6 517.6 112.3 0 0.226 1_adp: 0.2550 0.3179 0.005 0.758 65.3 512.6 130.7 0 0.226 1_regHadp: 0.2620 0.3157 0.005 0.758 65.3 512.6 130.7 0 0.226 2_bss: 0.2302 0.3004 0.005 0.758 30.7 478.1 96.1 0 0.226 2_settarget: 0.2302 0.3004 0.005 0.758 30.7 478.1 96.1 0 0.226 2_updatephipsi: 0.2302 0.3004 0.005 0.758 30.7 478.1 96.1 0 0.226 2_updatecdl: 0.2302 0.3004 0.005 0.805 30.7 478.1 96.1 0 0.226 2_weight: 0.2302 0.3004 0.005 0.805 30.7 478.1 96.1 0 0.226 2_xyzrec: 0.2346 0.3000 0.003 0.601 30.7 478.1 96.1 0 0.263 2_adp: 0.2530 0.2878 0.003 0.601 30.8 473.1 118.5 0 0.263 2_regHadp: 0.2566 0.2873 0.003 0.601 30.8 473.1 118.5 0 0.263 3_bss: 0.2471 0.2922 0.003 0.601 21.9 464.2 109.6 0 0.263 3_settarget: 0.2471 0.2922 0.003 0.601 21.9 464.2 109.6 0 0.263 3_updatephipsi: 0.2471 0.2922 0.003 0.601 21.9 464.2 109.6 0 0.263 3_updatecdl: 0.2471 0.2922 0.003 0.637 21.9 464.2 109.6 0 0.263 3_setrh: 0.2471 0.2922 0.003 0.637 21.9 464.2 109.6 0 0.262 3_weight: 0.2471 0.2922 0.003 0.637 21.9 464.2 109.6 0 0.262 3_xyzrec: 0.2469 0.2923 0.003 0.613 21.9 464.2 109.6 0 0.263 3_adp: 0.2609 0.2884 0.003 0.613 48.3 459.2 121.1 0 0.263 3_regHadp: 0.2617 0.2887 0.003 0.613 48.3 459.2 121.1 0 0.263 end: 0.2442 0.2882 0.003 0.613 30.9 441.8 103.7 0 0.263 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/3fm7_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/3fm7_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 10.1000 Refinement macro-cycles (run) : 267.4800 Write final files (write_after_run_outputs) : 23.0800 Total : 300.6600 Total CPU time: 5.70 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:42 PDT -0700 (1716251682.45 s) Start R-work = 0.2135, R-free = 0.3139 Final R-work = 0.2442, R-free = 0.2882 =============================================================================== Job complete usr+sys time: 364.20 seconds wall clock time: 18 minutes 2.08 seconds (1082.08 seconds total)