Starting phenix.refine on Mon May 20 17:15:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2fdq.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2fdq/2fdq.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+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2fdq.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2fdq.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2fdq/2fdq.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2fdq/2fdq.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 { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 4164 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1388 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "B" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1388 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "C" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1388 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Time building chain proxies: 0.81, per 1000 atoms: 0.19 Number of scatterers: 4164 At special positions: 0 Unit cell: (49.11, 49.11, 130.48, 90, 90, 90) Space group: P 41 (No. 76) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 411 8.00 N 342 7.00 C 1326 6.00 H 2076 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: 0.92 Conformation dependent library (CDL) restraints added in 123.7 milliseconds 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 0 sheets defined 68.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 4.294A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 35 Processing helix chain 'A' and resid 49 through 61 removed outlier: 3.653A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 84 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 49 through 61 removed outlier: 3.562A pdb=" N LYS B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 84 Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.705A pdb=" N GLU C 10 " --> pdb=" O ASP C 6 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 13 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN C 14 " --> pdb=" O GLU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 Processing helix chain 'C' and resid 49 through 60 Processing helix chain 'C' and resid 66 through 84 removed outlier: 3.595A pdb=" N SER C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 1.07 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: 2076 1.15 - 1.33: 551 1.33 - 1.50: 695 1.50 - 1.68: 863 1.68 - 1.85: 18 Bond restraints: 4203 Sorted by residual: bond pdb=" N LYS A 18 " pdb=" H LYS A 18 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N THR C 35 " pdb=" H THR C 35 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N THR B 64 " pdb=" H THR B 64 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLY A 63 " pdb=" H GLY A 63 " 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 B 5 " pdb=" H PHE B 5 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 4198 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.00: 110 106.00 - 113.00: 4926 113.00 - 119.99: 1188 119.99 - 126.99: 1387 126.99 - 133.98: 24 Bond angle restraints: 7635 Sorted by residual: angle pdb=" N GLU C 23 " pdb=" CA GLU C 23 " pdb=" C GLU C 23 " ideal model delta sigma weight residual 111.40 103.42 7.98 1.22e+00 6.72e-01 4.28e+01 angle pdb=" N TRP A 58 " pdb=" CA TRP A 58 " pdb=" C TRP A 58 " ideal model delta sigma weight residual 111.36 104.39 6.97 1.09e+00 8.42e-01 4.09e+01 angle pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" C LYS C 13 " ideal model delta sigma weight residual 113.15 105.67 7.48 1.19e+00 7.06e-01 3.95e+01 angle pdb=" N LYS B 82 " pdb=" CA LYS B 82 " pdb=" C LYS B 82 " ideal model delta sigma weight residual 111.03 104.08 6.95 1.11e+00 8.12e-01 3.92e+01 angle pdb=" N LEU C 61 " pdb=" CA LEU C 61 " pdb=" C LEU C 61 " ideal model delta sigma weight residual 113.18 120.69 -7.51 1.21e+00 6.83e-01 3.85e+01 ... (remaining 7630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 1730 17.57 - 35.13: 129 35.13 - 52.70: 61 52.70 - 70.26: 22 70.26 - 87.83: 5 Dihedral angle restraints: 1947 sinusoidal: 1056 harmonic: 891 Sorted by residual: dihedral pdb=" CB GLU C 42 " pdb=" CG GLU C 42 " pdb=" CD GLU C 42 " pdb=" OE1 GLU C 42 " ideal model delta sinusoidal sigma weight residual 0.00 87.83 -87.83 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB MET C 24 " pdb=" CG MET C 24 " pdb=" SD MET C 24 " pdb=" CE MET C 24 " ideal model delta sinusoidal sigma weight residual -60.00 -118.10 58.10 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET B 24 " pdb=" CG MET B 24 " pdb=" SD MET B 24 " pdb=" CE MET B 24 " ideal model delta sinusoidal sigma weight residual -60.00 -113.30 53.30 3 1.50e+01 4.44e-03 9.19e+00 ... (remaining 1944 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.054: 129 0.054 - 0.107: 96 0.107 - 0.160: 47 0.160 - 0.213: 12 0.213 - 0.266: 7 Chirality restraints: 291 Sorted by residual: chirality pdb=" CA VAL B 36 " pdb=" N VAL B 36 " pdb=" C VAL B 36 " pdb=" CB VAL B 36 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA LEU C 61 " pdb=" N LEU C 61 " pdb=" C LEU C 61 " pdb=" CB LEU C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 288 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 55 " -0.115 2.00e-02 2.50e+03 3.52e-02 4.95e+01 pdb=" CG TRP B 55 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 55 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 55 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP B 55 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 55 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 55 " 0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 55 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 55 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 55 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 TRP B 55 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 TRP B 55 " -0.005 2.00e-02 2.50e+03 pdb=" HE3 TRP B 55 " 0.044 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 55 " -0.029 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 55 " -0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP B 55 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " 0.097 2.00e-02 2.50e+03 3.78e-02 4.30e+01 pdb=" CG TYR C 28 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " 0.063 2.00e-02 2.50e+03 pdb=" HD1 TYR C 28 " -0.029 2.00e-02 2.50e+03 pdb=" HD2 TYR C 28 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR C 28 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR C 28 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 73 " 0.098 2.00e-02 2.50e+03 3.77e-02 4.27e+01 pdb=" CG TYR B 73 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR B 73 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 73 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 73 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 73 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 73 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 73 " 0.059 2.00e-02 2.50e+03 pdb=" HD1 TYR B 73 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR B 73 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 TYR B 73 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR B 73 " -0.004 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.98: 214 1.98 - 2.63: 5187 2.63 - 3.29: 13314 3.29 - 3.94: 16960 3.94 - 4.60: 25486 Nonbonded interactions: 61161 Sorted by model distance: nonbonded pdb=" HE ARG B 43 " pdb=" OD1 ASP B 56 " model vdw 1.324 1.850 nonbonded pdb=" HB2 ALA A 8 " pdb="HG23 ILE A 74 " model vdw 1.348 2.440 nonbonded pdb=" OE2 GLU B 23 " pdb=" HZ3 LYS B 83 " model vdw 1.372 1.850 nonbonded pdb=" HG2 LYS B 81 " pdb="HD11 ILE B 86 " model vdw 1.385 2.440 nonbonded pdb=" O TYR C 31 " pdb=" HG1 THR C 35 " model vdw 1.428 1.850 ... (remaining 61156 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 9 15.91 1 O 411 7.97 1 N 342 6.97 1 C 1326 5.97 1 H 2076 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: 2076 of 4164 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4164 n_use_u_iso = 4164 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 = 4164 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4164 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4164 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 { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 2 through 14 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 21 through 35 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 49 through 61 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 66 through 84 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'B' and resid 2 through 11 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'B' and resid 21 through 35 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 49 through 61 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 66 through 84 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'C' and resid 2 through 14 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'C' and resid 21 through 35 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'C' and resid 49 through 60 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'C' and resid 66 through 84 } } enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "2fdq_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2076 occupancy sum: 2076.00 (% of total atoms 49.86) Rotatable: count: 531 occupancy sum: 531.00 (% of total atoms 12.75) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 24.56 A, n_refl.=3901 (all), 4.54 % free)-------------| | | | r_work= 0.3367 r_free= 0.3847 coordinate error (max.-lik. estimate): 0.79 A | | | | normalized target function (ml) (work): 5.414009 | | target function (ml) not normalized (work): 20161.769398 | | target function (ml) not normalized (free): 955.736830 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 24.56 - 3.50 1.00 3724 177 0.3367 0.3847 5.414 5.3996| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 24.56 - 3.50 3724 177 0.80 27.40 1.00 0.42 10659.71| |alpha: min = 0.23 max = 0.54 mean = 0.42| |beta: min = 3856.36 max = 48303.69 mean = 10659.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.80| |phase err.(work): min = 0.00 max = 89.81 mean = 27.40| |phase err.(test): min = 0.00 max = 88.12 mean = 26.74| |-----------------------------------------------------------------------------| ----------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 : 0.009 0.063 2127 Z= 0.584 Angle : 1.450 14.176 2844 Z= 0.982 Chirality : 0.089 0.266 291 Planarity : 0.007 0.042 363 Dihedral : 15.771 87.829 822 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 36.98 Ramachandran Plot: Outliers : 5.56 % Allowed : 25.79 % Favored : 68.65 % Rotamer: Outliers : 0.91 % Allowed : 6.39 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.58 (0.37), residues: 252 helix: -4.70 (0.19), residues: 156 sheet: None (None), residues: 0 loop : -3.42 (0.60), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG C 43 TYR 0.079 0.021 TYR C 28 PHE 0.033 0.008 PHE C 49 TRP 0.078 0.015 TRP B 55 HIS 0.003 0.002 HIS A 30 Individual atomic B min max mean iso aniso Overall: 20.45 55.43 29.36 1.83 2088 0 Protein: 20.45 55.43 29.36 1.83 2088 0 Chain A: 20.45 53.24 31.53 N/A 696 0 Chain B: 20.45 55.43 28.80 N/A 696 0 Chain C: 20.45 53.74 27.73 N/A 696 0 Histogram: Values Number of atoms 20.45 - 23.95 483 23.95 - 27.45 430 27.45 - 30.94 501 30.94 - 34.44 253 34.44 - 37.94 186 37.94 - 41.44 93 41.44 - 44.94 81 44.94 - 48.43 32 48.43 - 51.93 25 51.93 - 55.43 4 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.50 - 24.56 A, n_refl.=3901 (all), 4.54 % free)-------------| | | | r_work= 0.3367 r_free= 0.3847 coordinate error (max.-lik. estimate): 0.79 A | | | | normalized target function (ml) (work): 5.414009 | | target function (ml) not normalized (work): 20161.769398 | | target function (ml) not normalized (free): 955.736830 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3389 0.3367 0.3847 n_refl.: 3901 re-set all scales: r(all,work,free)=0.3389 0.3367 0.3847 n_refl.: 3901 remove outliers: r(all,work,free)=0.3390 0.3368 0.3847 n_refl.: 3900 overall B=1.29 to atoms: r(all,work,free)=0.3430 0.3408 0.3898 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.2158 0.2170 0.1921 n_refl.: 3900 remove outliers: r(all,work,free)=0.2158 0.2170 0.1921 n_refl.: 3900 ======================== 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 24.555-11.554 100.00 97 4 0.1718 879.253 859.871 1.015 1.135 0.339 11.543-9.422 100.00 94 5 0.1500 860.103 832.148 1.071 1.117 0.339 9.405-7.656 100.00 172 7 0.1517 693.173 674.933 1.053 1.097 0.354 7.645-6.234 100.00 300 18 0.2153 507.673 488.103 1.003 1.068 0.357 6.230-5.074 100.00 574 24 0.2379 440.704 420.298 0.982 1.023 0.356 5.067-4.130 100.00 1040 46 0.2173 488.029 470.997 1.068 0.957 0.285 4.129-3.498 99.54 1446 73 0.2378 390.867 374.550 1.143 0.872 0.156 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.8065 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2170 r_free=0.1921 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2170 r_free=0.1921 ========================= Local real-space refinement ========================= Before: r_work=0.2170 r_free=0.1921 66 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.163 outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0512 time to fit residues: 0.3422 After: r_work=0.2183 r_free=0.1930 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.774362 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.450923 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1629 0.2149 0.0520 0.013 1.2 12.2 0.0 2.7 0 7.387 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1629 r_free=0.2149 70 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.167 outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0833 time to fit residues: 0.8221 After: r_work=0.1657 r_free=0.2109 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 16.57 21.09 4.53 1.305 30.879 0.451 0.032 16.49 21.33 4.85 1.847 31.015 0.014 0.032 15.95 21.01 5.06 1.823 31.023 0.056 0.030 15.15 20.48 5.33 2.837 31.163 0.225 0.027 14.12 20.01 5.89 5.468 31.583 0.451 0.023 13.73 19.84 6.10 6.682 31.935 0.676 0.022 13.50 19.72 6.22 7.589 32.206 0.902 0.021 13.41 19.70 6.29 7.973 32.301 1.127 0.021 13.10 19.56 6.47 9.463 32.812 1.353 0.020 13.02 19.55 6.53 9.933 32.939 1.578 0.020 12.95 19.53 6.58 10.341 33.054 1.804 0.020 12.90 19.54 6.64 10.707 33.158 2.029 0.020 12.61 19.57 6.97 12.679 33.867 2.255 0.019 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.451 Accepted refinement result: 14.12 20.01 5.89 5.468 31.583 0.451 0.023 Individual atomic B min max mean iso aniso Overall: 16.74 103.97 32.05 5.15 2088 0 Protein: 16.74 103.97 32.05 5.15 2088 0 Chain A: 18.85 92.07 36.15 N/A 696 0 Chain B: 16.74 70.39 30.66 N/A 696 0 Chain C: 16.74 103.97 29.34 N/A 696 0 Histogram: Values Number of atoms 16.74 - 25.46 561 25.46 - 34.19 800 34.19 - 42.91 442 42.91 - 51.63 199 51.63 - 60.35 69 60.35 - 69.08 14 69.08 - 77.80 1 77.80 - 86.52 0 86.52 - 95.24 1 95.24 - 103.97 1 =========================== Idealize ADP of riding H ========================== r_work=0.1412 r_free=0.2001 r_work=0.1388 r_free=0.1982 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1388 r_free= 0.1982 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ls_wunit_k1) (work): 0.022483 | | target function (ls_wunit_k1) not normalized (work): 83.705219 | | target function (ls_wunit_k1) not normalized (free): 8.707586 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1416 0.1388 0.1982 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3051 0.2999 0.3963 n_refl.: 3900 remove outliers: r(all,work,free)=0.3051 0.2999 0.3963 n_refl.: 3900 overall B=1.35 to atoms: r(all,work,free)=0.3099 0.3047 0.4007 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1421 0.1395 0.1970 n_refl.: 3900 remove outliers: r(all,work,free)=0.1421 0.1395 0.1970 n_refl.: 3900 ======================== 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 24.555-11.554 100.00 97 4 0.1140 606.348 604.348 1.142 1.012 0.339 11.543-9.422 100.00 94 5 0.1011 593.142 584.061 1.205 1.009 0.339 9.405-7.656 100.00 172 7 0.1015 478.024 473.255 1.182 1.006 0.348 7.645-6.234 100.00 300 18 0.1420 350.100 348.558 1.088 1.002 0.347 6.230-5.074 100.00 574 24 0.1578 303.917 299.892 1.002 0.994 0.346 5.067-4.130 100.00 1040 46 0.1323 336.553 333.948 1.030 0.984 0.295 4.129-3.498 99.54 1446 73 0.1544 269.549 265.573 1.021 0.970 0.131 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.0570 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1395 r_free=0.1970 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN B 59 ASN Total number of N/Q/H flips: 2 r_work=0.1398 r_free=0.1964 ========================= Local real-space refinement ========================= Before: r_work=0.1398 r_free=0.1964 60 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.258 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2647 After: r_work=0.1398 r_free=0.1964 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.447600 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.044881 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1508 0.1953 0.0445 0.004 0.6 3.6 0.0 0.0 0 0.072 0.1375 0.2016 0.0642 0.008 0.8 7.2 0.0 2.7 0 0.217 0.1307 0.2024 0.0717 0.013 1.2 12.0 0.0 2.3 0 0.434 0.1271 0.2030 0.0759 0.017 1.4 12.0 0.0 2.3 0 0.651 0.1237 0.2040 0.0803 0.021 1.6 13.0 0.4 2.3 0 0.869 0.1212 0.2047 0.0835 0.023 1.8 13.7 0.8 2.7 0 1.086 0.1190 0.2043 0.0853 0.027 1.9 14.9 0.8 2.7 0 1.303 0.1175 0.2046 0.0871 0.029 2.1 15.9 0.8 3.2 0 1.520 0.1258 0.2037 0.0779 0.018 1.5 12.5 0.0 2.3 0 0.724 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1508 0.1953 0.0445 0.004 0.6 3.6 0.0 0.0 0 0.072 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1508 r_free=0.1953 70 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.778 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4598 After: r_work=0.1508 r_free=0.1953 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 15.08 19.53 4.45 6.083 37.259 0.045 5.497 16.86 20.03 3.17 5.904 39.606 0.001 5.607 15.51 19.55 4.05 5.621 38.203 0.006 5.519 13.76 19.22 5.45 6.844 38.434 0.022 5.394 13.24 19.28 6.04 8.079 38.478 0.045 5.352 13.01 19.40 6.39 9.022 38.636 0.067 5.333 12.86 19.55 6.69 9.848 38.840 0.090 5.320 12.76 19.65 6.89 10.448 38.992 0.112 5.313 12.69 19.73 7.04 10.994 39.135 0.135 5.307 12.64 19.80 7.16 11.480 39.261 0.157 5.302 12.60 19.84 7.24 11.846 39.357 0.180 5.299 12.57 19.90 7.33 12.171 39.444 0.202 5.296 12.54 19.95 7.41 12.446 39.515 0.224 5.294 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.022 Accepted refinement result: 13.76 19.22 5.45 6.844 38.434 0.022 5.394 Individual atomic B min max mean iso aniso Overall: 13.09 143.13 35.74 6.99 2088 0 Protein: 13.09 143.13 35.74 6.99 2088 0 Chain A: 19.57 106.62 43.41 N/A 696 0 Chain B: 14.39 88.17 32.66 N/A 696 0 Chain C: 13.09 143.13 31.14 N/A 696 0 Histogram: Values Number of atoms 13.09 - 26.09 574 26.09 - 39.09 827 39.09 - 52.10 408 52.10 - 65.10 181 65.10 - 78.11 85 78.11 - 91.11 7 91.11 - 104.12 4 104.12 - 117.12 1 117.12 - 130.12 0 130.12 - 143.13 1 =========================== Idealize ADP of riding H ========================== r_work=0.1376 r_free=0.1922 r_work=0.1368 r_free=0.1925 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1368 r_free= 0.1925 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.388455 | | target function (ml) not normalized (work): 20061.218343 | | target function (ml) not normalized (free): 1075.945489 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1394 0.1368 0.1925 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3100 0.3051 0.3968 n_refl.: 3900 remove outliers: r(all,work,free)=0.3100 0.3051 0.3968 n_refl.: 3900 overall B=3.30 to atoms: r(all,work,free)=0.3221 0.3172 0.4090 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1374 0.1348 0.1900 n_refl.: 3900 remove outliers: r(all,work,free)=0.1374 0.1348 0.1900 n_refl.: 3900 ======================== 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 24.555-11.554 100.00 97 4 0.1242 606.348 603.157 1.049 1.086 0.339 11.543-9.422 100.00 94 5 0.1001 593.142 583.345 1.147 1.074 0.347 9.405-7.656 100.00 172 7 0.1043 478.024 473.488 1.119 1.060 0.346 7.645-6.234 100.00 300 18 0.1394 350.100 346.476 1.050 1.041 0.344 6.230-5.074 100.00 574 24 0.1468 303.917 300.409 0.988 1.011 0.341 5.067-4.130 100.00 1040 46 0.1267 336.553 332.703 1.047 0.966 0.297 4.129-3.498 99.54 1446 73 0.1483 269.549 264.125 1.101 0.909 0.147 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.7823 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1348 r_free=0.1900 After: r_work=0.1348 r_free=0.1901 ================================== NQH flips ================================== r_work=0.1348 r_free=0.1901 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 GLN Total number of N/Q/H flips: 1 r_work=0.1349 r_free=0.1901 ========================= Local real-space refinement ========================= Before: r_work=0.1349 r_free=0.1901 71 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.718 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8120 After: r_work=0.1349 r_free=0.1901 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.451095 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.037207 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1350 0.1893 0.0543 0.003 0.6 4.1 0.0 0.0 0 0.073 0.1300 0.1880 0.0581 0.007 0.7 5.0 0.0 0.0 0 0.218 0.1186 0.1908 0.0722 0.012 1.3 8.6 0.0 1.4 0 0.435 0.1157 0.1936 0.0779 0.013 1.4 9.1 0.0 1.8 0 0.653 0.1130 0.1975 0.0845 0.017 1.5 11.5 0.0 4.6 0 0.871 0.1123 0.1952 0.0829 0.017 1.6 11.0 0.0 4.6 0 1.088 0.1109 0.1972 0.0862 0.019 1.7 12.0 0.0 4.6 0 1.306 0.1095 0.1987 0.0892 0.022 1.8 13.7 0.0 4.6 0 1.524 0.1148 0.1943 0.0795 0.014 1.5 8.9 0.0 2.7 0 0.726 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1350 0.1893 0.0543 0.003 0.6 4.1 0.0 0.0 0 0.073 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1350 r_free=0.1893 72 residues out of total 219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.757 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7651 After: r_work=0.1350 r_free=0.1893 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 18.93 5.43 7.500 43.468 0.037 5.384 16.29 19.47 3.18 7.643 46.161 0.001 5.564 14.87 19.21 4.34 7.238 44.612 0.005 5.484 13.16 19.29 6.13 7.230 44.142 0.019 5.357 12.45 19.18 6.73 8.926 44.184 0.037 5.296 12.30 19.35 7.05 9.696 44.200 0.056 5.281 12.18 19.58 7.40 10.448 44.435 0.074 5.271 12.14 19.48 7.34 10.657 44.430 0.093 5.266 12.12 19.53 7.41 10.891 44.492 0.112 5.264 12.09 19.59 7.50 11.135 44.565 0.130 5.261 12.06 19.66 7.60 11.425 44.658 0.149 5.259 12.03 19.73 7.70 11.763 44.766 0.167 5.256 12.04 19.73 7.69 11.783 44.769 0.186 5.256 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.005 Accepted refinement result: 14.87 19.21 4.34 7.238 44.612 0.005 5.484 Individual atomic B min max mean iso aniso Overall: 18.95 141.43 41.32 4.37 2088 0 Protein: 18.95 141.43 41.32 4.37 2088 0 Chain A: 28.58 104.92 50.22 N/A 696 0 Chain B: 23.14 86.48 37.77 N/A 696 0 Chain C: 18.95 141.43 35.98 N/A 696 0 Histogram: Values Number of atoms 18.95 - 31.19 440 31.19 - 43.44 983 43.44 - 55.69 344 55.69 - 67.94 235 67.94 - 80.19 74 80.19 - 92.44 9 92.44 - 104.69 1 104.69 - 116.94 1 116.94 - 129.18 0 129.18 - 141.43 1 =========================== Idealize ADP of riding H ========================== r_work=0.1487 r_free=0.1921 r_work=0.1504 r_free=0.1909 ----------X-ray data---------- |--(resolution: 3.50 - 24.56 A, n_refl.=3900 (all), 4.54 % free)-------------| | | | r_work= 0.1504 r_free= 0.1909 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 5.494648 | | target function (ml) not normalized (work): 20456.573804 | | target function (ml) not normalized (free): 1045.806376 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 24.56 - 3.50 1.00 3723 177 0.1504 0.1909 5.4946 5.9085| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 24.56 - 3.50 3723 177 0.94 12.76 1.00 1.08 7793.53| |alpha: min = 1.03 max = 1.15 mean = 1.08| |beta: min = 6005.30 max = 13537.96 mean = 7793.53| |figures of merit: min = 0.05 max = 1.00 mean = 0.94| |phase err.(work): min = 0.00 max = 86.49 mean = 12.76| |phase err.(test): min = 0.00 max = 75.19 mean = 11.99| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1523 0.1504 0.1909 n_refl.: 3900 re-set all scales: r(all,work,free)=0.3379 0.3334 0.4194 n_refl.: 3900 remove outliers: r(all,work,free)=0.3379 0.3334 0.4194 n_refl.: 3900 overall B=0.00 to atoms: r(all,work,free)=0.3379 0.3334 0.4194 n_refl.: 3900 bulk-solvent and scaling: r(all,work,free)=0.1536 0.1519 0.1900 n_refl.: 3900 remove outliers: r(all,work,free)=0.1536 0.1519 0.1900 n_refl.: 3900 ======================== 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 24.555-11.554 100.00 97 4 0.1224 606.348 605.067 1.091 1.005 0.340 11.543-9.422 100.00 94 5 0.0969 593.142 585.378 1.184 1.004 0.350 9.405-7.656 100.00 172 7 0.1064 478.024 473.053 1.146 1.001 0.350 7.645-6.234 100.00 300 18 0.1497 350.100 349.381 1.071 0.998 0.350 6.230-5.074 100.00 574 24 0.1621 303.917 298.847 0.980 0.992 0.350 5.067-4.130 100.00 1040 46 0.1464 336.553 332.114 1.008 0.984 0.300 4.129-3.498 99.54 1446 73 0.1748 269.549 262.094 1.006 0.973 0.150 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.5250 ================= 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 : 0.3367 0.3847 0.009 1.450 20.4 55.4 29.4 0 0.000 1_bss: 0.2170 0.1921 0.009 1.450 21.7 56.7 30.6 0 0.000 1_settarget: 0.2170 0.1921 0.009 1.450 21.7 56.7 30.6 0 0.000 1_updatephipsi: 0.2170 0.1921 0.009 1.450 21.7 56.7 30.6 0 0.000 1_nqh: 0.2170 0.1921 0.009 1.450 21.7 56.7 30.6 0 0.000 1_realsrl: 0.2183 0.1930 0.009 1.450 21.7 56.7 30.6 0 0.001 1_weight: 0.2183 0.1930 0.009 1.450 21.7 56.7 30.6 0 0.001 1_xyzrec: 0.1629 0.2149 0.013 1.227 21.7 56.7 30.6 0 0.320 1_realsrl2: 0.1657 0.2109 0.013 1.227 21.7 56.7 30.6 0 0.322 1_adp: 0.1412 0.2001 0.013 1.227 16.7 104.0 32.1 0 0.322 1_regHadp: 0.1388 0.1982 0.013 1.227 16.7 104.0 32.1 0 0.322 2_bss: 0.1395 0.1970 0.013 1.227 18.1 105.3 33.4 0 0.322 2_settarget: 0.1395 0.1970 0.013 1.227 18.1 105.3 33.4 0 0.322 2_updatephipsi: 0.1395 0.1970 0.013 1.227 18.1 105.3 33.4 0 0.322 2_updatecdl: 0.1395 0.1970 0.013 1.245 18.1 105.3 33.4 0 0.322 2_nqh: 0.1398 0.1964 0.013 1.245 18.1 105.3 33.4 0 0.326 2_realsrl: 0.1398 0.1964 0.013 1.245 18.1 105.3 33.4 0 0.326 2_weight: 0.1398 0.1964 0.013 1.245 18.1 105.3 33.4 0 0.326 2_xyzrec: 0.1508 0.1953 0.004 0.557 18.1 105.3 33.4 0 0.348 2_realsrl2: 0.1508 0.1953 0.004 0.557 18.1 105.3 33.4 0 0.348 2_adp: 0.1376 0.1922 0.004 0.557 13.1 143.1 35.7 0 0.348 2_regHadp: 0.1368 0.1925 0.004 0.557 13.1 143.1 35.7 0 0.348 3_bss: 0.1348 0.1900 0.004 0.557 16.4 146.4 39.0 0 0.348 3_settarget: 0.1348 0.1900 0.004 0.557 16.4 146.4 39.0 0 0.348 3_updatephipsi: 0.1348 0.1900 0.004 0.557 16.4 146.4 39.0 0 0.348 3_updatecdl: 0.1348 0.1900 0.004 0.586 16.4 146.4 39.0 0 0.348 3_setrh: 0.1348 0.1901 0.004 0.586 16.4 146.4 39.0 0 0.348 3_nqh: 0.1349 0.1901 0.004 0.586 16.4 146.4 39.0 0 0.350 3_realsrl: 0.1349 0.1901 0.004 0.586 16.4 146.4 39.0 0 0.350 3_weight: 0.1349 0.1901 0.004 0.586 16.4 146.4 39.0 0 0.350 3_xyzrec: 0.1350 0.1893 0.003 0.558 16.4 146.4 39.0 0 0.351 3_realsrl2: 0.1350 0.1893 0.003 0.558 16.4 146.4 39.0 0 0.351 3_adp: 0.1487 0.1921 0.003 0.558 18.9 141.4 41.3 0 0.351 3_regHadp: 0.1504 0.1909 0.003 0.558 18.9 141.4 41.3 0 0.351 end: 0.1519 0.1900 0.003 0.558 18.9 141.4 41.3 0 0.351 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2fdq_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2fdq_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2200 Refinement macro-cycles (run) : 169.0200 Write final files (write_after_run_outputs) : 16.3500 Total : 188.5900 Total CPU time: 3.44 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:23:45 PDT -0700 (1716251025.43 s) Start R-work = 0.2170, R-free = 0.1921 Final R-work = 0.1519, R-free = 0.1900 =============================================================================== Job complete usr+sys time: 218.49 seconds wall clock time: 9 minutes 6.34 seconds (546.34 seconds total)