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/1fb5.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fb5/1fb5.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/1fb5.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fb5.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fb5/1fb5.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fb5/1fb5.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 "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 183": "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: 5100 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 5082 Classifications: {'peptide': 320} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Classifications: {'peptide': 1} Modifications used: {'NH3': 1} Time building chain proxies: 1.06, per 1000 atoms: 0.21 Number of scatterers: 5100 At special positions: 0 Unit cell: (184.7, 184.7, 184.7, 90, 90, 90) Space group: P 43 3 2 (No. 212) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 476 8.00 N 427 7.00 C 1617 6.00 H 2569 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: 1.26 Conformation dependent library (CDL) restraints added in 156.0 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 602 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 2 sheets defined 44.2% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 50 through 68 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 91 through 103 Processing helix chain 'A' and resid 124 through 133 removed outlier: 4.739A pdb=" N ARG A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 169 through 183 Processing helix chain 'A' and resid 199 through 211 removed outlier: 4.450A pdb=" N ALA A 209 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LYS A 210 " --> pdb=" O MET A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.937A pdb=" N LEU A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 272 through 275 No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 288 through 293 removed outlier: 4.026A pdb=" N VAL A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 316 No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 323 through 342 removed outlier: 4.539A pdb=" N LYS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TRP A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 107 through 111 Processing sheet with id= B, first strand: chain 'A' and resid 299 through 301 removed outlier: 3.539A pdb=" N VAL A 259 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 263 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N HIS A 214 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TRP A 193 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN A 216 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N GLY A 195 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ALA A 218 " --> pdb=" O GLY A 195 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 245 " --> pdb=" O LEU A 215 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 282 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: 1.19 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 565 1.05 - 1.25: 2357 1.25 - 1.44: 743 1.44 - 1.64: 1466 1.64 - 1.83: 20 Bond restraints: 5151 Sorted by residual: bond pdb=" NH2 ARG A 94 " pdb="HH22 ARG A 94 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" ND1 HIS A 117 " pdb=" HD1 HIS A 117 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ALA A 253 " pdb=" H ALA A 253 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 HIS A 168 " pdb=" HE2 HIS A 168 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LYS A 275 " pdb=" H LYS A 275 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 5146 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.38: 128 105.38 - 112.52: 5958 112.52 - 119.66: 1333 119.66 - 126.80: 1893 126.80 - 133.95: 34 Bond angle restraints: 9346 Sorted by residual: angle pdb=" N ALA A 280 " pdb=" CA ALA A 280 " pdb=" C ALA A 280 " ideal model delta sigma weight residual 113.38 99.63 13.75 1.23e+00 6.61e-01 1.25e+02 angle pdb=" N GLN A 279 " pdb=" CA GLN A 279 " pdb=" C GLN A 279 " ideal model delta sigma weight residual 114.09 99.75 14.34 1.55e+00 4.16e-01 8.56e+01 angle pdb=" N GLN A 145 " pdb=" CA GLN A 145 " pdb=" C GLN A 145 " ideal model delta sigma weight residual 110.97 101.49 9.48 1.09e+00 8.42e-01 7.57e+01 angle pdb=" N LEU A 186 " pdb=" CA LEU A 186 " pdb=" C LEU A 186 " ideal model delta sigma weight residual 113.72 103.13 10.59 1.30e+00 5.92e-01 6.64e+01 angle pdb=" N ALA A 253 " pdb=" CA ALA A 253 " pdb=" C ALA A 253 " ideal model delta sigma weight residual 113.41 104.47 8.94 1.22e+00 6.72e-01 5.37e+01 ... (remaining 9341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.04: 2174 22.04 - 44.07: 165 44.07 - 66.11: 60 66.11 - 88.14: 7 88.14 - 110.18: 2 Dihedral angle restraints: 2408 sinusoidal: 1323 harmonic: 1085 Sorted by residual: dihedral pdb=" CG NVA A 900 " pdb=" CA NVA A 900 " pdb=" CB NVA A 900 " pdb=" HA NVA A 900 " ideal model delta sinusoidal sigma weight residual -62.82 47.36 -110.18 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" N GLN A 348 " pdb=" C GLN A 348 " pdb=" CA GLN A 348 " pdb=" CB GLN A 348 " ideal model delta harmonic sigma weight residual 122.80 114.22 8.58 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" CG ARG A 40 " pdb=" CD ARG A 40 " pdb=" NE ARG A 40 " pdb=" CZ ARG A 40 " ideal model delta sinusoidal sigma weight residual -90.00 -43.56 -46.44 2 1.50e+01 4.44e-03 1.12e+01 ... (remaining 2405 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.077: 254 0.077 - 0.153: 94 0.153 - 0.229: 35 0.229 - 0.306: 10 0.306 - 0.382: 4 Chirality restraints: 397 Sorted by residual: chirality pdb=" CA TRP A 298 " pdb=" N TRP A 298 " pdb=" C TRP A 298 " pdb=" CB TRP A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA ASN A 329 " pdb=" N ASN A 329 " pdb=" C ASN A 329 " pdb=" CB ASN A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ALA A 280 " pdb=" N ALA A 280 " pdb=" C ALA A 280 " pdb=" CB ALA A 280 " both_signs ideal model delta sigma weight residual False 2.48 2.80 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 394 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 298 " -0.117 2.00e-02 2.50e+03 3.53e-02 5.00e+01 pdb=" CG TRP A 298 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 298 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 298 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP A 298 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 298 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 298 " 0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 298 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 298 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 298 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP A 298 " 0.039 2.00e-02 2.50e+03 pdb=" HE1 TRP A 298 " -0.008 2.00e-02 2.50e+03 pdb=" HE3 TRP A 298 " 0.036 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 298 " -0.022 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 298 " 0.008 2.00e-02 2.50e+03 pdb=" HH2 TRP A 298 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 193 " -0.080 2.00e-02 2.50e+03 2.41e-02 2.33e+01 pdb=" CG TRP A 193 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 193 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 193 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP A 193 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 193 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 193 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 193 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 193 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 193 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP A 193 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TRP A 193 " -0.007 2.00e-02 2.50e+03 pdb=" HE3 TRP A 193 " 0.025 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 193 " -0.016 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 193 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 193 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 317 " 0.057 2.00e-02 2.50e+03 2.24e-02 1.51e+01 pdb=" CG TYR A 317 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 317 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 317 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 317 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 317 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 317 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 317 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 317 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 TYR A 317 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 317 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 317 " -0.008 2.00e-02 2.50e+03 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 0.68 - 1.47: 36 1.47 - 2.25: 1116 2.25 - 3.03: 16007 3.03 - 3.82: 23925 3.82 - 4.60: 38499 Warning: very small nonbonded interaction distances. Nonbonded interactions: 79583 Sorted by model distance: nonbonded pdb=" HB3 ARG A 40 " pdb="HH11 ARG A 40 " model vdw 0.684 2.270 nonbonded pdb=" HG2 GLU A 87 " pdb=" HD1 HIS A 117 " model vdw 0.725 2.270 nonbonded pdb="HD13 ILE A 116 " pdb=" HB3 LEU A 124 " model vdw 0.838 2.440 nonbonded pdb=" HA ILE A 116 " pdb="HG21 VAL A 120 " model vdw 0.941 2.440 nonbonded pdb=" OE2 GLU A 122 " pdb=" HB3 PRO A 305 " model vdw sym.op. 0.998 2.620 z,x,y ... (remaining 79578 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 11 15.91 1 O 476 7.97 1 N 427 6.97 1 C 1617 5.97 1 H 2569 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: 2569 of 5100 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 5100 n_use_u_iso = 5100 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 = 5100 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (5100 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 5100 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 45 through 47 helix_type = alpha pi *3_10 unknown } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 50 through 68 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 75 through 77 helix_type = alpha pi *3_10 unknown } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 91 through 103 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 124 through 133 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 145 through 153 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 169 through 183 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 199 through 211 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 227 through 240 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 250 through 252 helix_type = alpha pi *3_10 unknown } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 272 through 275 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'A' and resid 277 through 279 helix_type = alpha pi *3_10 unknown } helix { serial_number = "13" helix_identifier = "13" selection = chain 'A' and resid 288 through 293 } helix { serial_number = "14" helix_identifier = "14" selection = chain 'A' and resid 308 through 310 helix_type = alpha pi *3_10 unknown } helix { serial_number = "15" helix_identifier = "15" selection = chain 'A' and resid 313 through 316 } helix { serial_number = "16" helix_identifier = "16" selection = chain 'A' and resid 323 through 342 } sheet { first_strand = chain 'A' and resid 107 through 111 sheet_id = " A" strand { selection = chain 'A' and resid 81 through 86 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 82 and name N bond_start_previous = chain 'A' and resid 107 and name O } strand { selection = chain 'A' and resid 138 through 141 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 139 and name N bond_start_previous = chain 'A' and resid 83 and name O } strand { selection = chain 'A' and resid 159 through 161 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 160 and name N bond_start_previous = chain 'A' and resid 138 and name O } } sheet { first_strand = chain 'A' and resid 299 through 301 sheet_id = " B" strand { selection = chain 'A' and resid 259 through 263 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 260 and name N bond_start_previous = chain 'A' and resid 299 and name O } strand { selection = chain 'A' and resid 190 through 195 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 192 and name N bond_start_previous = chain 'A' and resid 259 and name O } strand { selection = chain 'A' and resid 214 through 218 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 214 and name N bond_start_previous = chain 'A' and resid 191 and name O } strand { selection = chain 'A' and resid 244 through 247 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 245 and name N bond_start_previous = chain 'A' and resid 215 and name O } } } enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1fb5_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2569 occupancy sum: 2569.00 (% of total atoms 50.55) Rotatable: count: 751 occupancy sum: 751.00 (% of total atoms 14.78) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 55.69 A, n_refl.=13583 (all), 5.08 % free)------------| | | | r_work= 0.3934 r_free= 0.3841 coordinate error (max.-lik. estimate): 0.20 A | | | | normalized target function (ml) (work): 7.070147 | | target function (ml) not normalized (work): 91155.402602 | | target function (ml) not normalized (free): 4891.182011 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 55.69 - 5.99 0.96 2727 155 0.4383 0.4389 7.8547 7.6803| | 2: 5.98 - 4.75 0.97 2600 136 0.3400 0.3210 7.1228 7.1545| | 3: 4.75 - 4.15 0.98 2607 127 0.3675 0.3564 6.9337 6.9672| | 4: 4.15 - 3.77 0.95 2474 131 0.3917 0.3663 6.7408 6.855| | 5: 3.77 - 3.50 0.96 2485 141 0.4190 0.4058 6.6251 6.7013| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 55.69 - 5.99 2727 155 0.56 45.31 0.74 0.54 772694.27| | 2: 5.98 - 4.75 2600 136 0.62 41.75 1.31 0.69 464297.85| | 3: 4.75 - 4.15 2607 127 0.77 28.66 1.48 0.80 250471.84| | 4: 4.15 - 3.77 2474 131 0.82 24.66 1.52 0.86 130060.96| | 5: 3.77 - 3.50 2485 141 0.79 27.72 1.54 0.87 102817.37| |alpha: min = 0.54 max = 0.87 mean = 0.75| |beta: min = 102817.37 max = 772694.27 mean = 352483.04| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 33.87| |phase err.(test): min = 0.00 max = 89.68 mean = 32.98| |-----------------------------------------------------------------------------| ----------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 : 0.010 0.067 2582 Z= 0.664 Angle : 1.670 14.337 3492 Z= 1.077 Chirality : 0.099 0.382 397 Planarity : 0.008 0.083 441 Dihedral : 17.955 87.743 961 Min Nonbonded Distance : 1.472 Molprobity Statistics. All-atom Clashscore : 64.94 Ramachandran Plot: Outliers : 7.86 % Allowed : 20.75 % Favored : 71.38 % Rotamer: Outliers : 16.73 % Allowed : 15.64 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -6.37 (0.33), residues: 318 helix: -4.89 (0.20), residues: 119 sheet: -2.43 (0.57), residues: 57 loop : -4.35 (0.40), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 94 TYR 0.047 0.010 TYR A 317 PHE 0.031 0.012 PHE A 65 TRP 0.080 0.015 TRP A 298 HIS 0.003 0.001 HIS A 182 Individual atomic B min max mean iso aniso Overall: 9.34 143.19 50.12 1.69 2531 0 Protein: 9.34 143.19 50.12 1.69 2531 0 Chain A: 9.34 143.19 50.12 N/A 2531 0 Histogram: Values Number of atoms 9.34 - 22.73 309 22.73 - 36.11 663 36.11 - 49.50 541 49.50 - 62.88 410 62.88 - 76.27 277 76.27 - 89.65 96 89.65 - 103.03 41 103.03 - 116.42 41 116.42 - 129.81 78 129.81 - 143.19 75 |-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 - 55.69 A, n_refl.=13583 (all), 5.08 % free)------------| | | | r_work= 0.3934 r_free= 0.3841 coordinate error (max.-lik. estimate): 0.20 A | | | | normalized target function (ml) (work): 7.070147 | | target function (ml) not normalized (work): 91155.402602 | | target function (ml) not normalized (free): 4891.182011 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3926 0.3934 0.3841 n_refl.: 13583 re-set all scales: r(all,work,free)=0.3926 0.3934 0.3841 n_refl.: 13583 remove outliers: r(all,work,free)=0.3925 0.3933 0.3841 n_refl.: 13580 overall B=7.43 to atoms: r(all,work,free)=0.4217 0.4227 0.4091 n_refl.: 13580 bulk-solvent and scaling: r(all,work,free)=0.2182 0.2162 0.2544 n_refl.: 13580 remove outliers: r(all,work,free)=0.2181 0.2161 0.2544 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5432 2167.891 1699.946 1.237 1.215 0.394 19.362-15.234 92.45 91 7 0.4008 2001.516 1851.844 0.999 1.207 0.352 15.182-11.849 95.91 195 16 0.2182 2357.622 2247.797 1.016 1.196 0.346 11.824-9.235 95.44 396 23 0.1342 2602.458 2571.289 0.979 1.173 0.344 9.223-7.200 96.44 830 38 0.1832 1876.452 1853.962 0.974 1.135 0.330 7.195-5.615 96.35 1675 92 0.2488 1247.522 1185.861 0.934 1.073 0.276 5.612-4.379 97.24 3486 178 0.1919 1353.373 1301.390 0.987 0.969 0.222 4.378-3.502 95.73 6123 328 0.2280 1060.465 1008.484 1.225 0.812 0.131 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0575 b_overall=4.7221 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2161 r_free=0.2544 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2161 r_free=0.2544 ========================= Local real-space refinement ========================= Before: r_work=0.2161 r_free=0.2544 116 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 70 time to evaluate : 0.264 revert: symmetry clash outliers start: 46 outliers final: 30 residues processed: 46 average time/residue: 0.3124 time to fit residues: 20.5695 After: r_work=0.2268 r_free=0.2572 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.928022 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.251147 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 0.2454 0.2708 0.0254 0.003 0.8 12.8 1.6 11.6 0 0.125 0.2440 0.2690 0.0249 0.003 0.8 13.5 1.6 11.6 0 0.250 0.2375 0.2660 0.0285 0.004 0.8 14.9 1.6 12.4 0 0.500 0.2301 0.2614 0.0313 0.004 0.9 17.5 1.6 13.5 0 1.000 0.2227 0.2587 0.0360 0.006 0.9 21.6 1.6 14.9 0 2.000 0.2181 0.2571 0.0389 0.008 1.0 23.9 1.6 16.4 0 3.000 0.2152 0.2562 0.0410 0.009 1.1 28.4 1.6 17.1 0 4.000 0.2123 0.2535 0.0412 0.011 1.2 30.4 1.6 17.8 0 5.000 0.2105 0.2526 0.0422 0.011 1.3 32.8 1.9 17.5 0 6.000 0.2089 0.2516 0.0427 0.013 1.4 34.7 2.2 19.3 0 7.000 0.2075 0.2507 0.0432 0.014 1.5 35.3 2.2 20.4 0 8.000 0.2062 0.2501 0.0440 0.015 1.5 35.7 2.2 21.8 0 9.000 0.2052 0.2495 0.0443 0.016 1.6 36.9 2.5 21.8 0 10.000 0.2062 0.2497 0.0435 0.015 1.5 35.1 2.2 21.5 0 8.964 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2301 0.2614 0.0313 0.004 0.9 17.5 1.6 13.5 0 1.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2301 r_free=0.2614 115 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 78 time to evaluate : 1.182 revert: symmetry clash outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 0.4899 time to fit residues: 32.9016 After: r_work=0.2434 r_free=0.2682 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.34 26.82 2.48 1.196 57.300 0.251 0.074 24.35 26.62 2.27 2.636 57.535 0.008 0.074 24.12 26.54 2.41 2.662 57.586 0.031 0.073 23.53 26.32 2.79 3.449 57.775 0.126 0.069 22.79 26.06 3.27 6.194 58.284 0.251 0.066 22.51 25.99 3.49 7.269 58.513 0.377 0.064 22.24 25.88 3.64 8.632 58.887 0.502 0.063 22.10 25.83 3.73 9.441 59.070 0.628 0.062 22.01 25.77 3.77 10.074 59.227 0.753 0.062 21.92 25.71 3.80 10.762 59.416 0.879 0.061 21.88 25.70 3.82 11.053 59.474 1.005 0.061 21.79 25.63 3.84 11.812 59.694 1.130 0.061 21.62 25.53 3.91 13.286 60.153 1.256 0.060 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 1.256 Accepted refinement result: 21.62 25.53 3.91 13.286 60.153 1.256 0.060 Individual atomic B min max mean iso aniso Overall: 12.99 166.92 63.30 11.49 2531 0 Protein: 12.99 166.92 63.30 11.49 2531 0 Chain A: 12.99 166.92 63.30 N/A 2531 0 Histogram: Values Number of atoms 12.99 - 28.38 144 28.38 - 43.78 591 43.78 - 59.17 612 59.17 - 74.56 523 74.56 - 89.95 249 89.95 - 105.35 154 105.35 - 120.74 84 120.74 - 136.13 69 136.13 - 151.52 78 151.52 - 166.92 27 =========================== Idealize ADP of riding H ========================== r_work=0.2162 r_free=0.2553 r_work=0.2133 r_free=0.2521 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13579 (all), 5.08 % free)------------| | | | r_work= 0.2133 r_free= 0.2521 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ls_wunit_k1) (work): 0.058126 | | target function (ls_wunit_k1) not normalized (work): 749.191885 | | target function (ls_wunit_k1) not normalized (free): 56.149822 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2153 0.2133 0.2521 n_refl.: 13579 re-set all scales: r(all,work,free)=0.4309 0.4316 0.4221 n_refl.: 13579 remove outliers: r(all,work,free)=0.4309 0.4316 0.4221 n_refl.: 13579 overall B=0.00 to atoms: r(all,work,free)=0.4309 0.4316 0.4221 n_refl.: 13579 bulk-solvent and scaling: r(all,work,free)=0.2162 0.2142 0.2532 n_refl.: 13579 remove outliers: r(all,work,free)=0.2162 0.2142 0.2532 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5263 1172.757 942.074 1.007 1.160 0.374 19.362-15.234 92.45 91 7 0.3704 1082.754 1034.985 0.982 1.155 0.347 15.182-11.849 95.91 195 16 0.2273 1275.395 1219.707 1.048 1.149 0.337 11.824-9.235 95.44 396 23 0.1514 1407.843 1394.248 1.025 1.130 0.331 9.223-7.200 96.44 830 38 0.1972 1015.098 1003.641 1.006 1.102 0.320 7.195-5.615 96.35 1675 92 0.2499 674.868 640.518 0.956 1.053 0.280 5.612-4.379 97.24 3486 178 0.1907 732.129 707.248 0.982 0.972 0.210 4.378-3.502 95.73 6123 328 0.2183 573.676 546.960 1.194 0.848 0.117 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=1.6900 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2142 r_free=0.2532 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN Total number of N/Q/H flips: 1 r_work=0.2147 r_free=0.2538 ========================= Local real-space refinement ========================= Before: r_work=0.2147 r_free=0.2538 91 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.278 outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.8848 time to fit residues: 2.8210 After: r_work=0.2147 r_free=0.2538 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.597465 wxc_scale = 0.023 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.056188 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 0.2315 0.2581 0.0265 0.003 0.6 11.6 0.9 0.7 0 0.011 0.2265 0.2560 0.0295 0.003 0.6 10.4 0.9 0.7 0 0.032 0.2211 0.2523 0.0312 0.003 0.6 11.0 0.9 0.7 0 0.063 0.2156 0.2509 0.0353 0.003 0.7 13.9 0.9 0.4 0 0.095 0.2154 0.2483 0.0329 0.003 0.7 11.8 0.9 1.5 0 0.126 0.2140 0.2472 0.0332 0.003 0.7 12.8 0.9 2.5 0 0.158 0.2112 0.2474 0.0362 0.003 0.7 13.1 0.9 2.9 0 0.189 0.2107 0.2466 0.0359 0.004 0.7 13.9 0.9 2.9 0 0.221 0.2166 0.2486 0.0321 0.003 0.7 11.2 0.9 1.1 0 0.105 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2265 0.2560 0.0295 0.003 0.6 10.4 0.9 0.7 0 0.032 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2265 r_free=0.2560 97 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.126 revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.4609 time to fit residues: 2.6456 After: r_work=0.2267 r_free=0.2557 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.67 25.57 2.90 12.980 70.797 0.056 6.666 25.00 26.80 1.80 12.495 74.852 0.002 6.720 24.39 26.24 1.86 12.494 73.626 0.007 6.703 23.20 25.34 2.15 13.208 71.393 0.028 6.664 22.66 25.08 2.42 13.762 70.880 0.056 6.645 22.40 25.08 2.67 14.234 70.899 0.084 6.636 22.25 25.15 2.90 14.530 70.908 0.112 6.633 22.22 25.16 2.95 14.357 70.607 0.140 6.634 22.16 25.18 3.02 14.531 70.661 0.169 6.632 22.03 25.20 3.17 15.137 71.040 0.197 6.627 21.99 25.20 3.21 15.312 71.101 0.225 6.626 22.05 25.21 3.16 14.936 70.810 0.253 6.630 22.02 25.21 3.19 15.040 70.851 0.281 6.629 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.056 Accepted refinement result: 22.66 25.08 2.42 13.762 70.880 0.056 6.645 Individual atomic B min max mean iso aniso Overall: 18.51 163.98 63.47 10.52 2531 0 Protein: 18.51 163.98 63.47 10.52 2531 0 Chain A: 18.51 163.98 63.47 N/A 2531 0 Histogram: Values Number of atoms 18.51 - 33.06 183 33.06 - 47.61 742 47.61 - 62.15 603 62.15 - 76.70 388 76.70 - 91.25 219 91.25 - 105.80 138 105.80 - 120.34 81 120.34 - 134.89 54 134.89 - 149.44 76 149.44 - 163.98 47 =========================== Idealize ADP of riding H ========================== r_work=0.2266 r_free=0.2508 r_work=0.2273 r_free=0.2514 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13579 (all), 5.08 % free)------------| | | | r_work= 0.2273 r_free= 0.2514 coordinate error (max.-lik. estimate): 0.46 A | | | | normalized target function (ml) (work): 6.645520 | | target function (ml) not normalized (work): 85654.112308 | | target function (ml) not normalized (free): 4615.857574 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2287 0.2273 0.2514 n_refl.: 13579 re-set all scales: r(all,work,free)=0.4351 0.4359 0.4260 n_refl.: 13579 remove outliers: r(all,work,free)=0.4351 0.4359 0.4260 n_refl.: 13579 overall B=0.00 to atoms: r(all,work,free)=0.4351 0.4359 0.4260 n_refl.: 13579 bulk-solvent and scaling: r(all,work,free)=0.2291 0.2277 0.2525 n_refl.: 13579 remove outliers: r(all,work,free)=0.2291 0.2277 0.2525 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5320 1172.757 925.333 1.103 1.091 0.376 19.362-15.234 92.45 91 7 0.3707 1082.754 1019.780 1.055 1.091 0.350 15.182-11.849 95.91 195 16 0.2282 1275.395 1229.411 1.143 1.088 0.344 11.824-9.235 95.44 396 23 0.1626 1407.843 1393.575 1.100 1.077 0.340 9.223-7.200 96.44 830 38 0.2118 1015.098 999.201 1.081 1.059 0.340 7.195-5.615 96.35 1675 92 0.2719 674.868 635.903 1.016 1.029 0.290 5.612-4.379 97.24 3486 178 0.2115 732.129 697.837 0.961 0.977 0.220 4.378-3.502 95.73 6123 328 0.2255 573.676 540.819 1.096 0.899 0.120 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.8630 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2277 r_free=0.2525 After: r_work=0.2277 r_free=0.2526 ================================== NQH flips ================================== r_work=0.2277 r_free=0.2526 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2277 r_free=0.2526 ========================= Local real-space refinement ========================= Before: r_work=0.2277 r_free=0.2526 96 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.448 outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2755 time to fit residues: 0.9958 After: r_work=0.2277 r_free=0.2526 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.925576 wxc_scale = 0.026 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.055034 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 0.2277 0.2528 0.0251 0.002 0.6 11.4 0.9 0.4 0 0.010 0.2277 0.2527 0.0251 0.002 0.6 11.4 0.9 0.4 0 0.030 0.2276 0.2526 0.0250 0.003 0.6 11.4 0.9 0.4 0 0.061 0.2275 0.2525 0.0250 0.003 0.6 11.4 0.9 0.4 0 0.091 0.2273 0.2524 0.0250 0.003 0.6 11.4 0.9 0.4 0 0.121 0.2271 0.2523 0.0251 0.003 0.6 11.2 0.9 0.4 0 0.151 0.2269 0.2521 0.0252 0.003 0.6 11.2 0.9 0.4 0 0.182 0.2267 0.2518 0.0252 0.003 0.6 11.2 0.9 0.4 0 0.212 0.2274 0.2525 0.0250 0.003 0.6 11.4 0.9 0.4 0 0.101 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2267 0.2518 0.0252 0.003 0.6 11.2 0.9 0.4 0 0.212 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2267 r_free=0.2518 94 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.630 revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.3331 time to fit residues: 1.1781 After: r_work=0.2267 r_free=0.2518 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.67 25.18 2.52 12.501 70.585 0.055 6.646 25.52 27.19 1.67 11.685 74.665 0.002 6.728 25.32 27.09 1.77 12.024 74.100 0.007 6.727 23.07 25.40 2.33 12.548 70.165 0.028 6.660 22.61 25.18 2.57 12.724 70.286 0.055 6.643 22.52 25.16 2.63 12.896 70.284 0.083 6.640 22.43 25.21 2.78 13.223 70.150 0.110 6.637 22.31 25.18 2.88 13.619 70.030 0.138 6.632 22.02 25.19 3.17 14.784 70.182 0.165 6.623 21.97 25.19 3.22 15.034 70.324 0.193 6.621 21.94 25.20 3.26 15.160 70.399 0.220 6.620 21.90 25.22 3.32 15.469 70.564 0.248 6.618 21.87 25.22 3.35 15.644 70.657 0.275 6.617 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.083 Accepted refinement result: 22.52 25.16 2.63 12.896 70.284 0.083 6.640 Individual atomic B min max mean iso aniso Overall: 18.18 164.43 62.86 10.73 2531 0 Protein: 18.18 164.43 62.86 10.73 2531 0 Chain A: 18.18 164.43 62.86 N/A 2531 0 Histogram: Values Number of atoms 18.18 - 32.80 211 32.80 - 47.43 743 47.43 - 62.05 601 62.05 - 76.68 366 76.68 - 91.30 215 91.30 - 105.93 138 105.93 - 120.55 80 120.55 - 135.18 54 135.18 - 149.80 79 149.80 - 164.43 44 =========================== Idealize ADP of riding H ========================== r_work=0.2252 r_free=0.2516 r_work=0.2251 r_free=0.2515 ----------X-ray data---------- |--(resolution: 3.50 - 55.69 A, n_refl.=13579 (all), 5.08 % free)------------| | | | r_work= 0.2251 r_free= 0.2515 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 6.639660 | | target function (ml) not normalized (work): 85578.583095 | | target function (ml) not normalized (free): 4614.594808 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 55.69 - 5.99 0.96 2723 155 0.2379 0.2719 7.0523 7.1319| | 2: 5.98 - 4.75 0.97 2600 136 0.2354 0.2428 6.7143 6.7357| | 3: 4.75 - 4.15 0.98 2607 127 0.1910 0.2161 6.5831 6.6024| | 4: 4.15 - 3.77 0.95 2474 131 0.2152 0.2267 6.4758 6.5056| | 5: 3.77 - 3.50 0.96 2485 141 0.2483 0.2933 6.3319 6.3998| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 55.69 - 5.99 2723 155 0.79 26.02 1.00 0.90 205159.46| | 2: 5.98 - 4.75 2600 136 0.79 26.90 1.01 0.93 141259.54| | 3: 4.75 - 4.15 2607 127 0.87 20.11 1.01 0.93 94592.70| | 4: 4.15 - 3.77 2474 131 0.86 20.75 1.01 0.91 64897.43| | 5: 3.77 - 3.50 2485 141 0.84 23.19 0.96 0.88 52269.81| |alpha: min = 0.88 max = 0.93 mean = 0.91| |beta: min = 52269.81 max = 205159.46 mean = 113505.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.83| |phase err.(work): min = 0.00 max = 89.99 mean = 23.44| |phase err.(test): min = 0.00 max = 87.20 mean = 23.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2266 0.2251 0.2515 n_refl.: 13579 re-set all scales: r(all,work,free)=0.4313 0.4320 0.4225 n_refl.: 13579 remove outliers: r(all,work,free)=0.4313 0.4320 0.4225 n_refl.: 13579 overall B=0.00 to atoms: r(all,work,free)=0.4313 0.4320 0.4225 n_refl.: 13579 bulk-solvent and scaling: r(all,work,free)=0.2277 0.2262 0.2539 n_refl.: 13579 remove outliers: r(all,work,free)=0.2277 0.2262 0.2539 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5265 1172.757 930.954 1.416 1.045 0.400 19.362-15.234 92.45 91 7 0.3710 1082.754 1023.186 1.096 1.046 0.350 15.182-11.849 95.91 195 16 0.2305 1275.395 1229.476 1.184 1.047 0.344 11.824-9.235 95.44 396 23 0.1629 1407.843 1394.081 1.136 1.040 0.340 9.223-7.200 96.44 830 38 0.2113 1015.098 999.971 1.110 1.031 0.340 7.195-5.615 96.35 1675 92 0.2715 674.868 635.726 1.029 1.013 0.290 5.612-4.379 97.24 3486 178 0.2108 732.129 696.995 0.944 0.984 0.220 4.378-3.502 95.73 6123 328 0.2221 573.676 541.457 1.040 0.937 0.110 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=5.4385 ================= 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 : 0.3934 0.3841 0.010 1.670 9.3 143.2 50.1 0 0.000 1_bss: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_settarget: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_updatephipsi: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_nqh: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_realsrl: 0.2268 0.2572 0.010 1.670 16.8 150.6 57.6 0 0.040 1_weight: 0.2268 0.2572 0.010 1.670 16.8 150.6 57.6 0 0.040 1_xyzrec: 0.2301 0.2614 0.004 0.854 16.8 150.6 57.6 0 0.254 1_realsrl2: 0.2434 0.2682 0.004 0.854 16.8 150.6 57.6 0 0.294 1_adp: 0.2162 0.2553 0.004 0.854 13.0 166.9 63.3 0 0.294 1_regHadp: 0.2133 0.2521 0.004 0.854 13.0 166.9 63.3 0 0.294 2_bss: 0.2142 0.2532 0.004 0.854 13.0 166.9 63.3 0 0.294 2_settarget: 0.2142 0.2532 0.004 0.854 13.0 166.9 63.3 0 0.294 2_updatephipsi: 0.2142 0.2532 0.004 0.854 13.0 166.9 63.3 0 0.294 2_updatecdl: 0.2142 0.2532 0.005 0.900 13.0 166.9 63.3 0 0.294 2_nqh: 0.2147 0.2538 0.005 0.900 13.0 166.9 63.3 0 0.296 2_realsrl: 0.2147 0.2538 0.005 0.900 13.0 166.9 63.3 0 0.296 2_weight: 0.2147 0.2538 0.005 0.900 13.0 166.9 63.3 0 0.296 2_xyzrec: 0.2265 0.2560 0.003 0.632 13.0 166.9 63.3 0 0.369 2_realsrl2: 0.2267 0.2557 0.003 0.632 13.0 166.9 63.3 0 0.369 2_adp: 0.2266 0.2508 0.003 0.632 18.5 164.0 63.5 0 0.369 2_regHadp: 0.2273 0.2514 0.003 0.632 18.5 164.0 63.5 0 0.369 3_bss: 0.2277 0.2525 0.003 0.632 18.5 164.0 63.5 0 0.369 3_settarget: 0.2277 0.2525 0.003 0.632 18.5 164.0 63.5 0 0.369 3_updatephipsi: 0.2277 0.2525 0.003 0.632 18.5 164.0 63.5 0 0.369 3_updatecdl: 0.2277 0.2525 0.003 0.642 18.5 164.0 63.5 0 0.369 3_setrh: 0.2277 0.2526 0.003 0.642 18.5 164.0 63.5 0 0.369 3_nqh: 0.2277 0.2526 0.003 0.642 18.5 164.0 63.5 0 0.369 3_realsrl: 0.2277 0.2526 0.003 0.642 18.5 164.0 63.5 0 0.369 3_weight: 0.2277 0.2526 0.003 0.642 18.5 164.0 63.5 0 0.369 3_xyzrec: 0.2267 0.2518 0.003 0.645 18.5 164.0 63.5 0 0.369 3_realsrl2: 0.2267 0.2518 0.003 0.645 18.5 164.0 63.5 0 0.369 3_adp: 0.2252 0.2516 0.003 0.645 18.2 164.4 62.9 0 0.369 3_regHadp: 0.2251 0.2515 0.003 0.645 18.2 164.4 62.9 0 0.369 end: 0.2262 0.2539 0.003 0.645 18.2 164.4 62.9 0 0.369 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1fb5_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1fb5_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9700 Refinement macro-cycles (run) : 371.3900 Write final files (write_after_run_outputs) : 21.2400 Total : 396.6000 Total CPU time: 7.00 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:22 PDT -0700 (1716251722.06 s) Start R-work = 0.2161, R-free = 0.2544 Final R-work = 0.2262, R-free = 0.2539 =============================================================================== Job complete usr+sys time: 441.70 seconds wall clock time: 20 minutes 19.15 seconds (1219.15 seconds total)