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/1fp9.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fp9/1fp9.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/1fp9.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fp9.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fp9/1fp9.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fp9/1fp9.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 None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 7982 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7982 Classifications: {'peptide': 500} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 38, 'TRANS': 461} Time building chain proxies: 1.41, per 1000 atoms: 0.18 Number of scatterers: 7982 At special positions: 0 Unit cell: (104.913, 52.445, 104.908, 90, 96.42, 90) Space group: C 1 2 1 (No. 5) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 707 8.00 N 703 7.00 C 2641 6.00 H 3920 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: 1.97 Conformation dependent library (CDL) restraints added in 254.4 milliseconds 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 3 sheets defined 45.2% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 27 through 38 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.994A pdb=" N ARG A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 118 removed outlier: 3.803A pdb=" N TRP A 105 " --> pdb=" O TYR A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.572A pdb=" N GLU A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 135 through 150 removed outlier: 4.644A pdb=" N ASP A 140 " --> pdb=" O TRP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 161 through 164 No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 179 through 205 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 321 through 332 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 408 through 421 removed outlier: 3.814A pdb=" N ASP A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 441 Processing helix chain 'A' and resid 451 through 454 No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 484 through 496 removed outlier: 3.687A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 446 through 450 removed outlier: 7.402A pdb=" N ALA A 6 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR A 449 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY A 8 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR A 43 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG A 209 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 289 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N MET A 214 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG A 291 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 300 through 303 Processing sheet with id= C, first strand: chain 'A' and resid 360 through 363 129 hydrogen bonds defined for protein. 381 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: 1.76 Time building geometry restraints manager: 2.23 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: 3919 1.15 - 1.32: 661 1.32 - 1.48: 1834 1.48 - 1.65: 1688 1.65 - 1.82: 21 Bond restraints: 8123 Sorted by residual: bond pdb=" NH1 ARG A 84 " pdb="HH11 ARG A 84 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH2 ARG A 476 " pdb="HH22 ARG A 476 " 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 A 399 " pdb=" H THR A 399 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH2 ARG A 279 " pdb="HH22 ARG A 279 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE1 TRP A 159 " pdb=" HE1 TRP A 159 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8118 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.96: 414 106.96 - 113.72: 8838 113.72 - 120.48: 2791 120.48 - 127.23: 2538 127.23 - 133.99: 74 Bond angle restraints: 14655 Sorted by residual: angle pdb=" OE1 GLN A 27 " pdb=" CD GLN A 27 " pdb=" NE2 GLN A 27 " ideal model delta sigma weight residual 122.60 112.79 9.81 1.00e+00 1.00e+00 9.63e+01 angle pdb=" N THR A 391 " pdb=" CA THR A 391 " pdb=" C THR A 391 " ideal model delta sigma weight residual 111.36 102.64 8.72 1.09e+00 8.42e-01 6.40e+01 angle pdb=" CG GLN A 27 " pdb=" CD GLN A 27 " pdb=" NE2 GLN A 27 " ideal model delta sigma weight residual 116.40 126.40 -10.00 1.50e+00 4.44e-01 4.44e+01 angle pdb=" N GLY A 21 " pdb=" CA GLY A 21 " pdb=" C GLY A 21 " ideal model delta sigma weight residual 114.90 124.70 -9.80 1.54e+00 4.22e-01 4.05e+01 angle pdb=" N GLY A 114 " pdb=" CA GLY A 114 " pdb=" C GLY A 114 " ideal model delta sigma weight residual 114.67 108.55 6.12 1.10e+00 8.26e-01 3.10e+01 ... (remaining 14650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 3435 14.82 - 29.65: 193 29.65 - 44.47: 97 44.47 - 59.29: 91 59.29 - 74.12: 23 Dihedral angle restraints: 3839 sinusoidal: 2018 harmonic: 1821 Sorted by residual: dihedral pdb=" CG ARG A 84 " pdb=" CD ARG A 84 " pdb=" NE ARG A 84 " pdb=" CZ ARG A 84 " ideal model delta sinusoidal sigma weight residual 180.00 136.22 43.78 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" N GLU A 180 " pdb=" CA GLU A 180 " pdb=" CB GLU A 180 " pdb=" CG GLU A 180 " ideal model delta sinusoidal sigma weight residual 180.00 -129.53 -50.47 3 1.50e+01 4.44e-03 8.90e+00 dihedral pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " pdb=" CG ARG A 296 " pdb=" CD ARG A 296 " ideal model delta sinusoidal sigma weight residual 60.00 109.93 -49.93 3 1.50e+01 4.44e-03 8.84e+00 ... (remaining 3836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 255 0.056 - 0.112: 233 0.112 - 0.168: 47 0.168 - 0.224: 23 0.224 - 0.280: 6 Chirality restraints: 564 Sorted by residual: chirality pdb=" CA PRO A 469 " pdb=" N PRO A 469 " pdb=" C PRO A 469 " pdb=" CB PRO A 469 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA VAL A 349 " pdb=" N VAL A 349 " pdb=" C VAL A 349 " pdb=" CB VAL A 349 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA VAL A 182 " pdb=" N VAL A 182 " pdb=" C VAL A 182 " pdb=" CB VAL A 182 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 561 not shown) Planarity restraints: 1211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.051 2.00e-02 2.50e+03 2.06e-02 1.27e+01 pdb=" CG TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " -0.051 2.00e-02 2.50e+03 1.96e-02 1.15e+01 pdb=" CG TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " -0.032 2.00e-02 2.50e+03 pdb=" HD1 TYR A 59 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 TYR A 59 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR A 59 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 192 " 0.052 2.00e-02 2.50e+03 1.93e-02 1.11e+01 pdb=" CG PHE A 192 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 192 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 192 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 192 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 192 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 192 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 192 " -0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE A 192 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 192 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 192 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 192 " 0.017 2.00e-02 2.50e+03 ... (remaining 1208 not shown) Histogram of nonbonded interaction distances: 1.28 - 1.94: 353 1.94 - 2.61: 8938 2.61 - 3.27: 26654 3.27 - 3.94: 35141 3.94 - 4.60: 53231 Nonbonded interactions: 124317 Sorted by model distance: nonbonded pdb=" O PRO A 215 " pdb="HH22 ARG A 279 " model vdw 1.279 1.850 nonbonded pdb=" HG2 ARG A 75 " pdb=" HD3 PRO A 76 " model vdw 1.320 2.440 nonbonded pdb=" HB3 GLN A 27 " pdb="HH21 ARG A 30 " model vdw 1.321 2.270 nonbonded pdb=" HG3 GLU A 334 " pdb=" HD3 PRO A 336 " model vdw 1.355 2.440 nonbonded pdb="HH22 ARG A 291 " pdb=" HE1 HIS A 394 " model vdw 1.358 2.100 ... (remaining 124312 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 15.96 2 O 707 7.97 1 N 703 6.97 1 C 2641 5.97 2 H 3920 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: 3920 of 7982 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7982 n_use_u_iso = 7982 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 = 7982 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7982 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7982 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 13 through 15 helix_type = alpha pi *3_10 unknown } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 27 through 38 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 69 through 71 helix_type = alpha pi *3_10 unknown } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 75 through 80 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 97 through 118 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 123 through 133 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 135 through 150 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 156 through 158 helix_type = alpha pi *3_10 unknown } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 161 through 164 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 168 through 177 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 179 through 205 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'A' and resid 223 through 227 } helix { serial_number = "13" helix_identifier = "13" selection = chain 'A' and resid 229 through 231 helix_type = alpha pi *3_10 unknown } helix { serial_number = "14" helix_identifier = "14" selection = chain 'A' and resid 265 through 270 } helix { serial_number = "15" helix_identifier = "15" selection = chain 'A' and resid 274 through 286 } helix { serial_number = "16" helix_identifier = "16" selection = chain 'A' and resid 295 through 298 helix_type = alpha pi *3_10 unknown } helix { serial_number = "17" helix_identifier = "17" selection = chain 'A' and resid 321 through 332 } helix { serial_number = "18" helix_identifier = "18" selection = chain 'A' and resid 347 through 356 } helix { serial_number = "19" helix_identifier = "19" selection = chain 'A' and resid 364 through 366 helix_type = alpha pi *3_10 unknown } helix { serial_number = "20" helix_identifier = "20" selection = chain 'A' and resid 378 through 380 helix_type = alpha pi *3_10 unknown } helix { serial_number = "21" helix_identifier = "21" selection = chain 'A' and resid 399 through 403 } helix { serial_number = "22" helix_identifier = "22" selection = chain 'A' and resid 408 through 421 } helix { serial_number = "23" helix_identifier = "23" selection = chain 'A' and resid 431 through 441 } helix { serial_number = "24" helix_identifier = "24" selection = chain 'A' and resid 451 through 454 } helix { serial_number = "25" helix_identifier = "25" selection = chain 'A' and resid 459 through 461 helix_type = alpha pi *3_10 unknown } helix { serial_number = "26" helix_identifier = "26" selection = chain 'A' and resid 484 through 496 } sheet { first_strand = chain 'A' and resid 446 through 450 sheet_id = " A" strand { selection = chain 'A' and resid 6 through 10 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 6 and name N bond_start_previous = chain 'A' and resid 447 and name O } strand { selection = chain 'A' and resid 43 through 45 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 43 and name N bond_start_previous = chain 'A' and resid 9 and name O } strand { selection = chain 'A' and resid 209 through 215 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 209 and name N bond_start_previous = chain 'A' and resid 44 and name O } strand { selection = chain 'A' and resid 289 through 293 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 289 and name N bond_start_previous = chain 'A' and resid 212 and name O } strand { selection = chain 'A' and resid 337 through 339 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 338 and name N bond_start_previous = chain 'A' and resid 290 and name O } } sheet { first_strand = chain 'A' and resid 300 through 303 sheet_id = " B" strand { selection = chain 'A' and resid 315 through 318 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 317 and name N bond_start_previous = chain 'A' and resid 301 and name O } } sheet { first_strand = chain 'A' and resid 360 through 363 sheet_id = " C" strand { selection = chain 'A' and resid 387 through 390 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 388 and name N bond_start_previous = chain 'A' and resid 360 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 = "1fp9_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3920 occupancy sum: 3920.00 (% of total atoms 49.11) Rotatable: count: 903 occupancy sum: 903.00 (% of total atoms 11.31) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.10 - 52.13 A, n_refl.=10132 (all), 10.01 % free)------------| | | | r_work= 0.4298 r_free= 0.5329 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.559026 | | target function (ml) not normalized (work): 50687.195951 | | target function (ml) not normalized (free): 5601.206097 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 52.13 - 5.93 0.97 1355 151 0.4603 0.4878 6.2066 6.1554| | 2: 5.93 - 4.71 0.96 1323 147 0.3547 0.4794 5.7546 5.7028| | 3: 4.71 - 4.11 0.96 1288 144 0.4084 0.5271 5.5696 5.4451| | 4: 4.11 - 3.74 0.96 1288 143 0.4551 0.5640 5.5142 5.619| | 5: 3.74 - 3.47 0.96 1281 142 0.4754 0.5967 5.4726 5.2661| | 6: 3.47 - 3.26 0.97 1282 142 0.4418 0.5860 5.2538 5.3947| | 7: 3.26 - 3.10 0.97 1301 145 0.4200 0.5257 5.1055 5.0481| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 52.13 - 5.93 1355 151 0.16 77.62 0.60 0.03 59863.03| | 2: 5.93 - 4.71 1323 147 0.58 46.10 1.30 0.17 26644.58| | 3: 4.71 - 4.11 1288 144 0.83 24.31 1.53 0.26 9202.68| | 4: 4.11 - 3.74 1288 143 0.82 25.71 1.67 0.28 8178.16| | 5: 3.74 - 3.47 1281 142 0.80 27.27 1.71 0.29 7239.08| | 6: 3.47 - 3.26 1282 142 0.77 30.37 1.60 0.27 6252.41| | 7: 3.26 - 3.10 1301 145 0.73 33.46 1.45 0.23 4577.34| |alpha: min = 0.03 max = 0.29 mean = 0.22| |beta: min = 4577.34 max = 59863.03 mean = 17766.58| |figures of merit: min = 0.00 max = 1.00 mean = 0.67| |phase err.(work): min = 0.00 max = 90.00 mean = 38.16| |phase err.(test): min = 0.00 max = 89.99 mean = 38.55| |-----------------------------------------------------------------------------| ----------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 : 0.005 0.046 4203 Z= 0.337 Angle : 1.249 9.998 5718 Z= 0.861 Chirality : 0.082 0.280 564 Planarity : 0.005 0.040 750 Dihedral : 14.688 74.118 1524 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 28.95 Ramachandran Plot: Outliers : 1.81 % Allowed : 12.25 % Favored : 85.94 % Rotamer: Outliers : 2.24 % Allowed : 2.24 % Favored : 95.51 % 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: -5.15 (0.30), residues: 498 helix: -4.21 (0.20), residues: 229 sheet: -1.62 (0.66), residues: 60 loop : -2.83 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 279 TYR 0.043 0.007 TYR A 141 PHE 0.032 0.005 PHE A 192 TRP 0.033 0.006 TRP A 159 HIS 0.002 0.000 HIS A 384 Individual atomic B min max mean iso aniso Overall: 12.70 77.70 33.40 2.74 4062 0 Protein: 12.70 77.70 33.40 2.74 4062 0 Chain A: 12.70 77.70 33.40 N/A 4062 0 Histogram: Values Number of atoms 12.70 - 19.20 560 19.20 - 25.70 851 25.70 - 32.20 919 32.20 - 38.70 595 38.70 - 45.20 378 45.20 - 51.70 244 51.70 - 58.20 183 58.20 - 64.70 129 64.70 - 71.20 85 71.20 - 77.70 118 |-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: 3.10 - 52.13 A, n_refl.=10132 (all), 10.01 % free)------------| | | | r_work= 0.4298 r_free= 0.5329 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.559026 | | target function (ml) not normalized (work): 50687.195951 | | target function (ml) not normalized (free): 5601.206097 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4407 0.4298 0.5329 n_refl.: 10132 re-set all scales: r(all,work,free)=0.4407 0.4298 0.5329 n_refl.: 10132 remove outliers: r(all,work,free)=0.4160 0.4027 0.5329 n_refl.: 10127 overall B=3.30 to atoms: r(all,work,free)=0.4309 0.4168 0.5513 n_refl.: 10127 bulk-solvent and scaling: r(all,work,free)=0.2399 0.2398 0.2416 n_refl.: 10127 remove outliers: r(all,work,free)=0.2397 0.2397 0.2400 n_refl.: 10125 ======================== 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 52.125-14.829 89.91 87 11 0.2450 1487.728 1446.815 1.051 1.275 0.404 14.763-11.705 97.09 91 9 0.1774 1550.646 1541.206 0.930 1.260 0.398 11.688-9.266 96.82 191 22 0.1307 1812.092 1781.536 0.927 1.236 0.395 9.245-7.329 97.77 355 40 0.1746 1351.329 1327.100 0.906 1.200 0.392 7.324-5.801 97.35 727 80 0.2319 959.455 924.737 0.843 1.146 0.389 5.796-4.593 96.03 1414 157 0.2081 1149.827 1113.607 0.910 1.055 0.352 4.593-3.637 95.90 2818 313 0.2376 1063.229 1016.166 1.121 0.912 0.295 3.636-3.100 96.41 3429 381 0.2953 729.417 669.032 1.293 0.739 0.111 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.8055 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2397 r_free=0.2400 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2397 r_free=0.2400 ========================= Local real-space refinement ========================= Before: r_work=0.2397 r_free=0.2400 106 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.325 revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 9 average time/residue: 0.2136 time to fit residues: 2.8094 After: r_work=0.2417 r_free=0.2449 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.280358 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.302638 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 0.1997 0.2714 0.0717 0.014 1.3 21.1 0.4 4.2 0 7.140 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1997 r_free=0.2714 104 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.095 outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.3711 time to fit residues: 9.6931 After: r_work=0.2039 r_free=0.2729 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.39 27.29 6.90 1.968 36.488 0.303 0.050 20.76 27.31 6.55 4.038 37.031 0.009 0.051 20.31 27.32 7.01 3.972 36.978 0.038 0.049 19.23 27.44 8.21 4.457 36.892 0.151 0.044 18.64 27.60 8.96 5.394 36.965 0.303 0.041 18.29 27.72 9.43 6.431 37.199 0.454 0.040 18.09 27.81 9.72 7.109 37.343 0.605 0.039 17.96 27.89 9.92 7.660 37.471 0.757 0.038 17.87 27.95 10.08 8.108 37.579 0.908 0.038 17.79 28.00 10.21 8.506 37.678 1.059 0.038 17.73 28.06 10.33 8.879 37.777 1.211 0.037 17.62 28.14 10.51 9.505 37.959 1.362 0.037 17.40 28.29 10.89 10.981 38.460 1.513 0.036 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.038 Accepted refinement result: 20.31 27.32 7.01 3.972 36.978 0.038 0.049 Individual atomic B min max mean iso aniso Overall: 18.36 82.00 37.67 2.52 4062 0 Protein: 18.36 82.00 37.67 2.52 4062 0 Chain A: 18.36 82.00 37.67 N/A 4062 0 Histogram: Values Number of atoms 18.36 - 24.72 307 24.72 - 31.09 1133 31.09 - 37.45 1062 37.45 - 43.81 579 43.81 - 50.18 397 50.18 - 56.54 201 56.54 - 62.91 150 62.91 - 69.27 93 69.27 - 75.63 74 75.63 - 82.00 66 =========================== Idealize ADP of riding H ========================== r_work=0.2031 r_free=0.2732 r_work=0.2029 r_free=0.2722 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 52.13 A, n_refl.=10125 (all), 10.00 % free)------------| | | | r_work= 0.2029 r_free= 0.2722 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ls_wunit_k1) (work): 0.049045 | | target function (ls_wunit_k1) not normalized (work): 446.899427 | | target function (ls_wunit_k1) not normalized (free): 94.235137 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2098 0.2029 0.2722 n_refl.: 10125 re-set all scales: r(all,work,free)=0.4226 0.4054 0.5561 n_refl.: 10125 remove outliers: r(all,work,free)=0.4226 0.4054 0.5561 n_refl.: 10125 overall B=0.00 to atoms: r(all,work,free)=0.4226 0.4054 0.5561 n_refl.: 10125 bulk-solvent and scaling: r(all,work,free)=0.2099 0.2028 0.2745 n_refl.: 10125 remove outliers: r(all,work,free)=0.2099 0.2028 0.2745 n_refl.: 10125 ======================== 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 52.125-14.829 89.91 87 11 0.2127 811.932 793.096 1.146 1.210 0.406 14.763-11.705 97.09 91 9 0.1426 846.270 850.780 1.030 1.198 0.403 11.688-9.266 96.82 191 22 0.1126 988.955 972.331 1.006 1.179 0.400 9.245-7.329 97.77 355 40 0.1502 737.492 726.579 0.973 1.150 0.393 7.324-5.801 97.35 727 80 0.1969 523.626 511.731 0.901 1.106 0.390 5.796-4.593 96.03 1414 157 0.1741 627.521 618.443 0.954 1.033 0.360 4.593-3.637 95.90 2818 313 0.1988 580.260 568.236 1.145 0.917 0.280 3.636-3.100 96.41 3429 381 0.2532 398.082 376.506 1.311 0.778 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.2584 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2028 r_free=0.2745 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.2028 r_free=0.2745 ========================= Local real-space refinement ========================= Before: r_work=0.2028 r_free=0.2745 97 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.569 outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2394 time to fit residues: 1.9459 After: r_work=0.2028 r_free=0.2745 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.963681 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.078820 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 0.2246 0.2687 0.0441 0.003 0.6 4.3 0.0 0.2 0 0.125 0.2179 0.2689 0.0510 0.004 0.6 5.6 0.0 1.2 0 0.250 0.2112 0.2702 0.0590 0.006 0.8 7.9 0.0 2.2 0 0.500 0.2033 0.2743 0.0710 0.011 1.1 13.7 0.0 5.5 0 1.000 0.1949 0.2830 0.0881 0.018 1.5 23.2 0.2 9.0 0 2.000 0.1900 0.2847 0.0947 0.024 1.9 28.4 0.6 12.2 0 3.000 0.1860 0.2856 0.0996 0.029 2.3 34.3 1.2 14.2 0 4.000 0.1839 0.2874 0.1035 0.034 2.6 38.8 2.0 14.7 0 5.000 0.1817 0.2893 0.1076 0.039 2.8 42.2 2.2 15.0 0 6.000 0.1801 0.2909 0.1108 0.043 3.0 46.9 2.4 16.2 1 7.000 0.1782 0.2912 0.1130 0.046 3.3 50.1 3.0 17.0 2 8.000 0.1765 0.2924 0.1160 0.050 3.5 53.4 3.0 18.0 2 9.000 0.1752 0.2945 0.1193 0.053 3.7 57.6 3.8 19.2 3 10.000 0.1983 0.2790 0.0807 0.014 1.3 20.1 0.0 7.2 0 1.482 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2246 0.2687 0.0441 0.003 0.6 4.3 0.0 0.2 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2246 r_free=0.2687 98 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.558 outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3563 time to fit residues: 1.8970 After: r_work=0.2249 r_free=0.2687 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.49 26.87 4.39 5.776 41.331 0.079 6.380 23.55 27.42 3.86 6.383 43.421 0.002 6.415 22.33 26.89 4.55 6.018 41.244 0.010 6.373 21.80 26.95 5.15 6.370 41.080 0.039 6.356 20.73 27.28 6.55 8.414 41.298 0.079 6.326 20.43 27.39 6.96 9.272 41.667 0.118 6.320 20.23 27.50 7.27 10.069 41.964 0.158 6.316 20.09 27.60 7.51 10.767 42.205 0.197 6.314 19.98 27.68 7.70 11.375 42.405 0.236 6.313 19.90 27.76 7.85 11.893 42.571 0.276 6.312 19.84 27.82 7.97 12.347 42.713 0.315 6.312 19.80 27.87 8.07 12.740 42.835 0.355 6.311 19.76 27.91 8.15 13.086 42.939 0.394 6.311 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.010 Accepted refinement result: 22.33 26.89 4.55 6.018 41.244 0.010 6.373 Individual atomic B min max mean iso aniso Overall: 15.88 83.09 37.50 2.55 4062 0 Protein: 15.88 83.09 37.50 2.55 4062 0 Chain A: 15.88 83.09 37.50 N/A 4062 0 Histogram: Values Number of atoms 15.88 - 22.60 105 22.60 - 29.32 954 29.32 - 36.04 1265 36.04 - 42.76 698 42.76 - 49.48 454 49.48 - 56.21 222 56.21 - 62.93 156 62.93 - 69.65 93 69.65 - 76.37 74 76.37 - 83.09 41 =========================== Idealize ADP of riding H ========================== r_work=0.2233 r_free=0.2689 r_work=0.2232 r_free=0.2689 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 52.13 A, n_refl.=10125 (all), 10.00 % free)------------| | | | r_work= 0.2232 r_free= 0.2689 coordinate error (max.-lik. estimate): 0.48 A | | | | normalized target function (ml) (work): 6.372024 | | target function (ml) not normalized (work): 58061.878347 | | target function (ml) not normalized (free): 6572.121647 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2277 0.2232 0.2689 n_refl.: 10125 re-set all scales: r(all,work,free)=0.4280 0.4118 0.5565 n_refl.: 10125 remove outliers: r(all,work,free)=0.4280 0.4118 0.5565 n_refl.: 10125 overall B=0.00 to atoms: r(all,work,free)=0.4280 0.4118 0.5565 n_refl.: 10125 bulk-solvent and scaling: r(all,work,free)=0.2264 0.2220 0.2663 n_refl.: 10125 remove outliers: r(all,work,free)=0.2264 0.2220 0.2663 n_refl.: 10125 ======================== 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 52.125-14.829 89.91 87 11 0.2137 811.932 794.088 1.229 1.207 0.410 14.763-11.705 97.09 91 9 0.1449 846.270 843.436 1.062 1.195 0.407 11.688-9.266 96.82 191 22 0.1142 988.955 974.665 1.039 1.176 0.406 9.245-7.329 97.77 355 40 0.1535 737.492 730.003 1.007 1.148 0.405 7.324-5.801 97.35 727 80 0.2115 523.626 510.840 0.932 1.104 0.400 5.796-4.593 96.03 1414 157 0.1870 627.521 614.436 0.967 1.032 0.400 4.593-3.637 95.90 2818 313 0.2252 580.260 559.119 1.127 0.917 0.320 3.636-3.100 96.41 3429 381 0.2767 398.082 369.303 1.285 0.779 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.8882 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2220 r_free=0.2663 After: r_work=0.2220 r_free=0.2664 ================================== NQH flips ================================== r_work=0.2220 r_free=0.2664 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 r_work=0.2220 r_free=0.2664 ========================= Local real-space refinement ========================= Before: r_work=0.2220 r_free=0.2664 95 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.173 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2080 After: r_work=0.2220 r_free=0.2664 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.997789 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.080686 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 0.2219 0.2667 0.0448 0.003 0.5 4.5 0.0 0.0 0 0.125 0.2210 0.2668 0.0458 0.003 0.6 4.6 0.0 0.0 0 0.250 0.2169 0.2674 0.0505 0.007 0.7 4.9 0.0 0.0 0 0.500 0.2045 0.2731 0.0686 0.014 1.4 14.5 0.2 0.2 0 1.000 0.1986 0.2780 0.0794 0.017 1.9 23.8 0.4 2.7 0 2.000 0.1941 0.2786 0.0844 0.023 2.2 25.1 0.4 3.2 0 3.000 0.1922 0.2807 0.0885 0.026 2.5 31.2 0.6 6.0 0 4.000 0.1877 0.2844 0.0968 0.033 3.2 37.3 0.6 6.5 0 5.000 0.1862 0.2837 0.0975 0.036 3.1 37.7 1.4 9.5 0 6.000 0.1832 0.2884 0.1052 0.041 3.7 44.1 1.2 9.2 1 7.000 0.1812 0.2896 0.1084 0.045 4.1 48.9 1.4 10.7 1 8.000 0.1795 0.2908 0.1112 0.048 4.3 53.9 2.0 11.2 3 9.000 0.1791 0.2881 0.1090 0.048 4.2 49.4 1.6 10.5 2 10.000 0.2009 0.2752 0.0743 0.016 1.7 20.9 0.2 1.5 0 1.499 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2219 0.2667 0.0448 0.003 0.5 4.5 0.0 0.0 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2219 r_free=0.2667 92 residues out of total 401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.592 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7834 After: r_work=0.2219 r_free=0.2667 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.19 26.67 4.48 5.748 41.159 0.081 6.371 23.54 27.26 3.72 6.182 42.736 0.002 6.416 22.18 26.69 4.51 5.825 41.113 0.010 6.371 21.69 26.75 5.06 6.203 40.960 0.040 6.355 20.52 27.20 6.68 8.464 40.984 0.081 6.324 20.24 27.35 7.11 9.302 41.369 0.121 6.318 20.06 27.49 7.43 10.079 41.674 0.161 6.315 19.94 27.61 7.67 10.764 41.920 0.202 6.314 19.86 27.72 7.86 11.362 42.124 0.242 6.313 19.80 27.81 8.01 11.876 42.293 0.282 6.313 19.75 27.88 8.14 12.319 42.436 0.323 6.313 19.71 27.95 8.23 12.708 42.559 0.363 6.313 19.68 28.00 8.32 13.055 42.667 0.403 6.313 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.010 Accepted refinement result: 22.18 26.69 4.51 5.825 41.113 0.010 6.371 Individual atomic B min max mean iso aniso Overall: 16.55 83.46 37.41 2.52 4062 0 Protein: 16.55 83.46 37.41 2.52 4062 0 Chain A: 16.55 83.46 37.41 N/A 4062 0 Histogram: Values Number of atoms 16.55 - 23.24 152 23.24 - 29.93 1041 29.93 - 36.63 1225 36.63 - 43.32 653 43.32 - 50.01 446 50.01 - 56.70 200 56.70 - 63.39 153 63.39 - 70.08 94 70.08 - 76.77 66 76.77 - 83.46 32 =========================== Idealize ADP of riding H ========================== r_work=0.2218 r_free=0.2669 r_work=0.2218 r_free=0.2669 ----------X-ray data---------- |--(resolution: 3.10 - 52.13 A, n_refl.=10125 (all), 10.00 % free)------------| | | | r_work= 0.2218 r_free= 0.2669 coordinate error (max.-lik. estimate): 0.46 A | | | | normalized target function (ml) (work): 6.370655 | | target function (ml) not normalized (work): 58049.409760 | | target function (ml) not normalized (free): 6569.942270 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 52.13 - 5.93 0.97 1352 151 0.1680 0.1995 6.3692 6.5339| | 2: 5.93 - 4.71 0.96 1323 147 0.1916 0.2407 6.411 6.5033| | 3: 4.71 - 4.11 0.96 1288 144 0.2064 0.2224 6.494 6.5368| | 4: 4.11 - 3.74 0.96 1286 142 0.2295 0.3092 6.4718 6.7173| | 5: 3.74 - 3.47 0.96 1281 142 0.2618 0.2981 6.4438 6.4647| | 6: 3.47 - 3.26 0.97 1281 142 0.2684 0.3295 6.2851 6.4747| | 7: 3.26 - 3.10 0.97 1301 145 0.2934 0.3553 6.1212 6.1708| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 52.13 - 5.93 1352 151 0.88 18.36 0.99 0.94 57322.52| | 2: 5.93 - 4.71 1323 147 0.86 20.91 1.00 0.90 64884.39| | 3: 4.71 - 4.11 1288 144 0.86 21.45 1.00 0.89 70257.50| | 4: 4.11 - 3.74 1286 142 0.82 25.11 1.00 0.89 75886.08| | 5: 3.74 - 3.47 1281 142 0.79 28.16 1.05 0.90 72150.55| | 6: 3.47 - 3.26 1281 142 0.75 32.18 1.02 0.86 62257.34| | 7: 3.26 - 3.10 1301 145 0.72 34.75 0.93 0.74 43762.22| |alpha: min = 0.74 max = 0.94 mean = 0.88| |beta: min = 43762.22 max = 75886.08 mean = 63710.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.81| |phase err.(work): min = 0.00 max = 89.80 mean = 25.78| |phase err.(test): min = 0.00 max = 89.59 mean = 26.37| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2263 0.2218 0.2669 n_refl.: 10125 re-set all scales: r(all,work,free)=0.4279 0.4117 0.5564 n_refl.: 10125 remove outliers: r(all,work,free)=0.4279 0.4117 0.5564 n_refl.: 10125 overall B=0.00 to atoms: r(all,work,free)=0.4279 0.4117 0.5564 n_refl.: 10125 bulk-solvent and scaling: r(all,work,free)=0.2282 0.2236 0.2697 n_refl.: 10125 remove outliers: r(all,work,free)=0.2282 0.2236 0.2697 n_refl.: 10125 ======================== 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 52.125-14.829 89.91 87 11 0.2131 811.932 799.196 1.314 1.105 0.410 14.763-11.705 97.09 91 9 0.1420 846.270 849.149 1.129 1.099 0.407 11.688-9.266 96.82 191 22 0.1141 988.955 978.881 1.097 1.088 0.406 9.245-7.329 97.77 355 40 0.1538 737.492 733.650 1.052 1.071 0.405 7.324-5.801 97.35 727 80 0.2114 523.626 512.145 0.957 1.046 0.400 5.796-4.593 96.03 1414 157 0.1875 627.521 614.666 0.960 1.004 0.390 4.593-3.637 95.90 2818 313 0.2262 580.260 558.405 1.070 0.936 0.310 3.636-3.100 96.41 3429 381 0.2809 398.082 367.819 1.130 0.856 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.3582 ================= 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 : 0.4298 0.5329 0.005 1.249 12.7 77.7 33.4 0 0.000 1_bss: 0.2397 0.2400 0.005 1.249 16.0 81.0 36.7 0 0.000 1_settarget: 0.2397 0.2400 0.005 1.249 16.0 81.0 36.7 0 0.000 1_updatephipsi: 0.2397 0.2400 0.005 1.249 16.0 81.0 36.7 0 0.000 1_nqh: 0.2397 0.2400 0.005 1.249 16.0 81.0 36.7 0 0.000 1_realsrl: 0.2417 0.2449 0.005 1.249 16.0 81.0 36.7 0 0.005 1_weight: 0.2417 0.2449 0.005 1.249 16.0 81.0 36.7 0 0.005 1_xyzrec: 0.1997 0.2714 0.014 1.325 16.0 81.0 36.7 0 0.271 1_realsrl2: 0.2039 0.2729 0.014 1.325 16.0 81.0 36.7 0 0.276 1_adp: 0.2031 0.2732 0.014 1.325 18.4 82.0 37.7 0 0.276 1_regHadp: 0.2029 0.2722 0.014 1.325 18.4 82.0 37.7 0 0.276 2_bss: 0.2028 0.2745 0.014 1.325 18.4 82.0 37.7 0 0.276 2_settarget: 0.2028 0.2745 0.014 1.325 18.4 82.0 37.7 0 0.276 2_updatephipsi: 0.2028 0.2745 0.014 1.325 18.4 82.0 37.7 0 0.276 2_updatecdl: 0.2028 0.2745 0.014 1.348 18.4 82.0 37.7 0 0.276 2_nqh: 0.2028 0.2745 0.014 1.348 18.4 82.0 37.7 0 0.278 2_realsrl: 0.2028 0.2745 0.014 1.348 18.4 82.0 37.7 0 0.278 2_weight: 0.2028 0.2745 0.014 1.348 18.4 82.0 37.7 0 0.278 2_xyzrec: 0.2246 0.2687 0.003 0.551 18.4 82.0 37.7 0 0.267 2_realsrl2: 0.2249 0.2687 0.003 0.551 18.4 82.0 37.7 0 0.267 2_adp: 0.2233 0.2689 0.003 0.551 15.9 83.1 37.5 0 0.267 2_regHadp: 0.2232 0.2689 0.003 0.551 15.9 83.1 37.5 0 0.267 3_bss: 0.2220 0.2663 0.003 0.551 15.9 83.1 37.5 0 0.267 3_settarget: 0.2220 0.2663 0.003 0.551 15.9 83.1 37.5 0 0.267 3_updatephipsi: 0.2220 0.2663 0.003 0.551 15.9 83.1 37.5 0 0.267 3_updatecdl: 0.2220 0.2663 0.003 0.576 15.9 83.1 37.5 0 0.267 3_setrh: 0.2220 0.2664 0.003 0.576 15.9 83.1 37.5 0 0.267 3_nqh: 0.2220 0.2664 0.003 0.576 15.9 83.1 37.5 0 0.267 3_realsrl: 0.2220 0.2664 0.003 0.576 15.9 83.1 37.5 0 0.267 3_weight: 0.2220 0.2664 0.003 0.576 15.9 83.1 37.5 0 0.267 3_xyzrec: 0.2219 0.2667 0.003 0.550 15.9 83.1 37.5 0 0.267 3_realsrl2: 0.2219 0.2667 0.003 0.550 15.9 83.1 37.5 0 0.267 3_adp: 0.2218 0.2669 0.003 0.550 16.6 83.5 37.4 0 0.267 3_regHadp: 0.2218 0.2669 0.003 0.550 16.6 83.5 37.4 0 0.267 end: 0.2236 0.2697 0.003 0.550 16.6 83.5 37.4 0 0.267 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1fp9_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1fp9_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.1000 Refinement macro-cycles (run) : 379.6300 Write final files (write_after_run_outputs) : 27.7900 Total : 413.5200 Total CPU time: 7.34 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:00 PDT -0700 (1716251640.60 s) Start R-work = 0.2397, R-free = 0.2400 Final R-work = 0.2236, R-free = 0.2697 =============================================================================== Job complete usr+sys time: 467.15 seconds wall clock time: 19 minutes 4.85 seconds (1144.85 seconds total)