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/4iy2.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4iy2/4iy2.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/4iy2.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4iy2.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4iy2/4iy2.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4iy2/4iy2.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 PHE 560": "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: 4856 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2428 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 144} Chain: "C" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2428 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 144} Time building chain proxies: 0.96, per 1000 atoms: 0.20 Number of scatterers: 4856 At special positions: 0 Unit cell: (102.513, 104.593, 105.694, 90, 90, 90) Space group: I 21 21 21 (No. 24) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Se 12 33.99 S 4 16.00 O 482 8.00 N 382 7.00 C 1558 6.00 H 2418 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 190.1 milliseconds 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 4 sheets defined 36.8% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 431 through 442 removed outlier: 4.526A pdb=" N ARG A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 468 through 476 removed outlier: 3.574A pdb=" N MSE A 474 " --> pdb=" O SER A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 500 Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 532 through 539 removed outlier: 3.513A pdb=" N LYS A 539 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 577 Processing helix chain 'C' and resid 431 through 442 removed outlier: 4.517A pdb=" N ARG C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 448 No H-bonds generated for 'chain 'C' and resid 446 through 448' Processing helix chain 'C' and resid 453 through 455 No H-bonds generated for 'chain 'C' and resid 453 through 455' Processing helix chain 'C' and resid 468 through 476 removed outlier: 3.543A pdb=" N MSE C 474 " --> pdb=" O SER C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 500 Processing helix chain 'C' and resid 505 through 507 No H-bonds generated for 'chain 'C' and resid 505 through 507' Processing helix chain 'C' and resid 511 through 518 Processing helix chain 'C' and resid 532 through 539 removed outlier: 3.519A pdb=" N LYS C 539 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 577 Processing sheet with id= A, first strand: chain 'A' and resid 524 through 526 removed outlier: 7.505A pdb=" N VAL A 525 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE A 547 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 565 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG A 550 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL A 563 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN A 552 " --> pdb=" O TYR A 561 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR A 561 " --> pdb=" O ASN A 552 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 480 through 484 Processing sheet with id= C, first strand: chain 'C' and resid 524 through 526 removed outlier: 7.590A pdb=" N VAL C 525 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE C 547 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C 565 " --> pdb=" O VAL C 548 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG C 550 " --> pdb=" O VAL C 563 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL C 563 " --> pdb=" O ARG C 550 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN C 552 " --> pdb=" O TYR C 561 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR C 561 " --> pdb=" O ASN C 552 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 480 through 484 66 hydrogen bonds defined for protein. 138 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: 1.22 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.19: 2414 1.19 - 1.39: 976 1.39 - 1.60: 1480 1.60 - 1.81: 3 1.81 - 2.02: 25 Bond restraints: 4898 Sorted by residual: bond pdb=" N VAL C 572 " pdb=" H VAL C 572 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N MSE A 470 " pdb=" H MSE A 470 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N CYS A 456 " pdb=" H CYS A 456 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N VAL A 449 " pdb=" H VAL A 449 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" ND2 ASN C 468 " pdb="HD21 ASN C 468 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 4893 not shown) Histogram of bond angle deviations from ideal: 96.68 - 103.60: 39 103.60 - 110.52: 4917 110.52 - 117.44: 1798 117.44 - 124.36: 2024 124.36 - 131.29: 120 Bond angle restraints: 8898 Sorted by residual: angle pdb=" C HIS A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta sigma weight residual 119.76 125.62 -5.86 1.03e+00 9.43e-01 3.23e+01 angle pdb=" C HIS C 520 " pdb=" N PRO C 521 " pdb=" CA PRO C 521 " ideal model delta sigma weight residual 119.78 124.36 -4.58 1.03e+00 9.43e-01 1.98e+01 angle pdb=" C ASP A 558 " pdb=" N PRO A 559 " pdb=" CA PRO A 559 " ideal model delta sigma weight residual 119.76 123.72 -3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" C VAL C 497 " pdb=" N LYS C 498 " pdb=" CA LYS C 498 " ideal model delta sigma weight residual 120.38 125.51 -5.13 1.37e+00 5.33e-01 1.40e+01 angle pdb=" N ASP A 493 " pdb=" CA ASP A 493 " pdb=" C ASP A 493 " ideal model delta sigma weight residual 108.74 113.88 -5.14 1.38e+00 5.25e-01 1.39e+01 ... (remaining 8893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 2041 16.89 - 33.77: 153 33.77 - 50.65: 67 50.65 - 67.54: 24 67.54 - 84.42: 3 Dihedral angle restraints: 2288 sinusoidal: 1262 harmonic: 1026 Sorted by residual: dihedral pdb=" C VAL C 572 " pdb=" N VAL C 572 " pdb=" CA VAL C 572 " pdb=" CB VAL C 572 " ideal model delta harmonic sigma weight residual -122.00 -129.82 7.82 0 2.50e+00 1.60e-01 9.78e+00 dihedral pdb=" C VAL A 572 " pdb=" N VAL A 572 " pdb=" CA VAL A 572 " pdb=" CB VAL A 572 " ideal model delta harmonic sigma weight residual -122.00 -129.79 7.79 0 2.50e+00 1.60e-01 9.71e+00 dihedral pdb=" CB GLU C 574 " pdb=" CG GLU C 574 " pdb=" CD GLU C 574 " pdb=" OE1 GLU C 574 " ideal model delta sinusoidal sigma weight residual 0.00 -84.42 84.42 1 3.00e+01 1.11e-03 9.63e+00 ... (remaining 2285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 198 0.044 - 0.088: 121 0.088 - 0.132: 47 0.132 - 0.176: 17 0.176 - 0.220: 7 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA GLU C 556 " pdb=" N GLU C 556 " pdb=" C GLU C 556 " pdb=" CB GLU C 556 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLU A 556 " pdb=" N GLU A 556 " pdb=" C GLU A 556 " pdb=" CB GLU A 556 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE A 573 " pdb=" N ILE A 573 " pdb=" C ILE A 573 " pdb=" CB ILE A 573 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 387 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 523 " 0.023 2.00e-02 2.50e+03 1.27e-02 3.64e+00 pdb=" CG HIS A 523 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS A 523 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 HIS A 523 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS A 523 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 523 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 HIS A 523 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 HIS A 523 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 HIS A 523 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 538 " 0.004 2.00e-02 2.50e+03 7.38e-03 1.63e+00 pdb=" CG PHE A 538 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE A 538 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 538 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 538 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 538 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 538 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 538 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 PHE A 538 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 538 " -0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE A 538 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 538 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 467 " -0.012 2.00e-02 2.50e+03 7.27e-03 1.59e+00 pdb=" CG PHE A 467 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE A 467 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 467 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 467 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 467 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 467 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 467 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE A 467 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 467 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 467 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 467 " -0.001 2.00e-02 2.50e+03 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.03: 221 2.03 - 2.72: 7474 2.72 - 3.41: 16274 3.41 - 4.11: 21898 4.11 - 4.80: 34964 Nonbonded interactions: 80831 Sorted by model distance: nonbonded pdb=" HA ASP A 504 " pdb=" HE2 PHE C 467 " model vdw 1.334 2.270 nonbonded pdb=" HE2 PHE A 467 " pdb=" HA ASP C 504 " model vdw 1.337 2.270 nonbonded pdb=" O GLU C 485 " pdb="HD22 ASN C 490 " model vdw 1.340 1.850 nonbonded pdb=" O GLU A 485 " pdb="HD22 ASN A 490 " model vdw 1.343 1.850 nonbonded pdb="HH22 ARG A 550 " pdb=" OE1 GLU A 554 " model vdw 1.350 1.850 ... (remaining 80826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians Se 12 33.79 1 S 4 15.91 1 O 482 7.97 1 N 382 6.97 1 C 1558 5.97 1 H 2418 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: 2418 of 4856 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4856 n_use_u_iso = 4856 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 = 4856 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4856 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4856 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 431 through 442 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 446 through 448 helix_type = alpha pi *3_10 unknown } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 453 through 455 helix_type = alpha pi *3_10 unknown } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 468 through 476 helix_type = alpha pi *3_10 unknown } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 497 through 500 helix_type = alpha pi *3_10 unknown } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 505 through 507 helix_type = alpha pi *3_10 unknown } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 511 through 518 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 532 through 539 helix_type = alpha pi *3_10 unknown } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 569 through 577 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'C' and resid 431 through 442 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'C' and resid 446 through 448 helix_type = alpha pi *3_10 unknown } helix { serial_number = "12" helix_identifier = "12" selection = chain 'C' and resid 453 through 455 helix_type = alpha pi *3_10 unknown } helix { serial_number = "13" helix_identifier = "13" selection = chain 'C' and resid 468 through 476 helix_type = alpha pi *3_10 unknown } helix { serial_number = "14" helix_identifier = "14" selection = chain 'C' and resid 497 through 500 helix_type = alpha pi *3_10 unknown } helix { serial_number = "15" helix_identifier = "15" selection = chain 'C' and resid 505 through 507 helix_type = alpha pi *3_10 unknown } helix { serial_number = "16" helix_identifier = "16" selection = chain 'C' and resid 511 through 518 } helix { serial_number = "17" helix_identifier = "17" selection = chain 'C' and resid 532 through 539 helix_type = alpha pi *3_10 unknown } helix { serial_number = "18" helix_identifier = "18" selection = chain 'C' and resid 569 through 577 } sheet { first_strand = chain 'A' and resid 524 through 526 sheet_id = " A" strand { selection = chain 'A' and resid 545 through 552 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 547 and name N bond_start_previous = chain 'A' and resid 525 and name O } strand { selection = chain 'A' and resid 560 through 568 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 567 and name N bond_start_previous = chain 'A' and resid 546 and name O } } sheet { first_strand = chain 'A' and resid 480 through 484 sheet_id = " B" strand { selection = chain 'A' and resid 491 through 496 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 495 and name N bond_start_previous = chain 'A' and resid 481 and name O } } sheet { first_strand = chain 'C' and resid 524 through 526 sheet_id = " C" strand { selection = chain 'C' and resid 545 through 552 sense = *parallel antiparallel unknown bond_start_current = chain 'C' and resid 547 and name N bond_start_previous = chain 'C' and resid 525 and name O } strand { selection = chain 'C' and resid 560 through 568 sense = parallel *antiparallel unknown bond_start_current = chain 'C' and resid 567 and name N bond_start_previous = chain 'C' and resid 546 and name O } } sheet { first_strand = chain 'C' and resid 480 through 484 sheet_id = " D" strand { selection = chain 'C' and resid 491 through 496 sense = parallel *antiparallel unknown bond_start_current = chain 'C' and resid 495 and name N bond_start_previous = chain 'C' and resid 481 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 = "4iy2_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2418 occupancy sum: 2418.00 (% of total atoms 49.89) Rotatable: count: 714 occupancy sum: 714.00 (% of total atoms 14.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.60 - 42.85 A, n_refl.=6670 (all), 4.74 % free)-------------| | | | r_work= 0.6305 r_free= 0.6362 coordinate error (max.-lik. estimate): 0.17 A | | | | normalized target function (ml) (work): 6.476566 | | target function (ml) not normalized (work): 41152.101576 | | target function (ml) not normalized (free): 2067.378995 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 42.85 - 4.54 1.00 3313 159 0.5995 0.6281 7.0436 7.1411| | 2: 4.54 - 3.60 0.95 3041 157 0.6997 0.6514 5.8588 5.936| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 42.85 - 4.54 3313 159 0.29 67.64 0.94 0.33 277885.05| | 2: 4.54 - 3.60 3041 157 0.70 35.82 3.03 0.97 23390.81| |alpha: min = 0.33 max = 0.97 mean = 0.63| |beta: min = 23390.81 max = 277885.05 mean = 156085.09| |figures of merit: min = 0.00 max = 1.00 mean = 0.48| |phase err.(work): min = 0.00 max = 89.99 mean = 52.41| |phase err.(test): min = 0.00 max = 89.77 mean = 51.68| |-----------------------------------------------------------------------------| ----------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 : 0.008 0.080 2480 Z= 0.511 Angle : 1.169 6.740 3354 Z= 0.826 Chirality : 0.068 0.220 390 Planarity : 0.002 0.016 436 Dihedral : 15.008 84.424 936 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.76 % Allowed : 5.40 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -0.97 (0.44), residues: 300 helix: -1.35 (0.39), residues: 120 sheet: -2.25 (0.57), residues: 36 loop : 0.76 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 454 TYR 0.007 0.001 TYR A 518 PHE 0.016 0.003 PHE A 467 HIS 0.006 0.002 HIS A 523 Individual atomic B min max mean iso aniso Overall: 80.79 182.44 119.09 7.70 2438 0 Protein: 80.79 182.44 119.09 7.70 2438 0 Chain A: 85.18 181.31 119.19 N/A 1219 0 Chain C: 80.79 182.44 119.00 N/A 1219 0 Histogram: Values Number of atoms 80.79 - 90.96 131 90.96 - 101.12 407 101.12 - 111.28 688 111.28 - 121.45 445 121.45 - 131.62 247 131.62 - 141.78 122 141.78 - 151.94 59 151.94 - 162.11 62 162.11 - 172.27 71 172.27 - 182.44 206 |-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: 3.60 - 42.85 A, n_refl.=6670 (all), 4.74 % free)-------------| | | | r_work= 0.6305 r_free= 0.6362 coordinate error (max.-lik. estimate): 0.17 A | | | | normalized target function (ml) (work): 6.476566 | | target function (ml) not normalized (work): 41152.101576 | | target function (ml) not normalized (free): 2067.378995 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.6313 0.6305 0.6362 n_refl.: 6670 re-set all scales: r(all,work,free)=0.6313 0.6305 0.6362 n_refl.: 6670 remove outliers: r(all,work,free)=0.6040 0.6042 0.5817 n_refl.: 6654 overall B=-14.21 to atoms: r(all,work,free)=0.5615 0.5617 0.5404 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2925 0.2929 0.2829 n_refl.: 6654 remove outliers: r(all,work,free)=0.2925 0.2929 0.2829 n_refl.: 6654 ======================== 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 36.793-15.524 96.91 93 1 0.5073 3051.792 2508.221 1.225 0.998 0.351 15.485-12.238 97.00 96 1 0.2476 3058.961 3020.909 1.312 1.001 0.336 12.212-9.617 100.00 192 10 0.2091 3276.350 3135.582 1.304 1.002 0.299 9.605-7.558 100.00 374 15 0.2628 2059.388 1987.213 1.306 0.995 0.295 7.551-5.945 99.50 761 39 0.3183 1127.282 1051.045 1.060 0.987 0.250 5.945-4.677 99.31 1515 77 0.2774 988.552 902.197 0.990 0.970 0.183 4.676-3.603 95.60 3309 171 0.3058 695.546 649.590 1.087 0.946 0.112 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.7331 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2929 r_free=0.2829 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2929 r_free=0.2829 ========================= Local real-space refinement ========================= Before: r_work=0.2929 r_free=0.2829 181 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 0.204 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 16 average time/residue: 0.3916 time to fit residues: 7.1940 After: r_work=0.2934 r_free=0.2801 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 12.890249 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.160524 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 0.2665 0.3022 0.0357 0.014 1.2 12.2 0.0 5.0 0 6.445 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2665 r_free=0.3022 176 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 0.341 revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.1573 time to fit residues: 3.2542 After: r_work=0.2719 r_free=0.3060 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 27.19 30.60 3.40 5.478 103.625 0.161 0.089 27.22 30.51 3.29 5.091 104.041 0.005 0.089 27.03 30.34 3.31 5.113 104.061 0.020 0.088 26.29 29.78 3.49 6.207 104.681 0.080 0.085 25.53 29.54 4.01 8.462 105.025 0.161 0.081 25.45 29.50 4.05 8.398 104.795 0.241 0.081 25.24 29.38 4.14 9.184 105.094 0.321 0.080 25.14 29.34 4.21 9.645 105.234 0.401 0.079 25.07 29.32 4.24 9.964 105.309 0.482 0.079 24.99 29.28 4.29 10.415 105.460 0.562 0.079 25.00 29.29 4.28 10.352 105.383 0.642 0.079 24.97 29.29 4.32 10.544 105.432 0.722 0.079 24.52 29.28 4.77 14.956 107.002 0.803 0.077 max suggested for this run: 20.73 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.562 Accepted refinement result: 24.99 29.28 4.29 10.415 105.460 0.562 0.079 Individual atomic B min max mean iso aniso Overall: 65.26 262.34 108.54 11.53 2438 0 Protein: 65.26 262.34 108.54 11.53 2438 0 Chain A: 65.97 262.34 108.56 N/A 1219 0 Chain C: 65.26 258.07 108.51 N/A 1219 0 Histogram: Values Number of atoms 65.26 - 84.97 309 84.97 - 104.67 1055 104.67 - 124.38 580 124.38 - 144.09 183 144.09 - 163.80 200 163.80 - 183.51 102 183.51 - 203.22 7 203.22 - 222.92 0 222.92 - 242.63 0 242.63 - 262.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.2499 r_free=0.2928 r_work=0.2484 r_free=0.2913 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.60 - 36.79 A, n_refl.=6654 (all), 4.72 % free)-------------| | | | r_work= 0.2484 r_free= 0.2913 coordinate error (max.-lik. estimate): 0.40 A | | | | normalized target function (ls_wunit_k1) (work): 0.077780 | | target function (ls_wunit_k1) not normalized (work): 493.128071 | | target function (ls_wunit_k1) not normalized (free): 26.313358 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2504 0.2484 0.2913 n_refl.: 6654 re-set all scales: r(all,work,free)=0.5460 0.5455 0.5456 n_refl.: 6654 remove outliers: r(all,work,free)=0.5460 0.5455 0.5456 n_refl.: 6654 overall B=0.00 to atoms: r(all,work,free)=0.5460 0.5455 0.5456 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2488 0.2465 0.2971 n_refl.: 6654 remove outliers: r(all,work,free)=0.2488 0.2465 0.2971 n_refl.: 6654 ======================== 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 36.793-15.524 96.91 93 1 0.4431 1151.852 1007.187 1.517 1.028 0.380 15.485-12.238 97.00 96 1 0.1982 1154.558 1174.467 1.227 1.027 0.330 12.212-9.617 100.00 192 10 0.1525 1236.608 1200.408 1.210 1.024 0.295 9.605-7.558 100.00 374 15 0.1917 777.285 776.583 1.251 1.015 0.290 7.551-5.945 99.50 761 39 0.2593 425.475 407.409 1.013 1.000 0.250 5.945-4.677 99.31 1515 77 0.2246 373.114 357.085 0.946 0.974 0.160 4.676-3.603 95.60 3309 171 0.2813 262.523 249.324 1.110 0.935 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=0.7103 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2465 r_free=0.2971 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2465 r_free=0.2971 ========================= Local real-space refinement ========================= Before: r_work=0.2465 r_free=0.2971 169 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 0.745 outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 2.3169 time to fit residues: 3.2758 After: r_work=0.2471 r_free=0.2969 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.218971 wxc_scale = 0.079 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049320 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 0.2647 0.2955 0.0309 0.003 0.5 2.7 0.0 0.0 0 0.033 0.2594 0.2930 0.0336 0.003 0.5 2.7 0.0 0.0 0 0.100 0.2538 0.2919 0.0381 0.004 0.6 3.9 0.0 0.4 0 0.199 0.2504 0.2925 0.0421 0.005 0.7 5.6 0.0 1.1 0 0.299 0.2487 0.2940 0.0453 0.006 0.7 7.2 0.0 2.2 0 0.398 0.2472 0.2965 0.0493 0.007 0.8 9.3 0.0 3.6 0 0.498 0.2458 0.2956 0.0498 0.007 0.9 10.9 0.0 3.6 0 0.597 0.2451 0.2980 0.0528 0.008 0.9 13.0 0.0 4.3 0 0.697 0.2495 0.2923 0.0428 0.005 0.7 6.2 0.0 1.4 0 0.332 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2594 0.2930 0.0336 0.003 0.5 2.7 0.0 0.0 0 0.100 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2594 r_free=0.2930 172 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.870 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7111 After: r_work=0.2594 r_free=0.2930 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.94 29.30 3.36 17.360 117.930 0.049 6.212 29.72 31.04 1.32 14.940 125.785 0.001 6.270 28.65 30.02 1.37 14.433 124.190 0.006 6.246 26.73 28.32 1.59 15.669 122.834 0.025 6.183 25.48 27.91 2.43 17.139 121.478 0.049 6.153 25.10 27.91 2.81 17.886 120.907 0.074 6.146 24.92 27.88 2.96 18.480 120.933 0.099 6.142 24.81 27.86 3.04 18.834 120.954 0.123 6.140 24.74 27.83 3.10 19.183 121.074 0.148 6.138 24.68 27.80 3.12 19.529 121.224 0.173 6.137 24.64 27.77 3.13 19.820 121.344 0.197 6.135 24.60 27.73 3.13 20.094 121.466 0.222 6.134 24.57 27.72 3.15 20.322 121.562 0.247 6.133 max suggested for this run: 23.59 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.247 Accepted refinement result: 24.57 27.72 3.15 20.322 121.562 0.247 6.133 Individual atomic B min max mean iso aniso Overall: 60.26 285.56 115.77 20.59 2438 0 Protein: 60.26 285.56 115.77 20.59 2438 0 Chain A: 61.65 273.91 115.80 N/A 1219 0 Chain C: 60.26 285.56 115.74 N/A 1219 0 Histogram: Values Number of atoms 60.26 - 82.79 256 82.79 - 105.32 807 105.32 - 127.85 631 127.85 - 150.38 375 150.38 - 172.91 264 172.91 - 195.44 89 195.44 - 217.97 13 217.97 - 240.50 1 240.50 - 263.03 0 263.03 - 285.56 2 =========================== Idealize ADP of riding H ========================== r_work=0.2457 r_free=0.2772 r_work=0.2455 r_free=0.2756 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.60 - 36.79 A, n_refl.=6654 (all), 4.72 % free)-------------| | | | r_work= 0.2455 r_free= 0.2756 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ml) (work): 6.128809 | | target function (ml) not normalized (work): 38856.647727 | | target function (ml) not normalized (free): 1948.292018 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2469 0.2455 0.2756 n_refl.: 6654 re-set all scales: r(all,work,free)=0.5675 0.5675 0.5495 n_refl.: 6654 remove outliers: r(all,work,free)=0.5675 0.5675 0.5495 n_refl.: 6654 overall B=-5.68 to atoms: r(all,work,free)=0.5496 0.5496 0.5330 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2467 0.2448 0.2845 n_refl.: 6654 remove outliers: r(all,work,free)=0.2467 0.2448 0.2845 n_refl.: 6654 ======================== 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 36.793-15.524 96.91 93 1 0.4333 1151.852 997.623 1.619 1.009 0.381 15.485-12.238 97.00 96 1 0.2013 1154.558 1165.351 1.313 1.007 0.333 12.212-9.617 100.00 192 10 0.1558 1236.608 1186.002 1.262 1.004 0.298 9.605-7.558 100.00 374 15 0.2133 777.285 762.547 1.303 1.000 0.286 7.551-5.945 99.50 761 39 0.2789 425.475 400.782 1.049 0.992 0.238 5.945-4.677 99.31 1515 77 0.2404 373.114 351.854 0.959 0.981 0.148 4.676-3.603 95.60 3309 171 0.2516 262.523 251.812 1.072 0.966 0.076 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.5656 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2448 r_free=0.2845 After: r_work=0.2449 r_free=0.2844 ================================== NQH flips ================================== r_work=0.2449 r_free=0.2844 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 433 ASN Total number of N/Q/H flips: 1 r_work=0.2449 r_free=0.2842 ========================= Local real-space refinement ========================= Before: r_work=0.2449 r_free=0.2842 170 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.267 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5481 After: r_work=0.2449 r_free=0.2842 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.176205 wxc_scale = 0.031 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.046471 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 0.2451 0.2824 0.0372 0.003 0.5 2.7 0.0 0.0 0 0.013 0.2451 0.2826 0.0375 0.003 0.5 2.7 0.0 0.0 0 0.039 0.2450 0.2827 0.0376 0.003 0.5 2.7 0.0 0.0 0 0.079 0.2449 0.2826 0.0377 0.003 0.5 2.7 0.0 0.0 0 0.118 0.2449 0.2829 0.0380 0.003 0.5 2.9 0.0 0.0 0 0.158 0.2447 0.2829 0.0381 0.003 0.5 2.7 0.0 0.0 0 0.197 0.2443 0.2824 0.0381 0.003 0.5 2.9 0.0 0.0 0 0.237 0.2437 0.2824 0.0387 0.004 0.5 2.9 0.0 0.0 0 0.276 0.2449 0.2827 0.0378 0.003 0.5 2.7 0.0 0.0 0 0.132 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2451 0.2824 0.0372 0.003 0.5 2.7 0.0 0.0 0 0.013 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2451 r_free=0.2824 170 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.175 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0882 After: r_work=0.2451 r_free=0.2824 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.51 28.24 3.72 21.941 119.814 0.046 6.140 28.51 29.27 0.76 17.621 128.002 0.001 6.225 27.72 28.77 1.05 17.039 126.924 0.006 6.209 26.05 27.98 1.93 17.430 124.063 0.023 6.176 25.24 27.77 2.54 18.364 122.985 0.046 6.154 24.71 27.67 2.96 19.151 122.369 0.070 6.138 24.30 27.61 3.31 19.719 122.222 0.093 6.129 24.09 27.60 3.51 20.331 122.476 0.116 6.122 23.94 27.62 3.68 20.892 122.033 0.139 6.118 23.84 27.62 3.78 21.375 122.256 0.163 6.115 23.77 27.65 3.87 21.762 122.280 0.186 6.113 23.72 27.66 3.95 22.115 122.401 0.209 6.112 23.67 27.66 4.00 22.456 122.561 0.232 6.110 max suggested for this run: 23.96 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.116 Accepted refinement result: 24.09 27.60 3.51 20.331 122.476 0.116 6.122 Individual atomic B min max mean iso aniso Overall: 49.62 294.11 115.39 20.23 2438 0 Protein: 49.62 294.11 115.39 20.23 2438 0 Chain A: 52.91 286.28 115.50 N/A 1219 0 Chain C: 49.62 294.11 115.28 N/A 1219 0 Histogram: Values Number of atoms 49.62 - 74.07 111 74.07 - 98.52 602 98.52 - 122.96 926 122.96 - 147.41 475 147.41 - 171.86 193 171.86 - 196.31 106 196.31 - 220.76 19 220.76 - 245.21 4 245.21 - 269.66 0 269.66 - 294.11 2 =========================== Idealize ADP of riding H ========================== r_work=0.2409 r_free=0.2760 r_work=0.2410 r_free=0.2749 ----------X-ray data---------- |--(resolution: 3.60 - 36.79 A, n_refl.=6654 (all), 4.72 % free)-------------| | | | r_work= 0.2410 r_free= 0.2749 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 6.122151 | | target function (ml) not normalized (work): 38814.439801 | | target function (ml) not normalized (free): 1949.298982 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 36.79 - 4.54 0.99 3304 158 0.2400 0.2645 6.4819 6.5055| | 2: 4.54 - 3.60 0.95 3036 156 0.2431 0.2951 5.7306 5.9066| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 36.79 - 4.54 3304 158 0.76 29.33 1.00 1.04 64394.04| | 2: 4.54 - 3.60 3036 156 0.77 29.04 1.02 0.97 19624.75| |alpha: min = 0.97 max = 1.04 mean = 1.00| |beta: min = 19624.75 max = 64394.04 mean = 42955.62| |figures of merit: min = 0.01 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 89.52 mean = 29.19| |phase err.(test): min = 0.00 max = 89.76 mean = 28.21| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2425 0.2410 0.2749 n_refl.: 6654 re-set all scales: r(all,work,free)=0.5657 0.5657 0.5484 n_refl.: 6654 remove outliers: r(all,work,free)=0.5657 0.5657 0.5484 n_refl.: 6654 overall B=0.00 to atoms: r(all,work,free)=0.5657 0.5657 0.5484 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2412 0.2394 0.2789 n_refl.: 6654 remove outliers: r(all,work,free)=0.2412 0.2394 0.2789 n_refl.: 6654 ======================== 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 36.793-15.524 96.91 93 1 0.4283 1151.852 1046.460 1.657 1.058 0.390 15.485-12.238 97.00 96 1 0.2004 1154.558 1168.445 1.193 1.050 0.330 12.212-9.617 100.00 192 10 0.1553 1236.608 1191.437 1.152 1.039 0.294 9.605-7.558 100.00 374 15 0.2076 777.285 765.766 1.218 1.023 0.280 7.551-5.945 99.50 761 39 0.2734 425.475 401.424 1.011 0.996 0.230 5.945-4.677 99.31 1515 77 0.2362 373.114 352.493 0.966 0.953 0.140 4.676-3.603 95.60 3309 171 0.2434 262.523 249.821 1.166 0.884 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=1.1233 ================= 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 : 0.6305 0.6362 0.008 1.169 80.8 182.4 119.1 0 0.000 1_bss: 0.2929 0.2829 0.008 1.169 66.6 168.2 104.9 0 0.000 1_settarget: 0.2929 0.2829 0.008 1.169 66.6 168.2 104.9 0 0.000 1_updatephipsi: 0.2929 0.2829 0.008 1.169 66.6 168.2 104.9 0 0.000 1_nqh: 0.2929 0.2829 0.008 1.169 66.6 168.2 104.9 0 0.000 1_realsrl: 0.2934 0.2801 0.008 1.169 66.6 168.2 104.9 0 0.023 1_weight: 0.2934 0.2801 0.008 1.169 66.6 168.2 104.9 0 0.023 1_xyzrec: 0.2665 0.3022 0.014 1.247 66.6 168.2 104.9 0 0.380 1_realsrl2: 0.2719 0.3060 0.014 1.247 66.6 168.2 104.9 0 0.390 1_adp: 0.2499 0.2928 0.014 1.247 65.3 262.3 108.5 0 0.390 1_regHadp: 0.2484 0.2913 0.014 1.247 65.3 262.3 108.5 0 0.390 2_bss: 0.2465 0.2971 0.014 1.247 65.3 262.3 108.5 0 0.390 2_settarget: 0.2465 0.2971 0.014 1.247 65.3 262.3 108.5 0 0.390 2_updatephipsi: 0.2465 0.2971 0.014 1.247 65.3 262.3 108.5 0 0.390 2_updatecdl: 0.2465 0.2971 0.014 1.273 65.3 262.3 108.5 0 0.390 2_nqh: 0.2465 0.2971 0.014 1.273 65.3 262.3 108.5 0 0.390 2_realsrl: 0.2471 0.2969 0.014 1.273 65.3 262.3 108.5 0 0.395 2_weight: 0.2471 0.2969 0.014 1.273 65.3 262.3 108.5 0 0.395 2_xyzrec: 0.2594 0.2930 0.003 0.534 65.3 262.3 108.5 0 0.367 2_realsrl2: 0.2594 0.2930 0.003 0.534 65.3 262.3 108.5 0 0.367 2_adp: 0.2457 0.2772 0.003 0.534 60.3 285.6 115.8 0 0.367 2_regHadp: 0.2455 0.2756 0.003 0.534 60.3 285.6 115.8 0 0.367 3_bss: 0.2448 0.2845 0.003 0.534 54.6 279.9 110.1 0 0.367 3_settarget: 0.2448 0.2845 0.003 0.534 54.6 279.9 110.1 0 0.367 3_updatephipsi: 0.2448 0.2845 0.003 0.534 54.6 279.9 110.1 0 0.367 3_updatecdl: 0.2448 0.2845 0.003 0.575 54.6 279.9 110.1 0 0.367 3_setrh: 0.2449 0.2844 0.003 0.575 54.6 279.9 110.1 0 0.367 3_nqh: 0.2449 0.2842 0.003 0.575 54.6 279.9 110.1 0 0.368 3_realsrl: 0.2449 0.2842 0.003 0.575 54.6 279.9 110.1 0 0.368 3_weight: 0.2449 0.2842 0.003 0.575 54.6 279.9 110.1 0 0.368 3_xyzrec: 0.2451 0.2824 0.003 0.527 54.6 279.9 110.1 0 0.368 3_realsrl2: 0.2451 0.2824 0.003 0.527 54.6 279.9 110.1 0 0.368 3_adp: 0.2409 0.2760 0.003 0.527 49.6 294.1 115.4 0 0.368 3_regHadp: 0.2410 0.2749 0.003 0.527 49.6 294.1 115.4 0 0.368 end: 0.2394 0.2789 0.003 0.527 49.6 294.1 115.4 0 0.368 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/4iy2_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/4iy2_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6700 Refinement macro-cycles (run) : 231.8300 Write final files (write_after_run_outputs) : 19.0500 Total : 254.5500 Total CPU time: 4.56 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:27:41 PDT -0700 (1716251261.92 s) Start R-work = 0.2929, R-free = 0.2829 Final R-work = 0.2394, R-free = 0.2789 =============================================================================== Job complete usr+sys time: 291.53 seconds wall clock time: 12 minutes 59.73 seconds (779.73 seconds total)