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/1m10.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.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/1m10.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1m10.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites *individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B TYR 228": "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: 7468 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3250 Classifications: {'peptide': 199} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "B" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 4218 Classifications: {'peptide': 267} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 246} Time building chain proxies: 1.26, per 1000 atoms: 0.17 Number of scatterers: 7468 At special positions: 0 Unit cell: (89.84, 89.84, 124.63, 90, 90, 120) Space group: P 61 (No. 169) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 682 8.00 N 628 7.00 C 2366 6.00 H 3778 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 509 " - pdb=" SG CYS A 695 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 17 " distance=2.03 Simple disulfide: pdb=" SG CYS B 209 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 211 " - pdb=" SG CYS B 264 " distance=2.04 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: 1.76 Conformation dependent library (CDL) restraints added in 223.9 milliseconds 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 886 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 5 sheets defined 21.7% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 527 through 542 removed outlier: 3.711A pdb=" N VAL A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 594 through 604 Processing helix chain 'A' and resid 628 through 644 removed outlier: 4.322A pdb=" N ARG A 632 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASN A 633 " --> pdb=" O MET A 630 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL A 635 " --> pdb=" O ARG A 632 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 641 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 666 Processing helix chain 'A' and resid 680 through 695 removed outlier: 4.470A pdb=" N GLU A 684 " --> pdb=" O ASP A 681 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG A 687 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASP A 688 " --> pdb=" O GLN A 685 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 694 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 214 through 226 removed outlier: 6.240A pdb=" N GLU B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing sheet with id= A, first strand: chain 'A' and resid 646 through 650 removed outlier: 6.410A pdb=" N ARG A 616 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE A 649 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA A 618 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS A 559 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.355A pdb=" N PHE A 675 " --> pdb=" O GLY A 652 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 5 through 9 removed outlier: 6.610A pdb=" N ILE B 35 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLN B 59 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR B 81 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 104 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU B 128 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS B 152 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR B 176 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE B 199 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 45 through 47 removed outlier: 6.794A pdb=" N LYS B 69 " --> pdb=" O PHE B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 228 through 232 82 hydrogen bonds defined for protein. 177 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: 1.79 Time building geometry restraints manager: 2.03 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: 3777 1.15 - 1.32: 698 1.32 - 1.49: 1420 1.49 - 1.67: 1630 1.67 - 1.84: 19 Bond restraints: 7544 Sorted by residual: bond pdb=" N VAL B 256 " pdb=" H VAL B 256 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLU A 700 " pdb=" H GLU A 700 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N SER B 114 " pdb=" H SER B 114 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" ND1 HIS A 563 " pdb=" HD1 HIS A 563 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS B 195 " pdb=" H HIS B 195 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 7539 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.21: 392 106.21 - 113.18: 8799 113.18 - 120.15: 2310 120.15 - 127.12: 2204 127.12 - 134.09: 31 Bond angle restraints: 13736 Sorted by residual: angle pdb=" N VAL B 78 " pdb=" CA VAL B 78 " pdb=" C VAL B 78 " ideal model delta sigma weight residual 112.43 120.71 -8.28 9.20e-01 1.18e+00 8.10e+01 angle pdb=" C LEU B 76 " pdb=" N PRO B 77 " pdb=" CA PRO B 77 " ideal model delta sigma weight residual 119.84 130.41 -10.57 1.25e+00 6.40e-01 7.15e+01 angle pdb=" C LEU B 197 " pdb=" N PRO B 198 " pdb=" CA PRO B 198 " ideal model delta sigma weight residual 119.56 127.99 -8.43 1.02e+00 9.61e-01 6.83e+01 angle pdb=" N ILE B 213 " pdb=" CA ILE B 213 " pdb=" C ILE B 213 " ideal model delta sigma weight residual 112.90 105.33 7.57 9.60e-01 1.09e+00 6.21e+01 angle pdb=" N ARG A 511 " pdb=" CA ARG A 511 " pdb=" C ARG A 511 " ideal model delta sigma weight residual 108.45 118.26 -9.81 1.26e+00 6.30e-01 6.06e+01 ... (remaining 13731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 3167 17.57 - 35.14: 236 35.14 - 52.71: 102 52.71 - 70.28: 32 70.28 - 87.84: 4 Dihedral angle restraints: 3541 sinusoidal: 1982 harmonic: 1559 Sorted by residual: dihedral pdb=" CA LYS A 585 " pdb=" CB LYS A 585 " pdb=" CG LYS A 585 " pdb=" CD LYS A 585 " ideal model delta sinusoidal sigma weight residual -60.00 -118.49 58.49 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLN B 159 " pdb=" CB GLN B 159 " pdb=" CG GLN B 159 " pdb=" CD GLN B 159 " ideal model delta sinusoidal sigma weight residual 60.00 113.33 -53.33 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" C HIS B 195 " pdb=" N HIS B 195 " pdb=" CA HIS B 195 " pdb=" CB HIS B 195 " ideal model delta harmonic sigma weight residual -122.60 -115.04 -7.56 0 2.50e+00 1.60e-01 9.15e+00 ... (remaining 3538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 349 0.080 - 0.160: 177 0.160 - 0.240: 54 0.240 - 0.320: 12 0.320 - 0.400: 4 Chirality restraints: 596 Sorted by residual: chirality pdb=" CA PRO B 2 " pdb=" N PRO B 2 " pdb=" C PRO B 2 " pdb=" CB PRO B 2 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA GLN B 21 " pdb=" N GLN B 21 " pdb=" C GLN B 21 " pdb=" CB GLN B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA HIS B 195 " pdb=" N HIS B 195 " pdb=" C HIS B 195 " pdb=" CB HIS B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 593 not shown) Planarity restraints: 1091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 44 " -0.125 2.00e-02 2.50e+03 5.17e-02 8.01e+01 pdb=" CG TYR B 44 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 44 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 44 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 44 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 44 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 44 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 44 " -0.101 2.00e-02 2.50e+03 pdb=" HD1 TYR B 44 " 0.036 2.00e-02 2.50e+03 pdb=" HD2 TYR B 44 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TYR B 44 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR B 44 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 600 " 0.122 2.00e-02 2.50e+03 4.68e-02 6.58e+01 pdb=" CG TYR A 600 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 600 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 600 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 600 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 600 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 600 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 600 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 TYR A 600 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 TYR A 600 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 600 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 600 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 54 " 0.112 2.00e-02 2.50e+03 4.13e-02 5.13e+01 pdb=" CG TYR B 54 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 54 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 54 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 54 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 54 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 54 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR B 54 " 0.042 2.00e-02 2.50e+03 pdb=" HD1 TYR B 54 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR B 54 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR B 54 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 54 " 0.006 2.00e-02 2.50e+03 ... (remaining 1088 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.73: 110 1.73 - 2.45: 4470 2.45 - 3.17: 24469 3.17 - 3.88: 32738 3.88 - 4.60: 50864 Nonbonded interactions: 112651 Sorted by model distance: nonbonded pdb=" HA HIS A 559 " pdb=" HA ALA A 592 " model vdw 1.014 2.440 nonbonded pdb="HH22 ARG A 545 " pdb=" HG3 PRO A 703 " model vdw 1.092 2.270 nonbonded pdb=" HA ARG A 636 " pdb="HH11 ARG A 636 " model vdw 1.130 2.270 nonbonded pdb="HD22 LEU A 512 " pdb="HH21 ARG A 611 " model vdw 1.155 2.270 nonbonded pdb=" OE1 GLU A 613 " pdb=" H GLU A 613 " model vdw 1.278 1.850 ... (remaining 112646 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 14 15.96 2 O 682 7.97 1 N 628 6.97 1 C 2366 5.97 2 H 3778 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: 3778 of 7468 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7468 n_use_u_iso = 7468 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 = 7468 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7468 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7468 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 527 through 542 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 574 through 583 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 594 through 604 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 628 through 644 helix_type = alpha pi *3_10 unknown } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 659 through 666 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 680 through 695 helix_type = alpha pi *3_10 unknown } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 48 through 51 helix_type = alpha pi *3_10 unknown } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 214 through 226 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'B' and resid 243 through 245 helix_type = alpha pi *3_10 unknown } helix { serial_number = "10" helix_identifier = "10" selection = chain 'B' and resid 256 through 258 helix_type = alpha pi *3_10 unknown } sheet { first_strand = chain 'A' and resid 646 through 650 sheet_id = " A" strand { selection = chain 'A' and resid 615 through 621 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 616 and name N bond_start_previous = chain 'A' and resid 647 and name O } strand { selection = chain 'A' and resid 513 through 520 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 514 and name N bond_start_previous = chain 'A' and resid 615 and name O } strand { selection = chain 'A' and resid 551 through 559 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 552 and name N bond_start_previous = chain 'A' and resid 513 and name O } strand { selection = chain 'A' and resid 561 through 564 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 563 and name N bond_start_previous = chain 'A' and resid 557 and name O } } sheet { first_strand = chain 'A' and resid 651 through 653 sheet_id = " B" strand { selection = chain 'A' and resid 675 through 677 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 675 and name N bond_start_previous = chain 'A' and resid 652 and name O } } sheet { first_strand = chain 'B' and resid 5 through 9 sheet_id = " C" strand { selection = chain 'B' and resid 12 through 16 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 16 and name N bond_start_previous = chain 'B' and resid 5 and name O } strand { selection = chain 'B' and resid 35 through 37 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 35 and name N bond_start_previous = chain 'B' and resid 15 and name O } strand { selection = chain 'B' and resid 59 through 61 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 59 and name N bond_start_previous = chain 'B' and resid 36 and name O } strand { selection = chain 'B' and resid 81 through 83 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 81 and name N bond_start_previous = chain 'B' and resid 60 and name O } strand { selection = chain 'B' and resid 104 through 106 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 104 and name N bond_start_previous = chain 'B' and resid 82 and name O } strand { selection = chain 'B' and resid 128 through 130 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 128 and name N bond_start_previous = chain 'B' and resid 105 and name O } strand { selection = chain 'B' and resid 152 through 154 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 152 and name N bond_start_previous = chain 'B' and resid 129 and name O } strand { selection = chain 'B' and resid 176 through 178 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 176 and name N bond_start_previous = chain 'B' and resid 153 and name O } strand { selection = chain 'B' and resid 199 through 201 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 199 and name N bond_start_previous = chain 'B' and resid 177 and name O } } sheet { first_strand = chain 'B' and resid 45 through 47 sheet_id = " D" strand { selection = chain 'B' and resid 69 through 71 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 69 and name N bond_start_previous = chain 'B' and resid 46 and name O } } sheet { first_strand = chain 'B' and resid 228 through 232 sheet_id = " E" strand { selection = chain 'B' and resid 237 through 241 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 240 and name N bond_start_previous = chain 'B' and resid 229 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 = "1m10_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3778 occupancy sum: 3778.00 (% of total atoms 50.59) Rotatable: count: 1103 occupancy sum: 1103.00 (% of total atoms 14.77) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.09 - 30.50 A, n_refl.=10454 (all), 5.11 % free)------------| | | | r_work= 0.3804 r_free= 0.4305 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.437560 | | target function (ml) not normalized (work): 53940.591815 | | target function (ml) not normalized (free): 2943.016547 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 30.50 - 4.90 1.00 2530 123 0.3660 0.4501 6.0037 5.8545| | 2: 4.90 - 3.90 1.00 2453 134 0.3747 0.3971 5.604 5.8298| | 3: 3.89 - 3.40 1.00 2476 150 0.4079 0.4323 5.2694 5.4009| | 4: 3.40 - 3.09 1.00 2461 127 0.3903 0.4710 4.8588 4.973| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 30.50 - 4.90 2530 123 0.59 44.84 0.82 0.19 23753.52| | 2: 4.90 - 3.90 2453 134 0.66 39.62 1.40 0.30 15554.07| | 3: 3.89 - 3.40 2476 150 0.61 43.67 1.52 0.32 9054.65| | 4: 3.40 - 3.09 2461 127 0.53 49.92 1.29 0.25 4255.28| |alpha: min = 0.19 max = 0.32 mean = 0.27| |beta: min = 4255.28 max = 23753.52 mean = 13219.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.60| |phase err.(work): min = 0.00 max = 89.91 mean = 44.52| |phase err.(test): min = 0.00 max = 89.08 mean = 44.81| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.119 3766 Z= 0.613 Angle : 1.710 10.944 5117 Z= 1.081 Chirality : 0.104 0.400 596 Planarity : 0.010 0.086 656 Dihedral : 15.487 87.844 1425 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 35.50 Ramachandran Plot: Outliers : 4.98 % Allowed : 12.77 % Favored : 82.25 % Rotamer: Outliers : 5.28 % Allowed : 6.24 % Favored : 88.49 % 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: -5.24 (0.31), residues: 462 helix: -4.51 (0.29), residues: 98 sheet: -2.23 (0.51), residues: 89 loop : -3.68 (0.30), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG A 545 TYR 0.104 0.022 TYR B 44 PHE 0.051 0.010 PHE B 201 TRP 0.058 0.016 TRP B 219 HIS 0.003 0.001 HIS B 86 Individual atomic B min max mean iso aniso Overall: 15.65 95.55 52.24 1.37 3690 0 Protein: 15.65 95.55 52.24 1.37 3690 0 Chain A: 21.62 95.55 60.64 N/A 1602 0 Chain B: 15.65 77.97 45.80 N/A 2088 0 Histogram: Values Number of atoms 15.65 - 23.64 14 23.64 - 31.63 190 31.63 - 39.62 520 39.62 - 47.61 817 47.61 - 55.60 852 55.60 - 63.59 530 63.59 - 71.58 302 71.58 - 79.57 236 79.57 - 87.56 164 87.56 - 95.55 65 |-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: 3.09 - 30.50 A, n_refl.=10454 (all), 5.11 % free)------------| | | | r_work= 0.3804 r_free= 0.4305 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.437560 | | target function (ml) not normalized (work): 53940.591815 | | target function (ml) not normalized (free): 2943.016547 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3828 0.3804 0.4305 n_refl.: 10454 re-set all scales: r(all,work,free)=0.3828 0.3804 0.4305 n_refl.: 10454 remove outliers: r(all,work,free)=0.3829 0.3805 0.4299 n_refl.: 10449 overall B=16.31 to atoms: r(all,work,free)=0.4448 0.4429 0.4826 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2288 0.2260 0.2819 n_refl.: 10449 remove outliers: r(all,work,free)=0.2288 0.2260 0.2819 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2311 1395.912 1343.970 1.051 1.212 0.395 14.512-11.594 100.00 95 5 0.1560 1328.531 1301.200 0.918 1.199 0.369 11.568-9.227 100.00 193 11 0.1404 1283.724 1248.849 0.929 1.180 0.359 9.162-7.352 100.00 368 15 0.2071 850.463 820.636 0.919 1.149 0.348 7.349-5.862 100.00 740 33 0.2226 628.811 611.546 0.853 1.103 0.326 5.858-4.671 100.00 1425 79 0.1948 673.689 650.894 0.916 1.028 0.283 4.669-3.723 99.86 2790 156 0.2269 618.917 593.677 1.202 0.910 0.181 3.723-3.092 99.93 4210 230 0.2720 337.947 316.886 1.511 0.750 0.063 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-5.7724 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2260 r_free=0.2819 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2260 r_free=0.2819 ========================= Local real-space refinement ========================= Before: r_work=0.2260 r_free=0.2819 125 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 0.317 revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 22 average time/residue: 0.2500 time to fit residues: 7.5026 After: r_work=0.2269 r_free=0.2819 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 16.483662 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.200522 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 0.2352 0.2728 0.0376 0.004 0.8 11.5 0.9 2.6 0 0.125 0.2341 0.2725 0.0383 0.004 0.8 11.3 0.6 2.6 0 0.250 0.2316 0.2718 0.0402 0.004 0.8 9.5 0.6 2.6 0 0.500 0.2260 0.2661 0.0401 0.004 0.7 6.6 0.4 2.6 0 1.000 0.2199 0.2656 0.0457 0.006 0.8 8.2 0.4 2.9 0 2.000 0.2162 0.2653 0.0492 0.007 1.0 10.2 0.6 3.1 0 3.000 0.2105 0.2687 0.0582 0.008 1.0 10.7 0.6 4.1 0 4.000 0.2103 0.2687 0.0585 0.010 1.1 13.3 1.3 4.6 0 5.000 0.2054 0.2715 0.0661 0.011 1.2 13.3 0.9 6.2 0 6.000 0.2034 0.2734 0.0700 0.012 1.3 14.7 0.9 7.0 0 7.000 0.2016 0.2751 0.0735 0.013 1.4 15.4 0.9 7.4 0 8.000 0.2001 0.2744 0.0744 0.014 1.5 16.6 1.3 7.7 0 9.000 0.1991 0.2751 0.0760 0.015 1.5 17.8 1.3 8.6 0 10.000 0.2013 0.2739 0.0726 0.013 1.4 15.7 1.1 7.2 0 8.242 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2260 0.2661 0.0401 0.004 0.7 6.6 0.4 2.6 0 1.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2260 r_free=0.2661 120 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 1.237 outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3877 time to fit residues: 7.3784 After: r_work=0.2281 r_free=0.2653 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.81 26.53 3.72 0.970 68.287 0.201 0.057 23.00 26.51 3.50 1.930 68.383 0.006 0.057 22.62 26.45 3.82 2.006 68.432 0.025 0.056 21.86 26.37 4.51 2.853 68.535 0.100 0.052 20.88 26.24 5.36 5.878 69.038 0.201 0.048 20.58 26.25 5.67 6.978 69.299 0.301 0.046 20.29 26.25 5.97 8.210 69.695 0.401 0.045 20.15 26.29 6.15 8.907 69.889 0.501 0.044 20.05 26.33 6.29 9.463 70.048 0.602 0.044 19.94 26.38 6.44 10.099 70.244 0.702 0.044 19.84 26.43 6.59 10.747 70.446 0.802 0.043 19.81 26.45 6.64 10.967 70.500 0.902 0.043 19.59 26.57 6.98 12.523 71.017 1.003 0.042 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.201 Accepted refinement result: 20.88 26.24 5.36 5.878 69.038 0.201 0.048 Individual atomic B min max mean iso aniso Overall: 35.26 120.00 70.07 5.88 3690 0 Protein: 35.26 120.00 70.07 5.88 3690 0 Chain A: 35.26 120.00 77.90 N/A 1602 0 Chain B: 35.92 115.43 64.07 N/A 2088 0 Histogram: Values Number of atoms 35.26 - 43.74 62 43.74 - 52.21 322 52.21 - 60.69 706 60.69 - 69.16 901 69.16 - 77.63 652 77.63 - 86.11 422 86.11 - 94.58 311 94.58 - 103.06 218 103.06 - 111.53 82 111.53 - 120.00 14 =========================== Idealize ADP of riding H ========================== r_work=0.2088 r_free=0.2624 r_work=0.2067 r_free=0.2612 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2067 r_free= 0.2612 coordinate error (max.-lik. estimate): 0.50 A | | | | normalized target function (ls_wunit_k1) (work): 0.046514 | | target function (ls_wunit_k1) not normalized (work): 461.230199 | | target function (ls_wunit_k1) not normalized (free): 42.467717 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2095 0.2067 0.2612 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4370 0.4352 0.4720 n_refl.: 10449 remove outliers: r(all,work,free)=0.4370 0.4352 0.4720 n_refl.: 10449 overall B=-6.17 to atoms: r(all,work,free)=0.4119 0.4100 0.4492 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2109 0.2081 0.2637 n_refl.: 10449 remove outliers: r(all,work,free)=0.2109 0.2081 0.2637 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2138 773.916 752.434 1.294 1.121 0.392 14.512-11.594 100.00 95 5 0.1401 736.559 731.761 1.138 1.112 0.372 11.568-9.227 100.00 193 11 0.1320 711.718 700.534 1.129 1.101 0.369 9.162-7.352 100.00 368 15 0.1756 471.511 461.951 1.097 1.081 0.369 7.349-5.862 100.00 740 33 0.1994 348.623 344.807 0.975 1.053 0.342 5.858-4.671 100.00 1425 79 0.1846 373.504 364.065 0.977 1.008 0.286 4.669-3.723 99.93 2790 156 0.1992 343.137 335.050 1.184 0.935 0.197 3.723-3.092 100.00 4210 230 0.2633 187.363 178.321 1.324 0.838 0.057 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=-0.4742 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2081 r_free=0.2637 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2081 r_free=0.2637 ========================= Local real-space refinement ========================= Before: r_work=0.2081 r_free=0.2637 110 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.245 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8839 After: r_work=0.2081 r_free=0.2637 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.519825 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.043460 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 0.2109 0.2652 0.0544 0.002 0.6 5.0 0.4 1.0 0 0.125 0.2057 0.2669 0.0612 0.004 0.6 5.5 0.4 1.4 0 0.250 0.2004 0.2692 0.0688 0.006 0.8 8.0 0.4 2.6 0 0.500 0.1952 0.2694 0.0742 0.009 1.0 10.4 0.4 3.4 0 1.000 0.1907 0.2711 0.0804 0.015 1.4 16.5 0.4 6.5 0 2.000 0.1873 0.2697 0.0824 0.020 1.7 19.4 0.9 9.1 0 3.000 0.1851 0.2681 0.0829 0.024 2.0 23.3 1.1 11.8 0 4.000 0.1837 0.2687 0.0851 0.028 2.3 25.7 1.3 12.9 0 5.000 0.1826 0.2694 0.0869 0.032 2.5 28.3 1.3 14.9 0 6.000 0.1815 0.2703 0.0888 0.035 2.7 30.7 1.3 15.3 0 7.000 0.1809 0.2716 0.0907 0.038 2.9 32.3 1.3 16.5 0 8.000 0.1799 0.2705 0.0906 0.041 3.1 35.1 1.5 17.7 1 9.000 0.1790 0.2727 0.0937 0.044 3.2 35.4 1.7 18.5 1 10.000 0.1918 0.2706 0.0788 0.014 1.3 14.7 0.4 6.0 0 1.760 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2109 0.2652 0.0544 0.002 0.6 5.0 0.4 1.0 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2109 r_free=0.2652 118 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 1.200 outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.7896 time to fit residues: 5.1830 After: r_work=0.2111 r_free=0.2646 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.11 26.46 5.35 10.972 71.054 0.043 5.751 24.03 27.90 3.87 8.888 74.996 0.001 5.818 23.34 27.18 3.83 10.763 73.157 0.005 5.802 21.18 26.35 5.17 11.153 70.834 0.022 5.745 20.96 26.39 5.43 11.350 70.790 0.043 5.740 20.70 26.30 5.60 11.889 70.599 0.065 5.729 20.07 26.19 6.12 13.589 71.451 0.087 5.707 20.17 26.20 6.03 12.984 70.904 0.109 5.710 20.09 26.22 6.12 13.124 71.013 0.130 5.708 20.04 26.24 6.20 13.251 71.102 0.152 5.707 19.99 26.26 6.27 13.360 71.177 0.174 5.705 19.96 26.28 6.32 13.457 71.240 0.196 5.705 19.93 26.29 6.36 13.547 71.296 0.217 5.704 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.065 Accepted refinement result: 20.70 26.30 5.60 11.889 70.599 0.065 5.729 Individual atomic B min max mean iso aniso Overall: 25.28 115.15 62.99 7.13 3690 0 Protein: 25.28 115.15 62.99 7.13 3690 0 Chain A: 28.07 115.15 70.74 N/A 1602 0 Chain B: 25.28 114.54 57.04 N/A 2088 0 Histogram: Values Number of atoms 25.28 - 34.27 52 34.27 - 43.25 286 43.25 - 52.24 653 52.24 - 61.23 914 61.23 - 70.22 696 70.22 - 79.20 443 79.20 - 88.19 326 88.19 - 97.18 222 97.18 - 106.17 82 106.17 - 115.15 16 =========================== Idealize ADP of riding H ========================== r_work=0.2070 r_free=0.2630 r_work=0.2067 r_free=0.2633 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2067 r_free= 0.2633 coordinate error (max.-lik. estimate): 0.53 A | | | | normalized target function (ml) (work): 5.728145 | | target function (ml) not normalized (work): 56800.289415 | | target function (ml) not normalized (free): 3146.320362 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2096 0.2067 0.2633 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4039 0.4022 0.4380 n_refl.: 10449 remove outliers: r(all,work,free)=0.4039 0.4022 0.4380 n_refl.: 10449 overall B=0.00 to atoms: r(all,work,free)=0.4039 0.4022 0.4380 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2111 0.2080 0.2681 n_refl.: 10449 remove outliers: r(all,work,free)=0.2111 0.2080 0.2681 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2056 885.886 870.782 1.508 1.028 0.405 14.512-11.594 100.00 95 5 0.1331 843.125 843.401 1.253 1.026 0.375 11.568-9.227 100.00 193 11 0.1274 814.689 806.467 1.223 1.023 0.370 9.162-7.352 100.00 368 15 0.1683 539.729 532.337 1.165 1.017 0.370 7.349-5.862 100.00 740 33 0.1994 399.062 393.973 1.035 1.010 0.360 5.858-4.671 100.00 1425 79 0.1835 427.543 415.119 0.975 0.998 0.290 4.669-3.723 99.86 2790 156 0.1992 392.783 382.142 1.112 0.978 0.200 3.723-3.092 99.93 4210 230 0.2681 214.471 202.952 1.125 0.952 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=0.5760 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2080 r_free=0.2681 After: r_work=0.2080 r_free=0.2681 ================================== NQH flips ================================== r_work=0.2080 r_free=0.2681 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN B 61 ASN Total number of N/Q/H flips: 2 r_work=0.2082 r_free=0.2679 ========================= Local real-space refinement ========================= Before: r_work=0.2082 r_free=0.2679 113 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.955 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0520 After: r_work=0.2082 r_free=0.2679 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.783305 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.045206 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 0.2081 0.2684 0.0603 0.002 0.6 5.2 0.4 0.0 0 0.125 0.2076 0.2679 0.0604 0.003 0.6 5.2 0.4 0.0 0 0.250 0.2045 0.2684 0.0639 0.006 0.6 5.9 0.4 0.0 0 0.500 0.1957 0.2717 0.0760 0.011 1.4 11.5 0.4 1.2 0 1.000 0.1934 0.2704 0.0770 0.014 1.4 12.7 0.4 1.7 0 2.000 0.1895 0.2739 0.0844 0.021 2.1 18.2 0.4 3.6 0 3.000 0.1877 0.2743 0.0866 0.023 2.4 21.7 0.6 4.6 0 4.000 0.1866 0.2734 0.0869 0.027 2.8 26.9 1.3 7.4 0 5.000 0.1862 0.2714 0.0852 0.028 2.8 26.1 0.9 8.6 0 6.000 0.1851 0.2710 0.0859 0.031 3.0 27.7 1.5 9.6 0 7.000 0.1832 0.2746 0.0914 0.036 3.6 31.6 1.3 8.9 0 8.000 0.1824 0.2746 0.0922 0.038 3.7 31.3 1.5 8.4 1 9.000 0.1815 0.2747 0.0932 0.040 3.8 32.2 1.3 8.4 1 10.000 0.1936 0.2708 0.0772 0.014 1.4 13.1 0.4 1.7 0 1.892 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2076 0.2679 0.0604 0.003 0.6 5.2 0.4 0.0 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2076 r_free=0.2679 113 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.777 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5270 After: r_work=0.2076 r_free=0.2679 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.76 26.79 6.04 10.501 69.444 0.045 5.875 24.15 28.21 4.05 8.722 73.886 0.001 5.956 23.15 27.53 4.39 9.946 71.566 0.006 5.938 21.01 26.70 5.69 10.601 69.163 0.023 5.876 20.76 26.79 6.04 10.501 69.444 0.045 5.875 20.73 26.78 6.06 10.630 69.356 0.068 5.873 20.60 26.80 6.20 11.181 69.058 0.090 5.865 20.03 26.60 6.57 12.994 69.097 0.113 5.846 19.93 26.57 6.64 13.736 69.495 0.136 5.842 19.85 26.59 6.74 14.128 69.734 0.158 5.840 19.80 26.60 6.80 14.504 69.940 0.181 5.839 20.02 26.67 6.65 13.127 69.083 0.203 5.845 19.99 26.67 6.68 13.198 69.137 0.226 5.845 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.023 Accepted refinement result: 21.01 26.70 5.69 10.601 69.163 0.023 5.876 Individual atomic B min max mean iso aniso Overall: 26.17 114.30 62.42 6.26 3690 0 Protein: 26.17 114.30 62.42 6.26 3690 0 Chain A: 30.51 114.30 70.17 N/A 1602 0 Chain B: 26.17 114.09 56.48 N/A 2088 0 Histogram: Values Number of atoms 26.17 - 34.98 50 34.98 - 43.79 329 43.79 - 52.61 714 52.61 - 61.42 919 61.42 - 70.23 633 70.23 - 79.05 410 79.05 - 87.86 319 87.86 - 96.67 219 96.67 - 105.49 81 105.49 - 114.30 16 =========================== Idealize ADP of riding H ========================== r_work=0.2101 r_free=0.2670 r_work=0.2104 r_free=0.2671 ----------X-ray data---------- |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2104 r_free= 0.2671 coordinate error (max.-lik. estimate): 0.53 A | | | | normalized target function (ml) (work): 5.876212 | | target function (ml) not normalized (work): 58268.521051 | | target function (ml) not normalized (free): 3221.414952 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 30.50 - 4.90 1.00 2530 123 0.1774 0.2205 6.1391 6.1906| | 2: 4.90 - 3.90 1.00 2451 133 0.1928 0.2444 6.0289 6.3209| | 3: 3.89 - 3.40 1.00 2475 150 0.2431 0.2967 5.8484 6.0283| | 4: 3.40 - 3.09 1.00 2460 127 0.2945 0.3909 5.4817 5.6303| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 30.50 - 4.90 2530 123 0.85 21.37 1.00 0.93 34476.17| | 2: 4.90 - 3.90 2451 133 0.84 23.04 1.01 0.96 31472.21| | 3: 3.89 - 3.40 2475 150 0.75 32.00 1.03 0.90 25031.76| | 4: 3.40 - 3.09 2460 127 0.66 39.57 0.89 0.75 15154.83| |alpha: min = 0.75 max = 0.96 mean = 0.89| |beta: min = 15154.83 max = 34476.17 mean = 26583.06| |figures of merit: min = 0.00 max = 1.00 mean = 0.78| |phase err.(work): min = 0.00 max = 89.86 mean = 28.95| |phase err.(test): min = 0.00 max = 88.20 mean = 29.94| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2133 0.2104 0.2671 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4020 0.4003 0.4357 n_refl.: 10449 remove outliers: r(all,work,free)=0.4020 0.4003 0.4357 n_refl.: 10449 overall B=0.00 to atoms: r(all,work,free)=0.4020 0.4003 0.4357 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2111 0.2083 0.2642 n_refl.: 10449 remove outliers: r(all,work,free)=0.2111 0.2083 0.2642 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2047 885.886 867.344 1.368 1.105 0.404 14.512-11.594 100.00 95 5 0.1325 843.125 838.899 1.140 1.097 0.375 11.568-9.227 100.00 193 11 0.1274 814.689 802.712 1.123 1.087 0.370 9.162-7.352 100.00 368 15 0.1673 539.729 530.884 1.082 1.070 0.370 7.349-5.862 100.00 740 33 0.1977 399.062 393.133 0.977 1.045 0.360 5.858-4.671 100.00 1425 79 0.1850 427.543 415.490 0.948 1.006 0.290 4.669-3.723 99.86 2790 156 0.2015 392.783 382.133 1.123 0.943 0.210 3.723-3.092 99.93 4210 230 0.2662 214.471 202.463 1.203 0.858 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=2.2353 ================= 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 : 0.3804 0.4305 0.010 1.710 15.7 95.5 52.2 0 0.000 1_bss: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_settarget: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_updatephipsi: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_nqh: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_realsrl: 0.2269 0.2819 0.010 1.719 32.0 111.9 68.6 0 0.010 1_weight: 0.2269 0.2819 0.010 1.719 32.0 111.9 68.6 0 0.010 1_xyzrec: 0.2260 0.2661 0.004 0.730 32.0 111.9 68.6 0 0.191 1_realsrl2: 0.2281 0.2653 0.004 0.730 32.0 111.9 68.6 0 0.195 1_adp: 0.2088 0.2624 0.004 0.730 35.3 120.0 70.1 0 0.195 1_regHadp: 0.2067 0.2612 0.004 0.730 35.3 120.0 70.1 0 0.195 2_bss: 0.2081 0.2637 0.004 0.730 29.1 113.8 63.9 0 0.195 2_settarget: 0.2081 0.2637 0.004 0.730 29.1 113.8 63.9 0 0.195 2_updatephipsi: 0.2081 0.2637 0.004 0.730 29.1 113.8 63.9 0 0.195 2_updatecdl: 0.2081 0.2637 0.004 0.766 29.1 113.8 63.9 0 0.195 2_nqh: 0.2081 0.2637 0.004 0.766 29.1 113.8 63.9 0 0.195 2_realsrl: 0.2081 0.2637 0.004 0.766 29.1 113.8 63.9 0 0.195 2_weight: 0.2081 0.2637 0.004 0.766 29.1 113.8 63.9 0 0.195 2_xyzrec: 0.2109 0.2652 0.002 0.555 29.1 113.8 63.9 0 0.264 2_realsrl2: 0.2111 0.2646 0.002 0.555 29.1 113.8 63.9 0 0.266 2_adp: 0.2070 0.2630 0.002 0.555 25.3 115.2 63.0 0 0.266 2_regHadp: 0.2067 0.2633 0.002 0.555 25.3 115.2 63.0 0 0.266 3_bss: 0.2080 0.2681 0.002 0.555 25.3 115.2 63.0 0 0.266 3_settarget: 0.2080 0.2681 0.002 0.555 25.3 115.2 63.0 0 0.266 3_updatephipsi: 0.2080 0.2681 0.002 0.555 25.3 115.2 63.0 0 0.266 3_updatecdl: 0.2080 0.2681 0.003 0.580 25.3 115.2 63.0 0 0.266 3_setrh: 0.2080 0.2681 0.003 0.580 25.3 115.2 63.0 0 0.265 3_nqh: 0.2082 0.2679 0.003 0.580 25.3 115.2 63.0 0 0.268 3_realsrl: 0.2082 0.2679 0.003 0.580 25.3 115.2 63.0 0 0.268 3_weight: 0.2082 0.2679 0.003 0.580 25.3 115.2 63.0 0 0.268 3_xyzrec: 0.2076 0.2679 0.003 0.556 25.3 115.2 63.0 0 0.268 3_realsrl2: 0.2076 0.2679 0.003 0.556 25.3 115.2 63.0 0 0.268 3_adp: 0.2101 0.2670 0.003 0.556 26.2 114.3 62.4 0 0.268 3_regHadp: 0.2104 0.2671 0.003 0.556 26.2 114.3 62.4 0 0.268 end: 0.2083 0.2642 0.003 0.556 26.2 114.3 62.4 0 0.268 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1m10_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1m10_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.7300 Refinement macro-cycles (run) : 359.4700 Write final files (write_after_run_outputs) : 24.7300 Total : 389.9300 Total CPU time: 6.93 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:35 PDT -0700 (1716251675.64 s) Start R-work = 0.2260, R-free = 0.2819 Final R-work = 0.2083, R-free = 0.2642 =============================================================================== Job complete usr+sys time: 439.49 seconds wall clock time: 19 minutes 34.56 seconds (1174.56 seconds total)