Starting phenix.real_space_refine on Tue Mar 3 18:45:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vcd_21149/03_2026/6vcd_21149.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vcd_21149/03_2026/6vcd_21149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vcd_21149/03_2026/6vcd_21149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vcd_21149/03_2026/6vcd_21149.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vcd_21149/03_2026/6vcd_21149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vcd_21149/03_2026/6vcd_21149.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 41 5.16 5 C 5169 2.51 5 N 1356 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8082 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5025 Classifications: {'peptide': 643} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 32, 'TRANS': 608} Chain breaks: 3 Chain: "B" Number of atoms: 1975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1975 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 242} Chain breaks: 2 Chain: "C" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1078 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6792 SG CYS B 662 73.515 60.156 67.240 1.00 26.24 S ATOM 6969 SG CYS B 687 73.996 59.465 63.013 1.00 16.01 S ATOM 6886 SG CYS B 676 69.000 54.956 65.606 1.00 24.32 S ATOM 6963 SG CYS B 686 70.184 55.459 61.928 1.00 16.92 S Time building chain proxies: 1.74, per 1000 atoms: 0.22 Number of scatterers: 8082 At special positions: 0 Unit cell: (108.768, 85.536, 119.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 41 16.00 O 1514 8.00 N 1356 7.00 C 5169 6.00 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 - 3.00 Amino acid : True - 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: 0.65 Conformation dependent library (CDL) restraints added in 265.4 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES B 800 " pdb="FE1 FES B 800 " - pdb=" SG CYS B 662 " pdb="FE2 FES B 800 " - pdb=" SG CYS B 686 " pdb="FE2 FES B 800 " - pdb=" SG CYS B 676 " pdb="FE1 FES B 800 " - pdb=" SG CYS B 687 " Number of angles added : 6 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 11 sheets defined 40.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.074A pdb=" N GLY A 32 " --> pdb=" O SER A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.703A pdb=" N LEU A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 92 through 108 removed outlier: 3.650A pdb=" N ASP A 98 " --> pdb=" O PRO A 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.798A pdb=" N GLU A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 239 removed outlier: 3.598A pdb=" N LEU A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 removed outlier: 3.806A pdb=" N GLU A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.610A pdb=" N VAL A 286 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 331 through 347 removed outlier: 3.700A pdb=" N VAL A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 388 through 399 removed outlier: 3.622A pdb=" N HIS A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 415 removed outlier: 4.017A pdb=" N SER A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 673 through 678 removed outlier: 4.577A pdb=" N GLU A 677 " --> pdb=" O ARG A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 689 removed outlier: 3.973A pdb=" N SER A 682 " --> pdb=" O HIS A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 756 removed outlier: 3.512A pdb=" N ILE A 755 " --> pdb=" O THR A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 774 Processing helix chain 'A' and resid 790 through 796 Processing helix chain 'A' and resid 827 through 837 removed outlier: 3.651A pdb=" N GLU A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.511A pdb=" N TYR A 863 " --> pdb=" O ALA A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 885 removed outlier: 3.828A pdb=" N ASP A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 902 removed outlier: 3.580A pdb=" N SER A 901 " --> pdb=" O ASN A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 953 through 962 removed outlier: 3.502A pdb=" N LYS A 961 " --> pdb=" O PHE A 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 removed outlier: 3.568A pdb=" N SER B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.711A pdb=" N GLN B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 removed outlier: 3.776A pdb=" N ALA B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 320 Processing helix chain 'B' and resid 324 through 329 removed outlier: 4.337A pdb=" N GLY B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 removed outlier: 3.534A pdb=" N ARG B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 405 Processing helix chain 'B' and resid 612 through 618 Processing helix chain 'B' and resid 640 through 649 removed outlier: 3.709A pdb=" N ASP B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 647 " --> pdb=" O GLY B 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.922A pdb=" N GLN C 23 " --> pdb=" O GLU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 31 Processing helix chain 'C' and resid 51 through 65 removed outlier: 4.461A pdb=" N LYS C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS C 64 " --> pdb=" O GLN C 60 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS C 65 " --> pdb=" O TRP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 96 through 111 removed outlier: 3.810A pdb=" N GLU C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 131 through 140 removed outlier: 4.291A pdb=" N ARG C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.921A pdb=" N GLN C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.675A pdb=" N PHE A 272 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 356 removed outlier: 3.516A pdb=" N PHE A 356 " --> pdb=" O CYS A 320 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU A 321 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 841 through 844 removed outlier: 3.622A pdb=" N ILE A 842 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU A 844 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR A 745 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 815 through 817 Processing sheet with id=AA8, first strand: chain 'A' and resid 869 through 872 removed outlier: 5.902A pdb=" N VAL A 870 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N PHE A 893 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA A 872 " --> pdb=" O PHE A 893 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 922 " --> pdb=" O ALA A 938 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 247 through 248 removed outlier: 7.245A pdb=" N LEU B 248 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 631 through 632 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 16 removed outlier: 6.011A pdb=" N LYS C 5 " --> pdb=" O VAL C 45 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 687 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: 1.39 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 3356 1.42 - 1.61: 4837 1.61 - 1.80: 50 1.80 - 2.00: 6 2.00 - 2.19: 4 Bond restraints: 8253 Sorted by residual: bond pdb=" N TRP C 159 " pdb=" CA TRP C 159 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.60e+00 bond pdb=" CG1 ILE A 283 " pdb=" CD1 ILE A 283 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.26e+00 bond pdb=" CA ILE A 14 " pdb=" CB ILE A 14 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.22e+00 bond pdb=" CA MET A 64 " pdb=" C MET A 64 " ideal model delta sigma weight residual 1.524 1.499 0.025 2.25e-02 1.98e+03 1.19e+00 bond pdb=" CB ILE A 291 " pdb=" CG2 ILE A 291 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 ... (remaining 8248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 11089 2.81 - 5.61: 79 5.61 - 8.42: 6 8.42 - 11.22: 1 11.22 - 14.03: 5 Bond angle restraints: 11180 Sorted by residual: angle pdb=" S1 FES B 800 " pdb="FE2 FES B 800 " pdb=" S2 FES B 800 " ideal model delta sigma weight residual 104.33 90.38 13.95 1.14e+00 7.69e-01 1.50e+02 angle pdb=" S1 FES B 800 " pdb="FE1 FES B 800 " pdb=" S2 FES B 800 " ideal model delta sigma weight residual 104.33 90.30 14.03 1.20e+00 6.94e-01 1.37e+02 angle pdb="FE1 FES B 800 " pdb=" S2 FES B 800 " pdb="FE2 FES B 800 " ideal model delta sigma weight residual 75.66 88.87 -13.21 1.14e+00 7.69e-01 1.34e+02 angle pdb="FE1 FES B 800 " pdb=" S1 FES B 800 " pdb="FE2 FES B 800 " ideal model delta sigma weight residual 75.66 88.77 -13.11 1.20e+00 6.94e-01 1.19e+02 angle pdb=" C GLN C 158 " pdb=" N TRP C 159 " pdb=" CA TRP C 159 " ideal model delta sigma weight residual 121.70 131.70 -10.00 1.80e+00 3.09e-01 3.09e+01 ... (remaining 11175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 4346 16.02 - 32.05: 462 32.05 - 48.07: 96 48.07 - 64.10: 23 64.10 - 80.12: 8 Dihedral angle restraints: 4935 sinusoidal: 1969 harmonic: 2966 Sorted by residual: dihedral pdb=" CA SER B 377 " pdb=" C SER B 377 " pdb=" N TRP B 378 " pdb=" CA TRP B 378 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA HIS A 22 " pdb=" C HIS A 22 " pdb=" N LYS A 23 " pdb=" CA LYS A 23 " ideal model delta harmonic sigma weight residual 180.00 -152.31 -27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA GLN C 158 " pdb=" C GLN C 158 " pdb=" N TRP C 159 " pdb=" CA TRP C 159 " ideal model delta harmonic sigma weight residual 0.00 -26.63 26.63 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 4932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1042 0.055 - 0.110: 209 0.110 - 0.165: 22 0.165 - 0.220: 1 0.220 - 0.275: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA TRP C 159 " pdb=" N TRP C 159 " pdb=" C TRP C 159 " pdb=" CB TRP C 159 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB VAL A 277 " pdb=" CA VAL A 277 " pdb=" CG1 VAL A 277 " pdb=" CG2 VAL A 277 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CB VAL A 415 " pdb=" CA VAL A 415 " pdb=" CG1 VAL A 415 " pdb=" CG2 VAL A 415 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1272 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 45 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO C 46 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 46 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 46 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 325 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO B 326 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 326 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 326 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 861 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO A 862 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 862 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 862 " 0.023 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 385 2.72 - 3.26: 8130 3.26 - 3.81: 12681 3.81 - 4.35: 17286 4.35 - 4.90: 28308 Nonbonded interactions: 66790 Sorted by model distance: nonbonded pdb=" NH1 ARG A 103 " pdb=" O PRO A 113 " model vdw 2.170 3.120 nonbonded pdb=" OE1 GLU A 227 " pdb=" OG SER A 715 " model vdw 2.186 3.040 nonbonded pdb=" O SER B 634 " pdb=" ND2 ASN B 678 " model vdw 2.224 3.120 nonbonded pdb=" NH2 ARG A 779 " pdb=" O CYS B 662 " model vdw 2.225 3.120 nonbonded pdb=" OG SER A 783 " pdb=" O GLY B 690 " model vdw 2.238 3.040 ... (remaining 66785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.810 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.684 8257 Z= 0.360 Angle : 0.897 28.932 11186 Z= 0.424 Chirality : 0.044 0.275 1275 Planarity : 0.005 0.057 1424 Dihedral : 14.129 80.122 3019 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.07 % Favored : 89.73 % Rotamer: Outliers : 0.11 % Allowed : 7.36 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.83 (0.21), residues: 1013 helix: -3.31 (0.17), residues: 396 sheet: -3.37 (0.44), residues: 115 loop : -3.04 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.021 0.002 TYR B 661 PHE 0.014 0.001 PHE B 602 TRP 0.017 0.002 TRP B 378 HIS 0.005 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 8253) covalent geometry : angle 0.70099 (11180) hydrogen bonds : bond 0.23037 ( 243) hydrogen bonds : angle 7.63460 ( 687) metal coordination : bond 0.60693 ( 4) metal coordination : angle 24.14927 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8047 (m-80) cc_final: 0.7773 (m-80) REVERT: A 337 LEU cc_start: 0.8529 (mt) cc_final: 0.8275 (mp) REVERT: A 406 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7050 (mp0) REVERT: B 215 SER cc_start: 0.9050 (t) cc_final: 0.8827 (t) REVERT: B 314 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7920 (ttmm) REVERT: C 154 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7508 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.5185 time to fit residues: 74.9279 Evaluate side-chains 100 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 38 optimal weight: 0.0070 chunk 61 optimal weight: 0.7980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 65 ASN A 217 ASN A 241 ASN A 397 HIS A 678 HIS A 754 HIS A 773 ASN A 879 HIS ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 247 HIS B 318 HIS ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN C 108 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120316 restraints weight = 9087.190| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.75 r_work: 0.3225 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8257 Z= 0.140 Angle : 0.640 12.527 11186 Z= 0.323 Chirality : 0.043 0.280 1275 Planarity : 0.005 0.058 1424 Dihedral : 5.142 28.235 1093 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.79 % Favored : 90.92 % Rotamer: Outliers : 2.56 % Allowed : 13.04 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.23), residues: 1013 helix: -2.10 (0.21), residues: 405 sheet: -3.25 (0.42), residues: 128 loop : -2.36 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 344 TYR 0.016 0.002 TYR A 12 PHE 0.011 0.001 PHE B 602 TRP 0.018 0.001 TRP B 378 HIS 0.007 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8253) covalent geometry : angle 0.62774 (11180) hydrogen bonds : bond 0.03714 ( 243) hydrogen bonds : angle 4.91345 ( 687) metal coordination : bond 0.00767 ( 4) metal coordination : angle 5.34390 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.213 Fit side-chains REVERT: A 40 TYR cc_start: 0.8383 (m-80) cc_final: 0.8166 (m-80) REVERT: A 65 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7611 (t0) REVERT: A 114 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: A 302 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: A 337 LEU cc_start: 0.8383 (mt) cc_final: 0.8131 (mp) REVERT: A 341 LYS cc_start: 0.7906 (ttpt) cc_final: 0.7281 (tttm) REVERT: A 406 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7233 (mp0) REVERT: B 213 MET cc_start: 0.7208 (mmm) cc_final: 0.6810 (tpt) REVERT: B 215 SER cc_start: 0.9111 (t) cc_final: 0.8908 (t) REVERT: B 248 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8788 (pp) REVERT: B 314 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7811 (ttmm) REVERT: B 398 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7525 (p0) REVERT: C 154 ARG cc_start: 0.8155 (mtm110) cc_final: 0.7493 (ttm-80) outliers start: 23 outliers final: 6 residues processed: 129 average time/residue: 0.4194 time to fit residues: 58.5054 Evaluate side-chains 118 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 0.0470 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 322 HIS B 350 GLN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120932 restraints weight = 8965.517| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.87 r_work: 0.3234 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8257 Z= 0.148 Angle : 0.616 12.232 11186 Z= 0.310 Chirality : 0.043 0.270 1275 Planarity : 0.005 0.052 1424 Dihedral : 5.009 27.914 1093 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.19 % Favored : 91.61 % Rotamer: Outliers : 3.79 % Allowed : 14.27 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.25), residues: 1013 helix: -1.35 (0.23), residues: 408 sheet: -2.71 (0.43), residues: 128 loop : -2.12 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 103 TYR 0.016 0.002 TYR B 661 PHE 0.025 0.001 PHE A 25 TRP 0.018 0.001 TRP B 378 HIS 0.004 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8253) covalent geometry : angle 0.60610 (11180) hydrogen bonds : bond 0.03305 ( 243) hydrogen bonds : angle 4.52805 ( 687) metal coordination : bond 0.00753 ( 4) metal coordination : angle 4.80006 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.235 Fit side-chains REVERT: A 25 PHE cc_start: 0.8732 (p90) cc_final: 0.8493 (p90) REVERT: A 114 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: A 258 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: A 302 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: A 337 LEU cc_start: 0.8263 (mt) cc_final: 0.8019 (mp) REVERT: A 406 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7367 (mp0) REVERT: A 847 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7792 (mmtt) REVERT: A 855 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7550 (mmt90) REVERT: B 248 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8751 (pp) REVERT: B 314 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7773 (ttmm) REVERT: B 398 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7444 (p0) REVERT: C 154 ARG cc_start: 0.8131 (mtm110) cc_final: 0.7500 (ttm-80) outliers start: 34 outliers final: 11 residues processed: 128 average time/residue: 0.3970 time to fit residues: 55.1411 Evaluate side-chains 119 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 31 optimal weight: 0.9980 chunk 95 optimal weight: 0.0570 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.0000 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 0.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS B 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120382 restraints weight = 9176.113| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.81 r_work: 0.3241 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8257 Z= 0.136 Angle : 0.597 12.360 11186 Z= 0.299 Chirality : 0.043 0.271 1275 Planarity : 0.004 0.051 1424 Dihedral : 4.873 27.415 1093 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.46 % Allowed : 16.16 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.25), residues: 1013 helix: -0.92 (0.24), residues: 407 sheet: -2.58 (0.42), residues: 136 loop : -1.97 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 51 TYR 0.015 0.001 TYR B 661 PHE 0.020 0.001 PHE A 25 TRP 0.018 0.001 TRP B 378 HIS 0.005 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8253) covalent geometry : angle 0.58690 (11180) hydrogen bonds : bond 0.02961 ( 243) hydrogen bonds : angle 4.27595 ( 687) metal coordination : bond 0.00817 ( 4) metal coordination : angle 4.69284 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.258 Fit side-chains REVERT: A 65 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7786 (t0) REVERT: A 114 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: A 302 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: A 337 LEU cc_start: 0.8283 (mt) cc_final: 0.8043 (mp) REVERT: A 341 LYS cc_start: 0.7779 (ttpt) cc_final: 0.7138 (tttm) REVERT: A 406 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7388 (mp0) REVERT: A 847 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7827 (mmtt) REVERT: A 855 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7628 (mmt90) REVERT: B 248 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8776 (pp) REVERT: B 314 LYS cc_start: 0.8289 (ttpp) cc_final: 0.7799 (ttmm) REVERT: B 398 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7477 (p0) REVERT: C 154 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7415 (ttm-80) outliers start: 31 outliers final: 14 residues processed: 126 average time/residue: 0.4240 time to fit residues: 57.5253 Evaluate side-chains 121 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 93 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 73 optimal weight: 0.1980 chunk 94 optimal weight: 6.9990 chunk 56 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS B 323 ASN B 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.158100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.121213 restraints weight = 9238.071| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.16 r_work: 0.3237 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8257 Z= 0.142 Angle : 0.602 12.185 11186 Z= 0.300 Chirality : 0.043 0.268 1275 Planarity : 0.004 0.049 1424 Dihedral : 4.814 27.171 1093 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.88 % Favored : 91.02 % Rotamer: Outliers : 4.01 % Allowed : 16.72 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.26), residues: 1013 helix: -0.69 (0.25), residues: 412 sheet: -2.50 (0.42), residues: 136 loop : -1.86 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 51 TYR 0.020 0.002 TYR A 259 PHE 0.026 0.001 PHE A 25 TRP 0.018 0.001 TRP B 378 HIS 0.005 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8253) covalent geometry : angle 0.59266 (11180) hydrogen bonds : bond 0.02879 ( 243) hydrogen bonds : angle 4.17443 ( 687) metal coordination : bond 0.00905 ( 4) metal coordination : angle 4.63927 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.304 Fit side-chains REVERT: A 25 PHE cc_start: 0.8777 (p90) cc_final: 0.8498 (p90) REVERT: A 114 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7928 (mt-10) REVERT: A 302 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: A 337 LEU cc_start: 0.8267 (mt) cc_final: 0.8034 (mp) REVERT: A 374 MET cc_start: 0.8003 (mtp) cc_final: 0.7795 (mtp) REVERT: A 406 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7365 (mp0) REVERT: A 847 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7831 (mmtt) REVERT: A 855 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7644 (mmt90) REVERT: B 248 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8772 (pp) REVERT: B 314 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7685 (ttmm) REVERT: B 398 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7441 (p0) REVERT: C 154 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7386 (ttm-80) outliers start: 36 outliers final: 13 residues processed: 127 average time/residue: 0.4219 time to fit residues: 57.7150 Evaluate side-chains 112 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 97 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS B 350 GLN B 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.155104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119812 restraints weight = 9035.564| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.77 r_work: 0.3226 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8257 Z= 0.158 Angle : 0.626 12.286 11186 Z= 0.311 Chirality : 0.043 0.272 1275 Planarity : 0.004 0.049 1424 Dihedral : 4.837 27.004 1093 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.18 % Favored : 90.72 % Rotamer: Outliers : 3.57 % Allowed : 17.84 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.26), residues: 1013 helix: -0.64 (0.25), residues: 412 sheet: -2.40 (0.42), residues: 136 loop : -1.79 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 103 TYR 0.016 0.002 TYR B 661 PHE 0.025 0.002 PHE A 25 TRP 0.017 0.001 TRP B 378 HIS 0.005 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8253) covalent geometry : angle 0.61625 (11180) hydrogen bonds : bond 0.02916 ( 243) hydrogen bonds : angle 4.12601 ( 687) metal coordination : bond 0.01067 ( 4) metal coordination : angle 4.68359 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.275 Fit side-chains REVERT: A 114 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: A 302 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: A 337 LEU cc_start: 0.8316 (mt) cc_final: 0.8072 (mp) REVERT: A 374 MET cc_start: 0.8081 (mtp) cc_final: 0.7857 (mtt) REVERT: A 406 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7354 (mp0) REVERT: A 847 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7895 (mmtt) REVERT: A 855 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7763 (mmt90) REVERT: B 248 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8748 (pp) REVERT: B 314 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7700 (ttmm) REVERT: B 398 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7496 (p0) REVERT: C 139 PHE cc_start: 0.7343 (m-10) cc_final: 0.7095 (m-10) REVERT: C 154 ARG cc_start: 0.7983 (mtm110) cc_final: 0.7298 (ttm-80) outliers start: 32 outliers final: 15 residues processed: 118 average time/residue: 0.4056 time to fit residues: 51.7814 Evaluate side-chains 114 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 93 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS B 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116250 restraints weight = 9207.711| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.89 r_work: 0.3168 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8257 Z= 0.221 Angle : 0.683 12.610 11186 Z= 0.339 Chirality : 0.046 0.282 1275 Planarity : 0.005 0.049 1424 Dihedral : 5.044 27.375 1093 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.28 % Favored : 90.52 % Rotamer: Outliers : 3.68 % Allowed : 17.84 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.25), residues: 1013 helix: -0.76 (0.24), residues: 416 sheet: -2.36 (0.43), residues: 136 loop : -1.86 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 103 TYR 0.020 0.002 TYR B 661 PHE 0.028 0.002 PHE A 25 TRP 0.018 0.002 TRP B 378 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 8253) covalent geometry : angle 0.67278 (11180) hydrogen bonds : bond 0.03242 ( 243) hydrogen bonds : angle 4.24085 ( 687) metal coordination : bond 0.01686 ( 4) metal coordination : angle 5.06980 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.203 Fit side-chains REVERT: A 25 PHE cc_start: 0.8895 (p90) cc_final: 0.8633 (p90) REVERT: A 114 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: A 232 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8374 (m-10) REVERT: A 302 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: A 337 LEU cc_start: 0.8353 (mt) cc_final: 0.8099 (mp) REVERT: A 374 MET cc_start: 0.8149 (mtp) cc_final: 0.7905 (mtp) REVERT: A 406 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7405 (mp0) REVERT: A 855 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8265 (mmt90) REVERT: B 248 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8559 (pp) REVERT: B 314 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7749 (ttmm) REVERT: B 320 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8291 (pp) REVERT: C 50 VAL cc_start: 0.8552 (t) cc_final: 0.8296 (m) REVERT: C 154 ARG cc_start: 0.7989 (mtm110) cc_final: 0.7349 (tpp-160) outliers start: 33 outliers final: 13 residues processed: 121 average time/residue: 0.4041 time to fit residues: 52.9566 Evaluate side-chains 108 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 398 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 99 optimal weight: 0.0870 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.154620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120116 restraints weight = 9053.340| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.77 r_work: 0.3215 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8257 Z= 0.166 Angle : 0.644 12.368 11186 Z= 0.319 Chirality : 0.044 0.272 1275 Planarity : 0.004 0.047 1424 Dihedral : 4.939 27.233 1093 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.98 % Favored : 90.92 % Rotamer: Outliers : 3.34 % Allowed : 18.62 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.26), residues: 1013 helix: -0.57 (0.25), residues: 416 sheet: -2.30 (0.43), residues: 136 loop : -1.78 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 103 TYR 0.016 0.002 TYR B 661 PHE 0.027 0.002 PHE A 25 TRP 0.019 0.001 TRP B 378 HIS 0.005 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8253) covalent geometry : angle 0.63448 (11180) hydrogen bonds : bond 0.02898 ( 243) hydrogen bonds : angle 4.13380 ( 687) metal coordination : bond 0.01232 ( 4) metal coordination : angle 4.79391 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.238 Fit side-chains REVERT: A 114 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: A 337 LEU cc_start: 0.8388 (mt) cc_final: 0.8137 (mp) REVERT: A 406 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7420 (mp0) REVERT: A 417 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8209 (mm) REVERT: A 809 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8069 (mp) REVERT: A 847 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7905 (mmtt) REVERT: A 855 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7733 (mmt90) REVERT: B 233 MET cc_start: 0.8331 (tpt) cc_final: 0.8101 (tpp) REVERT: B 248 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8722 (pp) REVERT: B 314 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7739 (ttmm) REVERT: B 398 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7499 (p0) REVERT: C 50 VAL cc_start: 0.8571 (t) cc_final: 0.8315 (m) REVERT: C 154 ARG cc_start: 0.7977 (mtm110) cc_final: 0.7331 (ttm-80) outliers start: 30 outliers final: 16 residues processed: 119 average time/residue: 0.4336 time to fit residues: 55.6678 Evaluate side-chains 114 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 637 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 0.0370 chunk 100 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 0.0270 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.157227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123023 restraints weight = 8996.920| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.77 r_work: 0.3245 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8257 Z= 0.122 Angle : 0.623 11.956 11186 Z= 0.305 Chirality : 0.042 0.261 1275 Planarity : 0.004 0.046 1424 Dihedral : 4.702 27.052 1093 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.49 % Favored : 91.41 % Rotamer: Outliers : 2.90 % Allowed : 19.40 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.26), residues: 1013 helix: -0.33 (0.25), residues: 416 sheet: -2.21 (0.43), residues: 141 loop : -1.60 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 103 TYR 0.013 0.001 TYR B 627 PHE 0.026 0.001 PHE A 25 TRP 0.021 0.001 TRP B 378 HIS 0.004 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8253) covalent geometry : angle 0.61458 (11180) hydrogen bonds : bond 0.02540 ( 243) hydrogen bonds : angle 3.96917 ( 687) metal coordination : bond 0.00796 ( 4) metal coordination : angle 4.42964 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.311 Fit side-chains REVERT: A 25 PHE cc_start: 0.8769 (p90) cc_final: 0.8569 (p90) REVERT: A 102 MET cc_start: 0.9051 (ttp) cc_final: 0.8685 (ttm) REVERT: A 114 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: A 337 LEU cc_start: 0.8348 (mt) cc_final: 0.8114 (mp) REVERT: A 406 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7319 (mp0) REVERT: A 809 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8114 (mp) REVERT: A 847 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7880 (mmtt) REVERT: B 233 MET cc_start: 0.8290 (tpt) cc_final: 0.8088 (tpp) REVERT: B 314 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7675 (ttmm) REVERT: B 398 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7438 (p0) REVERT: C 50 VAL cc_start: 0.8529 (t) cc_final: 0.8269 (m) REVERT: C 154 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7375 (ttm-80) outliers start: 26 outliers final: 10 residues processed: 117 average time/residue: 0.4160 time to fit residues: 52.7588 Evaluate side-chains 106 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 398 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 HIS ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117049 restraints weight = 9152.022| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.88 r_work: 0.3193 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8257 Z= 0.208 Angle : 0.689 12.511 11186 Z= 0.339 Chirality : 0.045 0.279 1275 Planarity : 0.005 0.048 1424 Dihedral : 4.919 27.415 1093 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.58 % Favored : 90.33 % Rotamer: Outliers : 2.34 % Allowed : 20.51 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.26), residues: 1013 helix: -0.42 (0.25), residues: 412 sheet: -2.25 (0.43), residues: 141 loop : -1.63 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 598 TYR 0.019 0.002 TYR B 661 PHE 0.030 0.002 PHE A 25 TRP 0.017 0.002 TRP B 378 HIS 0.005 0.001 HIS A 678 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 8253) covalent geometry : angle 0.67959 (11180) hydrogen bonds : bond 0.03089 ( 243) hydrogen bonds : angle 4.12297 ( 687) metal coordination : bond 0.01644 ( 4) metal coordination : angle 4.91174 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.331 Fit side-chains REVERT: A 25 PHE cc_start: 0.8783 (p90) cc_final: 0.8520 (p90) REVERT: A 102 MET cc_start: 0.9117 (ttp) cc_final: 0.8522 (ttm) REVERT: A 114 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: A 337 LEU cc_start: 0.8347 (mt) cc_final: 0.8100 (mp) REVERT: A 367 ASP cc_start: 0.8711 (m-30) cc_final: 0.8475 (m-30) REVERT: A 406 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7407 (mp0) REVERT: A 417 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8227 (mm) REVERT: A 847 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7887 (mmtt) REVERT: B 314 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7722 (ttmm) REVERT: B 398 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7511 (p0) REVERT: C 50 VAL cc_start: 0.8560 (t) cc_final: 0.8303 (m) outliers start: 21 outliers final: 13 residues processed: 109 average time/residue: 0.4626 time to fit residues: 54.3655 Evaluate side-chains 109 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 403 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 HIS ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.155077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117793 restraints weight = 9197.478| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.90 r_work: 0.3202 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8257 Z= 0.178 Angle : 0.672 12.314 11186 Z= 0.330 Chirality : 0.044 0.273 1275 Planarity : 0.004 0.047 1424 Dihedral : 4.897 27.266 1093 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.38 % Favored : 90.52 % Rotamer: Outliers : 2.90 % Allowed : 19.73 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.26), residues: 1013 helix: -0.35 (0.25), residues: 412 sheet: -2.24 (0.43), residues: 141 loop : -1.57 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 154 TYR 0.016 0.002 TYR B 661 PHE 0.029 0.002 PHE A 25 TRP 0.019 0.001 TRP B 378 HIS 0.005 0.001 HIS A 678 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 8253) covalent geometry : angle 0.66285 (11180) hydrogen bonds : bond 0.02907 ( 243) hydrogen bonds : angle 4.08867 ( 687) metal coordination : bond 0.01302 ( 4) metal coordination : angle 4.75617 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2731.98 seconds wall clock time: 47 minutes 17.66 seconds (2837.66 seconds total)