Starting phenix.real_space_refine on Wed Mar 12 16:43:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vcd_21149/03_2025/6vcd_21149.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vcd_21149/03_2025/6vcd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vcd_21149/03_2025/6vcd_21149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vcd_21149/03_2025/6vcd_21149.map" model { file = "/net/cci-nas-00/data/ceres_data/6vcd_21149/03_2025/6vcd_21149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vcd_21149/03_2025/6vcd_21149.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.66, per 1000 atoms: 0.70 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: 2.15 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.17 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: 2.30 Time building geometry restraints manager: 2.50 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: 2.680 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.300 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:14.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.290 ------------------------------------------------------------------------------- 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 : 0.005 0.044 8253 Z= 0.299 Angle : 0.701 14.029 11180 Z= 0.419 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 (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: -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 TRP 0.017 0.002 TRP B 378 HIS 0.005 0.001 HIS B 387 PHE 0.014 0.001 PHE B 602 TYR 0.021 0.002 TYR B 661 ARG 0.004 0.000 ARG A 262 *********************** 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 : 0.911 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: 0.8274 (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: 0.8830 (t) REVERT: B 314 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7921 (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: 1.1212 time to fit residues: 163.0029 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 : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 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 = 0.3798 r_free = 0.3798 target = 0.152458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116975 restraints weight = 9015.592| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.74 r_work: 0.3183 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8253 Z= 0.339 Angle : 0.684 12.954 11180 Z= 0.350 Chirality : 0.045 0.294 1275 Planarity : 0.005 0.060 1424 Dihedral : 5.345 28.610 1093 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.18 % Favored : 90.52 % Rotamer: Outliers : 3.46 % Allowed : 12.82 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -3.86 (0.23), residues: 1013 helix: -2.30 (0.21), residues: 406 sheet: -3.28 (0.44), residues: 118 loop : -2.54 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 378 HIS 0.007 0.001 HIS B 318 PHE 0.019 0.002 PHE B 602 TYR 0.021 0.002 TYR B 661 ARG 0.006 0.001 ARG B 598 *********************** 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 141 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8380 (m-80) cc_final: 0.8173 (m-80) REVERT: A 114 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: A 258 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: A 302 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: A 337 LEU cc_start: 0.8441 (mt) cc_final: 0.8182 (mp) REVERT: A 825 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7781 (pp) REVERT: A 855 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8177 (mmt90) REVERT: A 936 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8110 (p) REVERT: B 215 SER cc_start: 0.9107 (t) cc_final: 0.8885 (t) REVERT: B 248 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8616 (pp) REVERT: B 314 LYS cc_start: 0.8254 (ttpp) cc_final: 0.7837 (ttmm) REVERT: C 154 ARG cc_start: 0.8184 (mtm110) cc_final: 0.7525 (ttm-80) outliers start: 31 outliers final: 10 residues processed: 134 average time/residue: 0.9090 time to fit residues: 132.1771 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 : 0.839 ------------------------------------------------------------------------------- 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 269 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain A residue 936 VAL 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 89 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 81 optimal weight: 0.0370 chunk 5 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 318 HIS ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.154410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118830 restraints weight = 9079.058| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.75 r_work: 0.3207 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8253 Z= 0.243 Angle : 0.613 12.426 11180 Z= 0.314 Chirality : 0.043 0.274 1275 Planarity : 0.005 0.051 1424 Dihedral : 5.091 27.886 1093 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.29 % Favored : 91.41 % Rotamer: Outliers : 3.46 % Allowed : 15.27 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -2.97 (0.25), residues: 1013 helix: -1.41 (0.23), residues: 406 sheet: -2.76 (0.41), residues: 139 loop : -2.13 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 378 HIS 0.008 0.001 HIS B 318 PHE 0.027 0.002 PHE A 25 TYR 0.016 0.002 TYR B 661 ARG 0.005 0.001 ARG A 103 *********************** 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 135 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.934 Fit side-chains REVERT: A 25 PHE cc_start: 0.8784 (p90) cc_final: 0.8524 (p90) REVERT: A 40 TYR cc_start: 0.8398 (m-80) cc_final: 0.8182 (m-80) REVERT: A 114 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: A 258 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: A 302 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: A 337 LEU cc_start: 0.8383 (mt) cc_final: 0.8138 (mp) REVERT: A 406 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7424 (mp0) REVERT: A 855 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8167 (mmt90) REVERT: B 215 SER cc_start: 0.9094 (t) cc_final: 0.8884 (t) REVERT: B 248 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8725 (pp) REVERT: B 314 LYS cc_start: 0.8309 (ttpp) cc_final: 0.7848 (ttmm) REVERT: B 320 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8264 (pp) REVERT: B 398 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7512 (p0) REVERT: C 154 ARG cc_start: 0.8173 (mtm110) cc_final: 0.7538 (ttm-80) outliers start: 31 outliers final: 12 residues processed: 126 average time/residue: 0.9082 time to fit residues: 124.1649 Evaluate side-chains 118 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 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 316 LEU Chi-restraints excluded: chain B residue 320 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 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.0980 chunk 83 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 323 ASN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.154223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118451 restraints weight = 9044.476| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.74 r_work: 0.3215 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8253 Z= 0.220 Angle : 0.587 12.476 11180 Z= 0.300 Chirality : 0.043 0.271 1275 Planarity : 0.004 0.051 1424 Dihedral : 4.941 27.983 1093 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.98 % Favored : 90.92 % Rotamer: Outliers : 4.01 % Allowed : 16.05 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -2.53 (0.25), residues: 1013 helix: -0.95 (0.24), residues: 407 sheet: -2.61 (0.42), residues: 139 loop : -1.96 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 378 HIS 0.006 0.001 HIS B 318 PHE 0.019 0.001 PHE A 25 TYR 0.014 0.001 TYR B 661 ARG 0.005 0.000 ARG A 51 *********************** 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 139 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.977 Fit side-chains REVERT: A 40 TYR cc_start: 0.8380 (m-80) cc_final: 0.8153 (m-80) REVERT: A 114 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: A 232 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8369 (m-10) REVERT: A 302 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: A 337 LEU cc_start: 0.8305 (mt) cc_final: 0.8062 (mp) REVERT: A 374 MET cc_start: 0.8145 (mtp) cc_final: 0.7877 (mtp) REVERT: A 406 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7400 (mp0) REVERT: A 683 MET cc_start: 0.5073 (ttp) cc_final: 0.4767 (ptm) REVERT: A 847 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7835 (mmtt) REVERT: B 248 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8715 (pp) REVERT: B 314 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7729 (ttmm) REVERT: B 398 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7479 (p0) REVERT: C 154 ARG cc_start: 0.8119 (mtm110) cc_final: 0.7457 (ttm-80) outliers start: 36 outliers final: 13 residues processed: 127 average time/residue: 0.8508 time to fit residues: 118.3738 Evaluate side-chains 117 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 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 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 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 63 optimal weight: 0.3980 chunk 95 optimal weight: 0.0040 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 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 = 0.3854 r_free = 0.3854 target = 0.157040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122275 restraints weight = 8898.325| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.78 r_work: 0.3269 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8253 Z= 0.187 Angle : 0.572 11.943 11180 Z= 0.290 Chirality : 0.042 0.260 1275 Planarity : 0.004 0.049 1424 Dihedral : 4.741 27.349 1093 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.29 % Favored : 91.61 % Rotamer: Outliers : 3.46 % Allowed : 17.61 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -2.18 (0.26), residues: 1013 helix: -0.59 (0.25), residues: 407 sheet: -2.52 (0.42), residues: 136 loop : -1.82 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 378 HIS 0.004 0.001 HIS B 318 PHE 0.027 0.001 PHE A 25 TYR 0.020 0.001 TYR A 259 ARG 0.004 0.000 ARG A 51 *********************** 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 131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.835 Fit side-chains REVERT: A 25 PHE cc_start: 0.8758 (p90) cc_final: 0.8545 (p90) REVERT: A 40 TYR cc_start: 0.8346 (m-80) cc_final: 0.8136 (m-80) REVERT: A 114 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: A 302 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: A 337 LEU cc_start: 0.8301 (mt) cc_final: 0.8068 (mp) REVERT: A 406 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7369 (mp0) REVERT: A 683 MET cc_start: 0.4932 (ttp) cc_final: 0.4717 (ptm) REVERT: A 809 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8062 (mp) REVERT: A 847 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7853 (mmtt) REVERT: B 248 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8705 (pp) REVERT: B 314 LYS cc_start: 0.8190 (ttpp) cc_final: 0.7673 (ttmm) REVERT: B 398 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7400 (p0) REVERT: C 20 ILE cc_start: 0.6757 (mp) cc_final: 0.6400 (pp) REVERT: C 154 ARG cc_start: 0.8026 (mtm110) cc_final: 0.7396 (ttm-80) outliers start: 31 outliers final: 10 residues processed: 124 average time/residue: 0.9103 time to fit residues: 122.7492 Evaluate side-chains 111 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 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 809 ILE Chi-restraints excluded: chain A residue 924 LEU 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 68 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 88 optimal weight: 0.9980 chunk 55 optimal weight: 0.0980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 892 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.159826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122889 restraints weight = 9149.573| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.90 r_work: 0.3267 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8253 Z= 0.165 Angle : 0.561 11.846 11180 Z= 0.283 Chirality : 0.041 0.258 1275 Planarity : 0.004 0.048 1424 Dihedral : 4.562 27.026 1093 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.23 % Allowed : 18.39 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.86 (0.26), residues: 1013 helix: -0.30 (0.26), residues: 408 sheet: -2.33 (0.42), residues: 132 loop : -1.67 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 378 HIS 0.004 0.001 HIS B 387 PHE 0.024 0.001 PHE A 25 TYR 0.014 0.001 TYR B 627 ARG 0.003 0.000 ARG A 103 *********************** 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 134 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.921 Fit side-chains REVERT: A 40 TYR cc_start: 0.8387 (m-80) cc_final: 0.8141 (m-80) REVERT: A 102 MET cc_start: 0.9087 (ttp) cc_final: 0.8701 (ttm) REVERT: A 114 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: A 406 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7371 (mp0) REVERT: A 809 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8137 (mp) REVERT: A 847 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7815 (mmtt) REVERT: B 314 LYS cc_start: 0.8196 (ttpp) cc_final: 0.7675 (ttmm) REVERT: B 398 ASP cc_start: 0.8156 (p0) cc_final: 0.7344 (p0) REVERT: C 154 ARG cc_start: 0.7960 (mtm110) cc_final: 0.7270 (ttm-80) outliers start: 29 outliers final: 13 residues processed: 125 average time/residue: 0.8263 time to fit residues: 112.9973 Evaluate side-chains 111 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 809 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 89 optimal weight: 0.0170 chunk 37 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.2618 ------------------------------------------------------------------------------- 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 318 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 = 0.3881 r_free = 0.3881 target = 0.159501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124957 restraints weight = 8937.937| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.76 r_work: 0.3283 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8253 Z= 0.164 Angle : 0.572 11.741 11180 Z= 0.283 Chirality : 0.042 0.256 1275 Planarity : 0.004 0.046 1424 Dihedral : 4.461 26.519 1093 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.68 % Allowed : 19.06 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.67 (0.26), residues: 1013 helix: -0.14 (0.26), residues: 407 sheet: -2.23 (0.42), residues: 132 loop : -1.57 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 378 HIS 0.003 0.001 HIS B 387 PHE 0.021 0.001 PHE A 25 TYR 0.018 0.001 TYR A 378 ARG 0.003 0.000 ARG A 855 *********************** 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 122 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.936 Fit side-chains REVERT: A 102 MET cc_start: 0.9066 (ttp) cc_final: 0.8502 (ttm) REVERT: A 114 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: A 406 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7425 (mp0) REVERT: A 809 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8113 (mp) REVERT: A 847 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7821 (mmtt) REVERT: B 314 LYS cc_start: 0.8142 (ttpp) cc_final: 0.7661 (ttmm) REVERT: B 398 ASP cc_start: 0.8127 (p0) cc_final: 0.7330 (p0) REVERT: C 154 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7269 (ttm-80) outliers start: 24 outliers final: 12 residues processed: 114 average time/residue: 0.8864 time to fit residues: 110.4319 Evaluate side-chains 110 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 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 727 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 93 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 322 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 = 0.3859 r_free = 0.3859 target = 0.157509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.123146 restraints weight = 9036.384| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.77 r_work: 0.3252 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8253 Z= 0.218 Angle : 0.599 11.797 11180 Z= 0.299 Chirality : 0.043 0.260 1275 Planarity : 0.004 0.048 1424 Dihedral : 4.560 26.532 1093 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.81 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 (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: -1.64 (0.26), residues: 1013 helix: -0.15 (0.26), residues: 408 sheet: -2.18 (0.43), residues: 132 loop : -1.54 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 378 HIS 0.004 0.001 HIS B 387 PHE 0.021 0.001 PHE A 25 TYR 0.017 0.001 TYR A 378 ARG 0.003 0.000 ARG A 103 *********************** 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 124 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.990 Fit side-chains REVERT: A 40 TYR cc_start: 0.8340 (m-80) cc_final: 0.8138 (m-80) REVERT: A 102 MET cc_start: 0.9095 (ttp) cc_final: 0.8640 (ttm) REVERT: A 114 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: A 367 ASP cc_start: 0.8698 (m-30) cc_final: 0.8477 (m-30) REVERT: A 406 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7438 (mp0) REVERT: A 847 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7854 (mmtt) REVERT: B 314 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7677 (ttmm) REVERT: B 398 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7315 (p0) outliers start: 26 outliers final: 12 residues processed: 116 average time/residue: 0.8526 time to fit residues: 108.3206 Evaluate side-chains 110 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 308 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 34 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.157614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120411 restraints weight = 9230.531| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.92 r_work: 0.3236 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8253 Z= 0.229 Angle : 0.615 11.797 11180 Z= 0.305 Chirality : 0.043 0.263 1275 Planarity : 0.004 0.047 1424 Dihedral : 4.618 26.853 1093 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.19 % Favored : 91.71 % Rotamer: Outliers : 2.90 % Allowed : 19.96 % 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 (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: -1.64 (0.26), residues: 1013 helix: -0.18 (0.25), residues: 413 sheet: -2.17 (0.43), residues: 132 loop : -1.52 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 378 HIS 0.005 0.001 HIS A 678 PHE 0.020 0.001 PHE A 25 TYR 0.016 0.001 TYR A 378 ARG 0.006 0.000 ARG C 154 *********************** 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 125 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.847 Fit side-chains REVERT: A 40 TYR cc_start: 0.8377 (m-80) cc_final: 0.8149 (m-80) REVERT: A 102 MET cc_start: 0.9108 (ttp) cc_final: 0.8492 (ttm) REVERT: A 114 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: A 337 LEU cc_start: 0.8317 (mt) cc_final: 0.8084 (mp) REVERT: A 406 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7391 (mp0) REVERT: A 678 HIS cc_start: 0.4780 (OUTLIER) cc_final: 0.4326 (t-90) REVERT: A 847 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7852 (mmtt) REVERT: B 314 LYS cc_start: 0.8161 (ttpp) cc_final: 0.7668 (ttmm) REVERT: B 398 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7361 (p0) REVERT: C 154 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7296 (ttm-80) outliers start: 26 outliers final: 17 residues processed: 116 average time/residue: 0.8769 time to fit residues: 110.8562 Evaluate side-chains 117 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 322 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 678 HIS 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 B residue 205 ILE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 27 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 322 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 = 0.3875 r_free = 0.3875 target = 0.158730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121686 restraints weight = 9092.111| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.91 r_work: 0.3248 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8253 Z= 0.204 Angle : 0.612 11.733 11180 Z= 0.302 Chirality : 0.043 0.260 1275 Planarity : 0.004 0.046 1424 Dihedral : 4.547 26.768 1093 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.19 % Favored : 91.71 % Rotamer: Outliers : 2.68 % Allowed : 20.07 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.48 (0.27), residues: 1013 helix: -0.01 (0.26), residues: 407 sheet: -2.14 (0.43), residues: 132 loop : -1.44 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 378 HIS 0.004 0.001 HIS A 678 PHE 0.020 0.001 PHE A 25 TYR 0.016 0.001 TYR A 378 ARG 0.007 0.000 ARG C 154 ********************** 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 129 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.910 Fit side-chains REVERT: A 40 TYR cc_start: 0.8384 (m-80) cc_final: 0.8180 (m-80) REVERT: A 102 MET cc_start: 0.9092 (ttp) cc_final: 0.8644 (ttm) REVERT: A 114 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: A 337 LEU cc_start: 0.8286 (mt) cc_final: 0.8049 (mp) REVERT: A 406 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7367 (mp0) REVERT: A 417 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8147 (mm) REVERT: A 847 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7813 (mmtt) REVERT: B 314 LYS cc_start: 0.8142 (ttpp) cc_final: 0.7649 (ttmm) REVERT: B 398 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7356 (p0) REVERT: C 154 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7284 (ttm-80) outliers start: 24 outliers final: 18 residues processed: 121 average time/residue: 0.8457 time to fit residues: 112.0829 Evaluate side-chains 122 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 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 322 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 681 LEU 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 809 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 241 THR 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 27 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 87 optimal weight: 0.0870 chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 322 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 = 0.3850 r_free = 0.3850 target = 0.156364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122081 restraints weight = 9049.495| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.78 r_work: 0.3241 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8253 Z= 0.240 Angle : 0.626 11.814 11180 Z= 0.309 Chirality : 0.043 0.264 1275 Planarity : 0.004 0.046 1424 Dihedral : 4.622 26.873 1093 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.49 % Favored : 91.41 % Rotamer: Outliers : 2.79 % Allowed : 20.29 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % 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: -1.49 (0.27), residues: 1013 helix: -0.04 (0.26), residues: 407 sheet: -2.18 (0.42), residues: 141 loop : -1.37 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 378 HIS 0.004 0.001 HIS A 678 PHE 0.020 0.001 PHE A 25 TYR 0.016 0.001 TYR A 378 ARG 0.007 0.001 ARG C 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6219.56 seconds wall clock time: 108 minutes 33.01 seconds (6513.01 seconds total)