Starting phenix.real_space_refine on Fri Jul 25 22:15:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vcd_21149/07_2025/6vcd_21149.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vcd_21149/07_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_21149/07_2025/6vcd_21149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vcd_21149/07_2025/6vcd_21149.map" model { file = "/net/cci-nas-00/data/ceres_data/6vcd_21149/07_2025/6vcd_21149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vcd_21149/07_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-5711/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: 5.18, per 1000 atoms: 0.64 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: 1.91 Conformation dependent library (CDL) restraints added in 1.1 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: 0.91 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: 2.08 Time building geometry restraints manager: 2.27 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: 1.690 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.960 Find NCS groups from input model: 0.070 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:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.500 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.23037 ( 243) hydrogen bonds : angle 7.63460 ( 687) metal coordination : bond 0.60693 ( 4) metal coordination : angle 24.14927 ( 6) covalent geometry : bond 0.00453 ( 8253) covalent geometry : angle 0.70099 (11180) *********************** 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 : 0.921 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: 1.1362 time to fit residues: 164.9375 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 : 0.853 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.152890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117482 restraints weight = 9009.111| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.73 r_work: 0.3191 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8257 Z= 0.201 Angle : 0.687 12.962 11186 Z= 0.346 Chirality : 0.045 0.294 1275 Planarity : 0.005 0.060 1424 Dihedral : 5.326 28.487 1093 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.28 % Favored : 90.42 % Rotamer: Outliers : 3.34 % Allowed : 12.93 % 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: -3.77 (0.23), residues: 1013 helix: -2.25 (0.21), residues: 406 sheet: -3.06 (0.43), residues: 119 loop : -2.51 (0.26), residues: 488 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 0.018 0.002 PHE B 602 TYR 0.020 0.002 TYR B 661 ARG 0.006 0.001 ARG B 598 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 243) hydrogen bonds : angle 5.00436 ( 687) metal coordination : bond 0.01527 ( 4) metal coordination : angle 5.43275 ( 6) covalent geometry : bond 0.00485 ( 8253) covalent geometry : angle 0.67511 (11180) *********************** 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 140 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8389 (m-80) cc_final: 0.8142 (m-80) REVERT: A 114 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: A 302 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: A 337 LEU cc_start: 0.8418 (mt) cc_final: 0.8151 (mp) REVERT: A 406 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7323 (mp0) REVERT: A 825 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7770 (pp) REVERT: A 855 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8171 (mmt90) REVERT: A 936 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.8094 (p) REVERT: B 215 SER cc_start: 0.9088 (t) cc_final: 0.8878 (t) REVERT: B 248 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8661 (pp) REVERT: B 314 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7816 (ttmm) REVERT: C 154 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7499 (ttm-80) outliers start: 30 outliers final: 9 residues processed: 133 average time/residue: 0.8923 time to fit residues: 128.9725 Evaluate side-chains 117 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 269 ASP 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: 0.9980 chunk 19 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.154356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118784 restraints weight = 9070.650| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.75 r_work: 0.3206 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8257 Z= 0.157 Angle : 0.625 12.262 11186 Z= 0.315 Chirality : 0.044 0.270 1275 Planarity : 0.005 0.052 1424 Dihedral : 5.101 28.030 1093 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.49 % Favored : 91.31 % Rotamer: Outliers : 3.34 % Allowed : 15.05 % Favored : 81.61 % 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: -2.98 (0.25), residues: 1013 helix: -1.40 (0.23), residues: 407 sheet: -2.77 (0.42), residues: 134 loop : -2.17 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 378 HIS 0.007 0.001 HIS B 318 PHE 0.026 0.001 PHE A 25 TYR 0.016 0.002 TYR B 661 ARG 0.005 0.001 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.03346 ( 243) hydrogen bonds : angle 4.52049 ( 687) metal coordination : bond 0.00905 ( 4) metal coordination : angle 4.89549 ( 6) covalent geometry : bond 0.00377 ( 8253) covalent geometry : angle 0.61444 (11180) *********************** 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 134 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.961 Fit side-chains REVERT: A 25 PHE cc_start: 0.8785 (p90) cc_final: 0.8521 (p90) REVERT: A 40 TYR cc_start: 0.8426 (m-80) cc_final: 0.8212 (m-80) REVERT: A 114 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: A 258 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: A 302 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: A 337 LEU cc_start: 0.8375 (mt) cc_final: 0.8121 (mp) REVERT: A 341 LYS cc_start: 0.7825 (ttpt) cc_final: 0.7178 (tttm) REVERT: A 406 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7392 (mp0) REVERT: B 215 SER cc_start: 0.9102 (t) cc_final: 0.8891 (t) REVERT: B 248 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8747 (pp) REVERT: B 314 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7838 (ttmm) REVERT: B 398 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7530 (p0) REVERT: C 50 VAL cc_start: 0.8626 (t) cc_final: 0.8346 (m) REVERT: C 154 ARG cc_start: 0.8175 (mtm110) cc_final: 0.7544 (ttm-80) outliers start: 30 outliers final: 11 residues processed: 125 average time/residue: 0.8891 time to fit residues: 120.7028 Evaluate side-chains 117 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 83 optimal weight: 0.0570 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.156506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119046 restraints weight = 9139.741| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.92 r_work: 0.3233 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1822 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 : 0.600 12.413 11186 Z= 0.301 Chirality : 0.043 0.271 1275 Planarity : 0.004 0.051 1424 Dihedral : 4.924 27.868 1093 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.98 % Favored : 90.92 % Rotamer: Outliers : 3.57 % Allowed : 16.61 % Favored : 79.82 % 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: -2.51 (0.25), residues: 1013 helix: -0.91 (0.25), residues: 406 sheet: -2.59 (0.42), residues: 134 loop : -1.99 (0.28), residues: 473 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 0.020 0.001 PHE A 25 TYR 0.014 0.001 TYR B 661 ARG 0.005 0.001 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.02936 ( 243) hydrogen bonds : angle 4.26085 ( 687) metal coordination : bond 0.00921 ( 4) metal coordination : angle 4.64731 ( 6) covalent geometry : bond 0.00341 ( 8253) covalent geometry : angle 0.59032 (11180) *********************** 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: 32 poor density : 104 time to evaluate : 0.846 Fit side-chains REVERT: A 40 TYR cc_start: 0.8365 (m-80) cc_final: 0.8125 (m-80) REVERT: A 114 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: A 302 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: A 337 LEU cc_start: 0.8319 (mt) cc_final: 0.8083 (mp) REVERT: A 406 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7389 (mp0) REVERT: A 683 MET cc_start: 0.5180 (ttp) cc_final: 0.4820 (ptm) REVERT: A 847 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7850 (mmtt) REVERT: B 248 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8765 (pp) REVERT: B 314 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7760 (ttmm) REVERT: B 398 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7500 (p0) REVERT: C 50 VAL cc_start: 0.8600 (t) cc_final: 0.8321 (m) REVERT: C 154 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7461 (ttm-80) outliers start: 32 outliers final: 13 residues processed: 125 average time/residue: 0.8181 time to fit residues: 111.5646 Evaluate side-chains 118 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.156460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119332 restraints weight = 9028.536| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.15 r_work: 0.3207 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8257 Z= 0.169 Angle : 0.627 12.323 11186 Z= 0.312 Chirality : 0.044 0.271 1275 Planarity : 0.005 0.050 1424 Dihedral : 4.931 27.255 1093 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.59 % Favored : 91.21 % Rotamer: Outliers : 4.12 % Allowed : 16.72 % Favored : 79.15 % 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: -2.34 (0.25), residues: 1013 helix: -0.73 (0.25), residues: 406 sheet: -2.50 (0.42), residues: 136 loop : -1.94 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 378 HIS 0.005 0.001 HIS B 318 PHE 0.027 0.002 PHE A 25 TYR 0.017 0.002 TYR A 378 ARG 0.005 0.001 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03048 ( 243) hydrogen bonds : angle 4.22502 ( 687) metal coordination : bond 0.01202 ( 4) metal coordination : angle 4.81114 ( 6) covalent geometry : bond 0.00413 ( 8253) covalent geometry : angle 0.61671 (11180) *********************** 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 135 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.996 Fit side-chains REVERT: A 25 PHE cc_start: 0.8812 (p90) cc_final: 0.8544 (p90) REVERT: A 40 TYR cc_start: 0.8372 (m-80) cc_final: 0.8147 (m-80) REVERT: A 114 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: A 337 LEU cc_start: 0.8260 (mt) cc_final: 0.8012 (mp) REVERT: A 406 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7372 (mp0) REVERT: A 683 MET cc_start: 0.4963 (ttp) cc_final: 0.4702 (ptm) REVERT: A 809 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8146 (mp) REVERT: A 847 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7826 (mmtt) REVERT: B 248 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8701 (pp) REVERT: B 314 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7688 (ttmm) REVERT: B 398 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7492 (p0) REVERT: C 50 VAL cc_start: 0.8540 (t) cc_final: 0.8266 (m) REVERT: C 154 ARG cc_start: 0.8006 (mtm110) cc_final: 0.7313 (ttm-80) outliers start: 37 outliers final: 15 residues processed: 125 average time/residue: 0.8868 time to fit residues: 120.6878 Evaluate side-chains 116 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 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 825 LEU 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 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: 0.7980 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 0.0170 chunk 55 optimal weight: 0.4980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 ** 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 = 0.3846 r_free = 0.3846 target = 0.156518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119141 restraints weight = 9165.851| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.94 r_work: 0.3235 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8257 Z= 0.133 Angle : 0.601 12.151 11186 Z= 0.299 Chirality : 0.043 0.266 1275 Planarity : 0.004 0.048 1424 Dihedral : 4.794 27.413 1093 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.69 % Favored : 91.21 % 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: -2.15 (0.26), residues: 1013 helix: -0.61 (0.25), residues: 416 sheet: -2.45 (0.41), residues: 141 loop : -1.77 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 A 378 ARG 0.003 0.000 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.02743 ( 243) hydrogen bonds : angle 4.08243 ( 687) metal coordination : bond 0.00892 ( 4) metal coordination : angle 4.57652 ( 6) covalent geometry : bond 0.00321 ( 8253) covalent geometry : angle 0.59147 (11180) *********************** 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: 29 poor density : 99 time to evaluate : 0.932 Fit side-chains REVERT: A 40 TYR cc_start: 0.8366 (m-80) cc_final: 0.8143 (m-80) REVERT: A 114 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: A 337 LEU cc_start: 0.8326 (mt) cc_final: 0.8080 (mp) REVERT: A 406 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7356 (mp0) REVERT: A 809 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8152 (mp) REVERT: A 847 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7852 (mmtt) REVERT: B 248 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8766 (pp) REVERT: B 314 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7709 (ttmm) REVERT: B 398 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7434 (p0) REVERT: C 50 VAL cc_start: 0.8607 (t) cc_final: 0.8333 (m) REVERT: C 154 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7358 (ttm-80) outliers start: 29 outliers final: 15 residues processed: 120 average time/residue: 0.8994 time to fit residues: 118.0082 Evaluate side-chains 111 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 255 ILE 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 727 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 350 GLN ** 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 = 0.3822 r_free = 0.3822 target = 0.154223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119034 restraints weight = 9071.509| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.78 r_work: 0.3222 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2091 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= 0.152 Angle : 0.628 12.214 11186 Z= 0.308 Chirality : 0.043 0.270 1275 Planarity : 0.004 0.049 1424 Dihedral : 4.788 27.206 1093 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.39 % Favored : 91.41 % Rotamer: Outliers : 3.79 % Allowed : 17.84 % 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: -2.03 (0.26), residues: 1013 helix: -0.49 (0.25), residues: 415 sheet: -2.38 (0.42), residues: 141 loop : -1.72 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 378 HIS 0.005 0.001 HIS B 387 PHE 0.022 0.001 PHE A 25 TYR 0.015 0.002 TYR B 661 ARG 0.004 0.000 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.02815 ( 243) hydrogen bonds : angle 4.05491 ( 687) metal coordination : bond 0.01090 ( 4) metal coordination : angle 4.66042 ( 6) covalent geometry : bond 0.00369 ( 8253) covalent geometry : angle 0.61847 (11180) *********************** 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 128 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.876 Fit side-chains REVERT: A 102 MET cc_start: 0.9119 (ttp) cc_final: 0.8734 (ttm) REVERT: A 337 LEU cc_start: 0.8333 (mt) cc_final: 0.8092 (mp) REVERT: A 406 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7388 (mp0) REVERT: A 417 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8200 (mm) REVERT: A 847 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7886 (mmtt) REVERT: B 233 MET cc_start: 0.8364 (tpt) cc_final: 0.8146 (tpp) REVERT: B 248 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8778 (pp) REVERT: B 314 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7738 (ttmm) REVERT: B 398 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7427 (p0) REVERT: C 50 VAL cc_start: 0.8634 (t) cc_final: 0.8354 (m) REVERT: C 154 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7348 (ttm-80) outliers start: 34 outliers final: 18 residues processed: 116 average time/residue: 0.8848 time to fit residues: 112.0229 Evaluate side-chains 112 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 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 727 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 0.9980 chunk 41 optimal weight: 0.0270 chunk 39 optimal weight: 0.3980 chunk 40 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.157827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120689 restraints weight = 9137.457| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.92 r_work: 0.3243 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8257 Z= 0.122 Angle : 0.602 12.016 11186 Z= 0.295 Chirality : 0.042 0.263 1275 Planarity : 0.004 0.047 1424 Dihedral : 4.654 27.009 1093 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.59 % Favored : 91.31 % Rotamer: Outliers : 2.79 % Allowed : 19.51 % 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: -1.80 (0.26), residues: 1013 helix: -0.30 (0.25), residues: 413 sheet: -2.27 (0.43), residues: 132 loop : -1.62 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 378 HIS 0.005 0.001 HIS B 387 PHE 0.020 0.001 PHE A 25 TYR 0.013 0.001 TYR A 378 ARG 0.004 0.000 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.02588 ( 243) hydrogen bonds : angle 3.94054 ( 687) metal coordination : bond 0.00778 ( 4) metal coordination : angle 4.46590 ( 6) covalent geometry : bond 0.00292 ( 8253) covalent geometry : angle 0.59358 (11180) *********************** 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 123 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.824 Fit side-chains REVERT: A 102 MET cc_start: 0.9043 (ttp) cc_final: 0.8653 (ttm) REVERT: A 337 LEU cc_start: 0.8297 (mt) cc_final: 0.8066 (mp) REVERT: A 406 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7284 (mp0) REVERT: A 417 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8177 (mm) REVERT: A 847 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7845 (mmtt) REVERT: B 248 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8784 (pp) REVERT: B 314 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7640 (ttmm) REVERT: B 398 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7377 (p0) REVERT: C 50 VAL cc_start: 0.8566 (t) cc_final: 0.8289 (m) outliers start: 25 outliers final: 15 residues processed: 113 average time/residue: 0.8128 time to fit residues: 100.6986 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 : 0.903 ------------------------------------------------------------------------------- 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 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 417 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 A residue 825 LEU 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 403 LYS 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 34 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 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 = 0.3846 r_free = 0.3846 target = 0.156221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118925 restraints weight = 9231.173| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.92 r_work: 0.3230 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2240 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= 0.155 Angle : 0.632 12.152 11186 Z= 0.309 Chirality : 0.043 0.269 1275 Planarity : 0.004 0.048 1424 Dihedral : 4.722 27.088 1093 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.79 % Favored : 91.12 % Rotamer: Outliers : 2.56 % Allowed : 20.29 % 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: -1.73 (0.26), residues: 1013 helix: -0.23 (0.25), residues: 413 sheet: -2.27 (0.42), residues: 141 loop : -1.55 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 378 HIS 0.006 0.001 HIS A 678 PHE 0.020 0.001 PHE A 25 TYR 0.017 0.002 TYR A 378 ARG 0.006 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.02760 ( 243) hydrogen bonds : angle 3.98591 ( 687) metal coordination : bond 0.01181 ( 4) metal coordination : angle 4.65323 ( 6) covalent geometry : bond 0.00378 ( 8253) covalent geometry : angle 0.62247 (11180) *********************** 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 120 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.981 Fit side-chains REVERT: A 102 MET cc_start: 0.9062 (ttp) cc_final: 0.8611 (ttm) REVERT: A 337 LEU cc_start: 0.8345 (mt) cc_final: 0.8110 (mp) REVERT: A 406 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7358 (mp0) REVERT: A 417 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8205 (mm) REVERT: A 847 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7870 (mmtt) REVERT: B 248 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 314 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7669 (ttmm) REVERT: B 398 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7426 (p0) REVERT: C 50 VAL cc_start: 0.8604 (t) cc_final: 0.8337 (m) REVERT: C 154 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7286 (ttm-80) outliers start: 23 outliers final: 15 residues processed: 113 average time/residue: 0.9169 time to fit residues: 112.9814 Evaluate side-chains 110 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 417 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119170 restraints weight = 9116.909| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.92 r_work: 0.3213 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2300 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= 0.160 Angle : 0.650 12.166 11186 Z= 0.317 Chirality : 0.044 0.270 1275 Planarity : 0.004 0.047 1424 Dihedral : 4.763 27.205 1093 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.98 % Favored : 90.92 % Rotamer: Outliers : 2.79 % Allowed : 20.74 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.70 (0.26), residues: 1013 helix: -0.20 (0.25), residues: 412 sheet: -2.24 (0.42), residues: 141 loop : -1.54 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 378 HIS 0.005 0.001 HIS B 387 PHE 0.020 0.001 PHE A 25 TYR 0.017 0.002 TYR A 378 ARG 0.007 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.02759 ( 243) hydrogen bonds : angle 3.99893 ( 687) metal coordination : bond 0.01187 ( 4) metal coordination : angle 4.65402 ( 6) covalent geometry : bond 0.00390 ( 8253) covalent geometry : angle 0.64124 (11180) ********************** 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 116 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.833 Fit side-chains REVERT: A 102 MET cc_start: 0.9062 (ttp) cc_final: 0.8604 (ttm) REVERT: A 337 LEU cc_start: 0.8312 (mt) cc_final: 0.8086 (mp) REVERT: A 406 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7414 (mp0) REVERT: A 417 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8211 (mm) REVERT: A 678 HIS cc_start: 0.4733 (OUTLIER) cc_final: 0.4340 (t-90) REVERT: A 847 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7845 (mmtt) REVERT: B 248 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8755 (pp) REVERT: B 314 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7667 (ttmm) REVERT: B 398 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7444 (p0) REVERT: C 50 VAL cc_start: 0.8612 (t) cc_final: 0.8353 (m) REVERT: C 154 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7306 (ttm-80) outliers start: 25 outliers final: 15 residues processed: 108 average time/residue: 0.9241 time to fit residues: 108.6773 Evaluate side-chains 110 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 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 417 LEU 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 809 ILE Chi-restraints excluded: chain A residue 825 LEU 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 403 LYS Chi-restraints excluded: chain B residue 637 LEU 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: 2.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 chunk 94 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 87 optimal weight: 0.0570 chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 0.0670 overall best weight: 0.3534 ------------------------------------------------------------------------------- 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 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.158412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121393 restraints weight = 9172.295| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.92 r_work: 0.3248 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8257 Z= 0.119 Angle : 0.611 11.823 11186 Z= 0.299 Chirality : 0.042 0.260 1275 Planarity : 0.004 0.046 1424 Dihedral : 4.576 26.868 1093 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.59 % Favored : 91.31 % Rotamer: Outliers : 2.45 % Allowed : 21.18 % Favored : 76.37 % 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: -1.54 (0.27), residues: 1013 helix: -0.05 (0.26), residues: 413 sheet: -2.16 (0.43), residues: 132 loop : -1.50 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 378 HIS 0.005 0.001 HIS B 387 PHE 0.019 0.001 PHE A 25 TYR 0.015 0.001 TYR A 378 ARG 0.006 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.02488 ( 243) hydrogen bonds : angle 3.90635 ( 687) metal coordination : bond 0.00717 ( 4) metal coordination : angle 4.38489 ( 6) covalent geometry : bond 0.00285 ( 8253) covalent geometry : angle 0.60241 (11180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6274.38 seconds wall clock time: 109 minutes 19.28 seconds (6559.28 seconds total)