Starting phenix.real_space_refine on Sun Sep 13 06:14:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jm6_22386/09_2026/7jm6_22386_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jm6_22386/09_2026/7jm6_22386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jm6_22386/09_2026/7jm6_22386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jm6_22386/09_2026/7jm6_22386.map" model { file = "/net/cci-nas-00/data/ceres_data/7jm6_22386/09_2026/7jm6_22386_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jm6_22386/09_2026/7jm6_22386_trim.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.427 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: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 64 5.16 5 Cl 6 4.86 5 C 6810 2.51 5 N 1744 2.21 5 O 1944 1.98 5 H 10504 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21084 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 10426 Classifications: {'peptide': 667} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 639} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 10426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 10426 Classifications: {'peptide': 667} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 639} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {' CL': 3, ' MG': 1, '0J1': 1, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {' CL': 3, ' MG': 1, '0J1': 1, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Time building chain proxies: 3.74, per 1000 atoms: 0.18 Number of scatterers: 21084 At special positions: 0 Unit cell: (85.784, 116.523, 101.511, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 6 17.00 S 64 16.00 P 10 15.00 Mg 2 11.99 O 1944 8.00 N 1744 7.00 C 6810 6.00 H 10504 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.12 Conformation dependent library (CDL) restraints added in 475.5 milliseconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2452 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 67.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 115 through 165 removed outlier: 4.473A pdb=" N ILE A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 218 through 235 Processing helix chain 'A' and resid 242 through 259 removed outlier: 4.229A pdb=" N ILE A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 315 through 342 Processing helix chain 'A' and resid 368 through 402 removed outlier: 4.614A pdb=" N ILE A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 431 removed outlier: 3.707A pdb=" N ARG A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 475 Processing helix chain 'A' and resid 481 through 498 Processing helix chain 'A' and resid 508 through 531 Processing helix chain 'A' and resid 538 through 555 removed outlier: 3.598A pdb=" N TYR A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 574 through 593 removed outlier: 3.631A pdb=" N PHE A 592 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 605 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 677 through 686 Processing helix chain 'A' and resid 703 through 711 removed outlier: 3.801A pdb=" N PHE A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 711 " --> pdb=" O PHE A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 779 through 785 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 115 through 165 removed outlier: 4.473A pdb=" N ILE B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 218 through 235 Processing helix chain 'B' and resid 242 through 259 removed outlier: 4.229A pdb=" N ILE B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 297 Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 315 through 342 Processing helix chain 'B' and resid 368 through 402 removed outlier: 4.614A pdb=" N ILE B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 431 removed outlier: 3.707A pdb=" N ARG B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 475 Processing helix chain 'B' and resid 481 through 498 Processing helix chain 'B' and resid 508 through 531 Processing helix chain 'B' and resid 538 through 555 removed outlier: 3.597A pdb=" N TYR B 542 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 574 through 593 removed outlier: 3.632A pdb=" N PHE B 592 " --> pdb=" O VAL B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 605 Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 639 through 648 Processing helix chain 'B' and resid 677 through 686 Processing helix chain 'B' and resid 703 through 711 removed outlier: 3.801A pdb=" N PHE B 707 " --> pdb=" O LYS B 703 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B 710 " --> pdb=" O ASP B 706 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 711 " --> pdb=" O PHE B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 728 Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 779 through 785 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91 removed outlier: 4.057A pdb=" N GLU A 90 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA3, first strand: chain 'A' and resid 633 through 634 removed outlier: 6.547A pdb=" N PHE A 656 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU A 674 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 658 " --> pdb=" O ARG A 672 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 636 through 638 Processing sheet with id=AA5, first strand: chain 'A' and resid 743 through 745 removed outlier: 6.621A pdb=" N LEU A 765 " --> pdb=" O MET A 777 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N MET A 777 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 767 " --> pdb=" O VAL A 775 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 91 removed outlier: 4.057A pdb=" N GLU B 90 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 260 through 261 Processing sheet with id=AA8, first strand: chain 'B' and resid 633 through 634 removed outlier: 6.547A pdb=" N PHE B 656 " --> pdb=" O LEU B 674 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU B 674 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 658 " --> pdb=" O ARG B 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 636 through 638 Processing sheet with id=AB1, first strand: chain 'B' and resid 743 through 745 removed outlier: 6.620A pdb=" N LEU B 765 " --> pdb=" O MET B 777 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET B 777 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 767 " --> pdb=" O VAL B 775 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 2022 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: 4.41 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10486 1.03 - 1.23: 40 1.23 - 1.42: 4450 1.42 - 1.62: 6158 1.62 - 1.81: 116 Bond restraints: 21250 Sorted by residual: bond pdb=" C4 ATP B 901 " pdb=" C5 ATP B 901 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.71e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.59e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.72e+01 bond pdb=" C5 ATP B 901 " pdb=" C6 ATP B 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C8 ATP A 901 " pdb=" N7 ATP A 901 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.33e+01 ... (remaining 21245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 38228 3.73 - 7.47: 124 7.47 - 11.20: 14 11.20 - 14.93: 4 14.93 - 18.67: 4 Bond angle restraints: 38374 Sorted by residual: angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 121.20 18.67 1.00e+00 1.00e+00 3.48e+02 angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 121.26 18.61 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 120.40 16.43 1.00e+00 1.00e+00 2.70e+02 angle pdb=" PA ATP B 901 " pdb=" O3A ATP B 901 " pdb=" PB ATP B 901 " ideal model delta sigma weight residual 136.83 120.43 16.40 1.00e+00 1.00e+00 2.69e+02 angle pdb=" C5 ATP B 901 " pdb=" C4 ATP B 901 " pdb=" N3 ATP B 901 " ideal model delta sigma weight residual 126.80 119.28 7.52 1.00e+00 1.00e+00 5.65e+01 ... (remaining 38369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9193 17.93 - 35.87: 593 35.87 - 53.80: 231 53.80 - 71.73: 75 71.73 - 89.67: 14 Dihedral angle restraints: 10106 sinusoidal: 5492 harmonic: 4614 Sorted by residual: dihedral pdb=" CA ILE A 213 " pdb=" C ILE A 213 " pdb=" N PRO A 214 " pdb=" CA PRO A 214 " ideal model delta harmonic sigma weight residual -180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ILE B 213 " pdb=" C ILE B 213 " pdb=" N PRO B 214 " pdb=" CA PRO B 214 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA PHE A 473 " pdb=" C PHE A 473 " pdb=" N HIS A 474 " pdb=" CA HIS A 474 " ideal model delta harmonic sigma weight residual -180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 10103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1385 0.051 - 0.102: 244 0.102 - 0.152: 47 0.152 - 0.203: 4 0.203 - 0.254: 2 Chirality restraints: 1682 Sorted by residual: chirality pdb=" C14 0J1 B 906 " pdb=" C13 0J1 B 906 " pdb=" C15 0J1 B 906 " pdb=" O36 0J1 B 906 " both_signs ideal model delta sigma weight residual False 2.26 2.52 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C14 0J1 A 906 " pdb=" C13 0J1 A 906 " pdb=" C15 0J1 A 906 " pdb=" O36 0J1 A 906 " both_signs ideal model delta sigma weight residual False 2.26 2.51 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C2' ATP A 901 " pdb=" C1' ATP A 901 " pdb=" C3' ATP A 901 " pdb=" O2' ATP A 901 " both_signs ideal model delta sigma weight residual False -2.68 -2.52 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1679 not shown) Planarity restraints: 3078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 364 " 0.027 2.00e-02 2.50e+03 5.41e-02 2.93e+01 pdb=" C GLY A 364 " -0.094 2.00e-02 2.50e+03 pdb=" O GLY A 364 " 0.035 2.00e-02 2.50e+03 pdb=" N TYR A 365 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 364 " -0.027 2.00e-02 2.50e+03 5.38e-02 2.89e+01 pdb=" C GLY B 364 " 0.093 2.00e-02 2.50e+03 pdb=" O GLY B 364 " -0.035 2.00e-02 2.50e+03 pdb=" N TYR B 365 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 191 " -0.019 2.00e-02 2.50e+03 1.53e-02 7.00e+00 pdb=" CG PHE B 191 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 191 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 191 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 191 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 191 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 191 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE B 191 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE B 191 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 191 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE B 191 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE B 191 " 0.001 2.00e-02 2.50e+03 ... (remaining 3075 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 165 2.05 - 2.68: 32295 2.68 - 3.32: 64510 3.32 - 3.96: 82983 3.96 - 4.60: 130869 Nonbonded interactions: 310822 Sorted by model distance: nonbonded pdb="HH12 ARG A 752 " pdb=" O SER B 740 " model vdw 1.408 2.450 nonbonded pdb=" O SER A 740 " pdb="HH12 ARG B 752 " model vdw 1.411 2.450 nonbonded pdb=" O MET A 363 " pdb=" HH TYR A 574 " model vdw 1.589 2.450 nonbonded pdb=" O MET B 363 " pdb=" HH TYR B 574 " model vdw 1.589 2.450 nonbonded pdb=" O SER A 86 " pdb=" HZ1 LYS A 781 " model vdw 1.616 2.450 ... (remaining 310817 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 5.020 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: 0.170 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.660 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.006 0.096 10746 Z= 0.317 Angle : 0.857 18.667 14596 Z= 0.544 Chirality : 0.041 0.254 1682 Planarity : 0.005 0.054 1804 Dihedral : 14.271 89.669 3962 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.72 % Allowed : 0.36 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.22), residues: 1322 helix: 1.80 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -0.75 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 638 TYR 0.009 0.001 TYR A 365 PHE 0.045 0.002 PHE B 191 TRP 0.019 0.002 TRP B 519 HIS 0.017 0.002 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.32 (10746) covalent geometry : angle 0.85710 / 0.54 (14596) hydrogen bonds : bond 0.14232 / 9.44 ( 680) hydrogen bonds : angle 6.74866 / 4.92 ( 2022) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.6598 (mtm110) cc_final: 0.6362 (mtm-85) REVERT: B 108 ARG cc_start: 0.6624 (mtm110) cc_final: 0.6387 (mtm-85) REVERT: B 376 MET cc_start: 0.8853 (mtm) cc_final: 0.8612 (mtm) outliers start: 8 outliers final: 0 residues processed: 186 average time/residue: 0.9880 time to fit residues: 202.5553 Evaluate side-chains 150 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.142425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.123036 restraints weight = 34973.700| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.45 r_work: 0.3154 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.003 0.041 10746 Z= 0.154 Angle : 0.548 5.359 14596 Z= 0.298 Chirality : 0.041 0.242 1682 Planarity : 0.005 0.040 1804 Dihedral : 10.685 88.130 1634 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.62 % Allowed : 6.91 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.22), residues: 1322 helix: 2.36 (0.17), residues: 840 sheet: None (None), residues: 0 loop : -0.72 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 780 TYR 0.009 0.001 TYR B 340 PHE 0.022 0.001 PHE A 324 TRP 0.018 0.001 TRP B 519 HIS 0.003 0.001 HIS B 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (10746) covalent geometry : angle 0.54765 / 0.30 (14596) hydrogen bonds : bond 0.05574 / 3.74 ( 680) hydrogen bonds : angle 4.62385 / 3.34 ( 2022) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 LYS cc_start: 0.7829 (mttm) cc_final: 0.7566 (mttp) REVERT: B 266 ARG cc_start: 0.7660 (ttp-170) cc_final: 0.7315 (ttm110) REVERT: B 467 LYS cc_start: 0.7868 (mttm) cc_final: 0.7531 (mtmt) outliers start: 18 outliers final: 9 residues processed: 177 average time/residue: 1.0140 time to fit residues: 197.8301 Evaluate side-chains 163 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 744 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 391 ASN B 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.138441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.118610 restraints weight = 34904.616| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.46 r_work: 0.3105 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10746 Z= 0.187 Angle : 0.536 6.380 14596 Z= 0.291 Chirality : 0.041 0.251 1682 Planarity : 0.005 0.041 1804 Dihedral : 10.216 85.954 1634 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.89 % Allowed : 8.80 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.22), residues: 1322 helix: 2.30 (0.17), residues: 842 sheet: None (None), residues: 0 loop : -0.91 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 785 TYR 0.009 0.001 TYR B 542 PHE 0.016 0.001 PHE B 576 TRP 0.016 0.002 TRP B 519 HIS 0.003 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (10746) covalent geometry : angle 0.53565 / 0.29 (14596) hydrogen bonds : bond 0.05779 / 3.87 ( 680) hydrogen bonds : angle 4.45946 / 3.21 ( 2022) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.5942 (ttmp) cc_final: 0.5704 (ttmp) REVERT: A 467 LYS cc_start: 0.7878 (mttm) cc_final: 0.7632 (mttp) REVERT: A 685 LYS cc_start: 0.7753 (tttt) cc_final: 0.7511 (tttp) REVERT: A 747 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: B 269 LYS cc_start: 0.8093 (mmmm) cc_final: 0.7390 (mmtt) REVERT: B 466 GLU cc_start: 0.8074 (mp0) cc_final: 0.7524 (mp0) REVERT: B 467 LYS cc_start: 0.7928 (mttm) cc_final: 0.7590 (mtmt) REVERT: B 685 LYS cc_start: 0.7757 (tttt) cc_final: 0.7485 (tttp) REVERT: B 747 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7218 (mp0) outliers start: 21 outliers final: 11 residues processed: 193 average time/residue: 1.0648 time to fit residues: 226.0569 Evaluate side-chains 191 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 627 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 747 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.139099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.119320 restraints weight = 35122.847| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.47 r_work: 0.3115 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10746 Z= 0.147 Angle : 0.507 5.628 14596 Z= 0.274 Chirality : 0.039 0.216 1682 Planarity : 0.005 0.042 1804 Dihedral : 10.044 82.536 1634 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.71 % Allowed : 10.59 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.22), residues: 1322 helix: 2.38 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -0.88 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 752 TYR 0.007 0.001 TYR B 542 PHE 0.015 0.001 PHE A 324 TRP 0.017 0.001 TRP B 519 HIS 0.003 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (10746) covalent geometry : angle 0.50722 / 0.27 (14596) hydrogen bonds : bond 0.05205 / 3.49 ( 680) hydrogen bonds : angle 4.32622 / 3.12 ( 2022) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.5961 (ttmp) cc_final: 0.5749 (ttmp) REVERT: A 467 LYS cc_start: 0.7908 (mttm) cc_final: 0.7657 (mttp) REVERT: A 747 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: B 309 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8417 (mp0) REVERT: B 466 GLU cc_start: 0.8107 (mp0) cc_final: 0.7553 (mp0) REVERT: B 467 LYS cc_start: 0.7922 (mttm) cc_final: 0.7587 (mtmt) REVERT: B 685 LYS cc_start: 0.7736 (tttt) cc_final: 0.7462 (tttp) REVERT: B 747 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7208 (mp0) outliers start: 19 outliers final: 11 residues processed: 183 average time/residue: 0.9724 time to fit residues: 196.5415 Evaluate side-chains 184 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 747 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.137102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.117449 restraints weight = 35213.576| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.46 r_work: 0.3085 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10746 Z= 0.193 Angle : 0.535 5.735 14596 Z= 0.289 Chirality : 0.041 0.231 1682 Planarity : 0.005 0.045 1804 Dihedral : 10.263 86.004 1634 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.80 % Allowed : 11.40 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.22), residues: 1322 helix: 2.30 (0.17), residues: 842 sheet: None (None), residues: 0 loop : -0.96 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 727 TYR 0.009 0.001 TYR A 542 PHE 0.015 0.001 PHE B 324 TRP 0.016 0.002 TRP A 519 HIS 0.003 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (10746) covalent geometry : angle 0.53542 / 0.29 (14596) hydrogen bonds : bond 0.05497 / 3.68 ( 680) hydrogen bonds : angle 4.32965 / 3.11 ( 2022) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 LYS cc_start: 0.7876 (mttm) cc_final: 0.7645 (mttp) REVERT: A 685 LYS cc_start: 0.7837 (tttt) cc_final: 0.7568 (tttp) REVERT: A 747 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: B 155 LYS cc_start: 0.6016 (ttmp) cc_final: 0.5775 (ttmp) REVERT: B 269 LYS cc_start: 0.8100 (mmmm) cc_final: 0.7396 (mmtt) REVERT: B 466 GLU cc_start: 0.8091 (mp0) cc_final: 0.7561 (mp0) REVERT: B 467 LYS cc_start: 0.7927 (mttm) cc_final: 0.7576 (mtmm) REVERT: B 685 LYS cc_start: 0.7856 (tttt) cc_final: 0.7560 (tttp) REVERT: B 747 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7290 (mp0) outliers start: 20 outliers final: 10 residues processed: 183 average time/residue: 1.0536 time to fit residues: 212.8785 Evaluate side-chains 183 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 747 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 76 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.137762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.117948 restraints weight = 35266.587| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.47 r_work: 0.3096 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10746 Z= 0.159 Angle : 0.515 6.009 14596 Z= 0.277 Chirality : 0.039 0.214 1682 Planarity : 0.005 0.044 1804 Dihedral : 10.230 87.977 1634 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.80 % Allowed : 11.94 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.22), residues: 1322 helix: 2.39 (0.17), residues: 842 sheet: None (None), residues: 0 loop : -0.92 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 260 TYR 0.007 0.001 TYR A 542 PHE 0.015 0.001 PHE B 324 TRP 0.016 0.001 TRP B 519 HIS 0.003 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (10746) covalent geometry : angle 0.51534 / 0.28 (14596) hydrogen bonds : bond 0.05193 / 3.48 ( 680) hydrogen bonds : angle 4.24791 / 3.06 ( 2022) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 TRP cc_start: 0.7428 (t60) cc_final: 0.7117 (t-100) REVERT: A 467 LYS cc_start: 0.7885 (mttm) cc_final: 0.7653 (mttp) REVERT: A 685 LYS cc_start: 0.7821 (tttt) cc_final: 0.7555 (tttp) REVERT: A 747 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: B 269 LYS cc_start: 0.8075 (mmmm) cc_final: 0.7383 (mmtt) REVERT: B 309 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: B 467 LYS cc_start: 0.7944 (mttm) cc_final: 0.7591 (mtmm) REVERT: B 685 LYS cc_start: 0.7761 (tttt) cc_final: 0.7502 (tttp) REVERT: B 747 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7251 (mp0) outliers start: 20 outliers final: 10 residues processed: 183 average time/residue: 1.0552 time to fit residues: 213.3847 Evaluate side-chains 186 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 747 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.138245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.118474 restraints weight = 35168.166| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.47 r_work: 0.3106 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10746 Z= 0.145 Angle : 0.508 6.051 14596 Z= 0.272 Chirality : 0.039 0.204 1682 Planarity : 0.005 0.044 1804 Dihedral : 10.247 89.565 1634 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.62 % Allowed : 12.57 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.22), residues: 1322 helix: 2.48 (0.17), residues: 842 sheet: None (None), residues: 0 loop : -0.91 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 260 TYR 0.010 0.001 TYR A 151 PHE 0.015 0.001 PHE A 324 TRP 0.016 0.001 TRP A 519 HIS 0.003 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (10746) covalent geometry : angle 0.50797 / 0.27 (14596) hydrogen bonds : bond 0.05030 / 3.36 ( 680) hydrogen bonds : angle 4.20710 / 3.03 ( 2022) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 TRP cc_start: 0.7437 (t60) cc_final: 0.7096 (t-100) REVERT: A 401 TYR cc_start: 0.7894 (m-80) cc_final: 0.7523 (m-80) REVERT: A 467 LYS cc_start: 0.7885 (mttm) cc_final: 0.7651 (mttp) REVERT: A 685 LYS cc_start: 0.7789 (tttt) cc_final: 0.7526 (tttp) REVERT: A 747 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: B 269 LYS cc_start: 0.8049 (mmmm) cc_final: 0.7354 (mmtt) REVERT: B 309 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: B 467 LYS cc_start: 0.7933 (mttm) cc_final: 0.7576 (mtmm) REVERT: B 685 LYS cc_start: 0.7756 (tttt) cc_final: 0.7495 (tttp) REVERT: B 747 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7218 (mp0) outliers start: 18 outliers final: 10 residues processed: 181 average time/residue: 0.9718 time to fit residues: 194.9185 Evaluate side-chains 185 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 747 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.136777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.117205 restraints weight = 35091.715| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.46 r_work: 0.3090 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10746 Z= 0.181 Angle : 0.535 6.452 14596 Z= 0.288 Chirality : 0.040 0.221 1682 Planarity : 0.005 0.044 1804 Dihedral : 10.246 82.788 1634 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.24 % Allowed : 12.21 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.22), residues: 1322 helix: 2.37 (0.17), residues: 842 sheet: None (None), residues: 0 loop : -0.93 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 260 TYR 0.010 0.001 TYR B 151 PHE 0.015 0.001 PHE A 324 TRP 0.015 0.002 TRP A 519 HIS 0.003 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (10746) covalent geometry : angle 0.53476 / 0.29 (14596) hydrogen bonds : bond 0.05317 / 3.56 ( 680) hydrogen bonds : angle 4.24457 / 3.05 ( 2022) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 TRP cc_start: 0.7506 (t60) cc_final: 0.7133 (t-100) REVERT: A 401 TYR cc_start: 0.7896 (m-80) cc_final: 0.7538 (m-80) REVERT: A 467 LYS cc_start: 0.7894 (mttm) cc_final: 0.7661 (mttp) REVERT: A 685 LYS cc_start: 0.7784 (tttt) cc_final: 0.7512 (tttp) REVERT: A 747 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: B 269 LYS cc_start: 0.8042 (mmmm) cc_final: 0.7362 (mmtt) REVERT: B 309 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: B 466 GLU cc_start: 0.8084 (mp0) cc_final: 0.7572 (mp0) REVERT: B 467 LYS cc_start: 0.7924 (mttm) cc_final: 0.7699 (mttp) REVERT: B 685 LYS cc_start: 0.7767 (tttt) cc_final: 0.7447 (ttmm) REVERT: B 747 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7275 (mp0) outliers start: 25 outliers final: 11 residues processed: 186 average time/residue: 0.9800 time to fit residues: 202.6971 Evaluate side-chains 184 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 747 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.137926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.118215 restraints weight = 35102.189| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.47 r_work: 0.3097 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10746 Z= 0.148 Angle : 0.517 6.514 14596 Z= 0.276 Chirality : 0.039 0.205 1682 Planarity : 0.005 0.044 1804 Dihedral : 9.906 72.650 1634 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.53 % Allowed : 13.11 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.22), residues: 1322 helix: 2.47 (0.17), residues: 842 sheet: None (None), residues: 0 loop : -0.93 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 260 TYR 0.011 0.001 TYR A 151 PHE 0.016 0.001 PHE A 324 TRP 0.017 0.001 TRP B 519 HIS 0.003 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (10746) covalent geometry : angle 0.51686 / 0.28 (14596) hydrogen bonds : bond 0.05047 / 3.38 ( 680) hydrogen bonds : angle 4.19529 / 3.02 ( 2022) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.5907 (ttmp) cc_final: 0.5601 (ttmp) REVERT: A 174 TRP cc_start: 0.7474 (t60) cc_final: 0.7093 (t-100) REVERT: A 401 TYR cc_start: 0.7871 (m-80) cc_final: 0.7514 (m-80) REVERT: A 467 LYS cc_start: 0.7883 (mttm) cc_final: 0.7653 (mttp) REVERT: A 685 LYS cc_start: 0.7755 (tttt) cc_final: 0.7491 (tttp) REVERT: A 747 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: B 266 ARG cc_start: 0.7505 (tpp-160) cc_final: 0.7229 (ttm110) REVERT: B 269 LYS cc_start: 0.8032 (mmmm) cc_final: 0.7367 (mmtt) REVERT: B 309 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: B 467 LYS cc_start: 0.7931 (mttm) cc_final: 0.7710 (mttp) REVERT: B 685 LYS cc_start: 0.7703 (tttt) cc_final: 0.7372 (ttmm) REVERT: B 747 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7254 (mp0) outliers start: 17 outliers final: 13 residues processed: 178 average time/residue: 0.9720 time to fit residues: 192.0571 Evaluate side-chains 185 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 747 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 77 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.139587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.119895 restraints weight = 35335.826| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.47 r_work: 0.3123 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10746 Z= 0.116 Angle : 0.492 6.582 14596 Z= 0.262 Chirality : 0.039 0.177 1682 Planarity : 0.005 0.044 1804 Dihedral : 9.255 61.344 1634 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.26 % Allowed : 13.46 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.23), residues: 1322 helix: 2.67 (0.17), residues: 842 sheet: None (None), residues: 0 loop : -0.86 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 260 TYR 0.011 0.001 TYR B 151 PHE 0.013 0.001 PHE A 324 TRP 0.017 0.001 TRP A 519 HIS 0.004 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (10746) covalent geometry : angle 0.49210 / 0.26 (14596) hydrogen bonds : bond 0.04605 / 3.08 ( 680) hydrogen bonds : angle 4.10561 / 2.97 ( 2022) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 TRP cc_start: 0.7427 (t60) cc_final: 0.7066 (t-100) REVERT: A 401 TYR cc_start: 0.7880 (m-80) cc_final: 0.7522 (m-80) REVERT: A 404 ARG cc_start: 0.6775 (ttt180) cc_final: 0.6203 (ttm-80) REVERT: A 466 GLU cc_start: 0.8056 (mp0) cc_final: 0.7540 (mp0) REVERT: A 467 LYS cc_start: 0.7866 (mttm) cc_final: 0.7642 (mttp) REVERT: A 747 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: B 155 LYS cc_start: 0.5867 (ttmp) cc_final: 0.5481 (ttmp) REVERT: B 266 ARG cc_start: 0.7572 (tpp-160) cc_final: 0.7296 (ttm110) REVERT: B 269 LYS cc_start: 0.7995 (mmmm) cc_final: 0.7357 (mmtt) REVERT: B 309 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: B 392 TYR cc_start: 0.8554 (t80) cc_final: 0.7922 (t80) REVERT: B 404 ARG cc_start: 0.6772 (ttt180) cc_final: 0.6233 (ttm-80) REVERT: B 467 LYS cc_start: 0.7918 (mttm) cc_final: 0.7698 (mttp) REVERT: B 685 LYS cc_start: 0.7668 (tttt) cc_final: 0.7341 (ttmm) REVERT: B 747 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: B 785 ARG cc_start: 0.8241 (ptp-170) cc_final: 0.7934 (ptt180) outliers start: 14 outliers final: 9 residues processed: 188 average time/residue: 1.0005 time to fit residues: 207.6504 Evaluate side-chains 188 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 320 TRP Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 320 TRP Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 747 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 65 optimal weight: 0.0070 chunk 100 optimal weight: 0.6980 chunk 131 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.139099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.119324 restraints weight = 35378.881| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.48 r_work: 0.3114 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10746 Z= 0.130 Angle : 0.501 6.379 14596 Z= 0.266 Chirality : 0.039 0.183 1682 Planarity : 0.005 0.050 1804 Dihedral : 9.175 58.572 1634 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.90 % Allowed : 14.00 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.23), residues: 1322 helix: 2.71 (0.17), residues: 842 sheet: None (None), residues: 0 loop : -0.85 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 635 TYR 0.009 0.001 TYR A 151 PHE 0.015 0.001 PHE B 324 TRP 0.016 0.001 TRP B 519 HIS 0.003 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10746) covalent geometry : angle 0.50110 / 0.27 (14596) hydrogen bonds : bond 0.04696 / 3.14 ( 680) hydrogen bonds : angle 4.09069 / 2.96 ( 2022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6664.18 seconds wall clock time: 113 minutes 49.15 seconds (6829.15 seconds total)