Starting phenix.real_space_refine on Sat Jul 4 14:10:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jm6_22386/07_2026/7jm6_22386_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jm6_22386/07_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_22386/07_2026/7jm6_22386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jm6_22386/07_2026/7jm6_22386.map" model { file = "/net/cci-nas-00/data/ceres_data/7jm6_22386/07_2026/7jm6_22386_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jm6_22386/07_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-dev-6108/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, 77 Ad-hoc single atom residues: {' CL': 3} Unusual residues: {' MG': 1, '0J1': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 3 Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 77 Ad-hoc single atom residues: {' CL': 3} Unusual residues: {' MG': 1, '0J1': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 3 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: 3.79, 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: 2.21 Conformation dependent library (CDL) restraints added in 564.8 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: 0.48 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: 5.05 Time building geometry restraints manager: 2.94 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: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.470 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.340 ------------------------------------------------------------------------------- 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 : 0.470 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: 0.9821 time to fit residues: 201.1532 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 : 0.523 ------------------------------------------------------------------------------- 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: 0.0060 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.142953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.123572 restraints weight = 34934.225| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.46 r_work: 0.3163 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10746 Z= 0.144 Angle : 0.536 5.272 14596 Z= 0.292 Chirality : 0.040 0.213 1682 Planarity : 0.005 0.040 1804 Dihedral : 10.632 88.726 1634 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.53 % Allowed : 7.00 % 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: 1.96 (0.22), residues: 1322 helix: 2.37 (0.17), residues: 840 sheet: None (None), residues: 0 loop : -0.68 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 404 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 A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10746) covalent geometry : angle 0.53638 / 0.29 (14596) hydrogen bonds : bond 0.05641 / 3.78 ( 680) hydrogen bonds : angle 4.67488 / 3.38 ( 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 186 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 LYS cc_start: 0.7825 (mttm) cc_final: 0.7552 (mttp) REVERT: B 144 GLU cc_start: 0.7891 (tt0) cc_final: 0.7680 (mm-30) REVERT: B 266 ARG cc_start: 0.7623 (ttp-170) cc_final: 0.7271 (ttm110) REVERT: B 467 LYS cc_start: 0.7848 (mttm) cc_final: 0.7511 (mtmt) outliers start: 17 outliers final: 8 residues processed: 176 average time/residue: 0.9498 time to fit residues: 183.8974 Evaluate side-chains 165 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 112 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.137833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.117979 restraints weight = 34871.868| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.46 r_work: 0.3096 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 : 0.005 0.052 10746 Z= 0.207 Angle : 0.551 6.455 14596 Z= 0.300 Chirality : 0.042 0.252 1682 Planarity : 0.005 0.041 1804 Dihedral : 10.350 87.142 1634 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.06 % Allowed : 8.80 % Favored : 89.14 % 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: 1.74 (0.22), residues: 1322 helix: 2.26 (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 0.004 0.001 ARG A 785 TYR 0.010 0.002 TYR A 542 PHE 0.017 0.002 PHE B 576 TRP 0.016 0.002 TRP B 519 HIS 0.004 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (10746) covalent geometry : angle 0.55112 / 0.30 (14596) hydrogen bonds : bond 0.05874 / 3.93 ( 680) hydrogen bonds : angle 4.47994 / 3.23 ( 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 205 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.628 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: symmetry clash REVERT: A 155 LYS cc_start: 0.5979 (ttmp) cc_final: 0.5738 (ttmp) REVERT: A 467 LYS cc_start: 0.7886 (mttm) cc_final: 0.7642 (mttp) REVERT: A 685 LYS cc_start: 0.7750 (tttt) cc_final: 0.7512 (tttp) REVERT: B 144 GLU cc_start: 0.7994 (tt0) cc_final: 0.7742 (mm-30) REVERT: B 466 GLU cc_start: 0.8095 (mp0) cc_final: 0.7545 (mp0) REVERT: B 467 LYS cc_start: 0.7936 (mttm) cc_final: 0.7615 (mtmt) REVERT: B 685 LYS cc_start: 0.7748 (tttt) cc_final: 0.7491 (tttp) REVERT: B 747 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7260 (mp0) outliers start: 23 outliers final: 12 residues processed: 190 average time/residue: 1.0492 time to fit residues: 218.4340 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 : 0.552 ------------------------------------------------------------------------------- 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 627 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 127 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: 0.0980 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 115 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.139875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.120067 restraints weight = 35071.279| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.48 r_work: 0.3126 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10746 Z= 0.130 Angle : 0.492 5.640 14596 Z= 0.266 Chirality : 0.039 0.207 1682 Planarity : 0.005 0.042 1804 Dihedral : 9.952 81.276 1634 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.08 % Allowed : 10.59 % Favored : 88.33 % 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: 1.94 (0.22), residues: 1322 helix: 2.43 (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 B 260 TYR 0.006 0.001 TYR B 542 PHE 0.014 0.001 PHE B 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 0.00279 / 0.13 (10746) covalent geometry : angle 0.49205 / 0.27 (14596) hydrogen bonds : bond 0.05050 / 3.38 ( 680) hydrogen bonds : angle 4.30368 / 3.11 ( 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 193 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.574 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: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.5964 (ttmp) cc_final: 0.5745 (ttmp) REVERT: A 467 LYS cc_start: 0.7903 (mttm) cc_final: 0.7653 (mttp) REVERT: B 144 GLU cc_start: 0.8002 (tt0) cc_final: 0.7776 (mm-30) REVERT: B 466 GLU cc_start: 0.8117 (mp0) cc_final: 0.7547 (mp0) REVERT: B 490 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7270 (mt) REVERT: B 747 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7197 (mp0) outliers start: 12 outliers final: 7 residues processed: 183 average time/residue: 0.8872 time to fit residues: 179.2819 Evaluate side-chains 180 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 B residue 320 TRP Chi-restraints excluded: chain B residue 490 LEU 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=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: 3.9990 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 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: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.136358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.116558 restraints weight = 35051.748| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.47 r_work: 0.3076 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10746 Z= 0.224 Angle : 0.564 5.899 14596 Z= 0.304 Chirality : 0.042 0.239 1682 Planarity : 0.005 0.045 1804 Dihedral : 10.437 87.691 1634 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.33 % Allowed : 10.95 % Favored : 86.71 % 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: 1.65 (0.22), residues: 1322 helix: 2.20 (0.17), residues: 842 sheet: None (None), residues: 0 loop : -0.98 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 260 TYR 0.010 0.001 TYR B 542 PHE 0.015 0.001 PHE B 576 TRP 0.016 0.002 TRP A 519 HIS 0.004 0.001 HIS B 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 (10746) covalent geometry : angle 0.56392 / 0.30 (14596) hydrogen bonds : bond 0.05755 / 3.86 ( 680) hydrogen bonds : angle 4.37134 / 3.14 ( 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 200 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 LYS cc_start: 0.7881 (mttm) cc_final: 0.7646 (mttp) REVERT: A 685 LYS cc_start: 0.7882 (tttt) cc_final: 0.7592 (tttp) REVERT: A 747 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: B 269 LYS cc_start: 0.8082 (mmmm) cc_final: 0.7385 (mmtt) REVERT: B 466 GLU cc_start: 0.8137 (mp0) cc_final: 0.7619 (mp0) REVERT: B 467 LYS cc_start: 0.7941 (mttm) cc_final: 0.7594 (mtmm) REVERT: B 685 LYS cc_start: 0.7848 (tttt) cc_final: 0.7565 (tttp) REVERT: B 747 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7345 (mp0) outliers start: 26 outliers final: 13 residues processed: 185 average time/residue: 0.9777 time to fit residues: 199.6833 Evaluate side-chains 183 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 740 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 527 LEU Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 740 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: 0.9990 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.137795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.118053 restraints weight = 35233.759| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.47 r_work: 0.3098 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10746 Z= 0.157 Angle : 0.518 5.952 14596 Z= 0.279 Chirality : 0.040 0.216 1682 Planarity : 0.005 0.045 1804 Dihedral : 10.314 89.633 1634 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.44 % Allowed : 12.39 % Favored : 86.18 % 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: 1.78 (0.22), residues: 1322 helix: 2.32 (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 0.004 0.000 ARG A 260 TYR 0.008 0.001 TYR B 542 PHE 0.015 0.001 PHE B 324 TRP 0.016 0.001 TRP B 519 HIS 0.003 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (10746) covalent geometry : angle 0.51834 / 0.28 (14596) hydrogen bonds : bond 0.05217 / 3.49 ( 680) hydrogen bonds : angle 4.26692 / 3.07 ( 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 189 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 TYR cc_start: 0.7922 (m-80) cc_final: 0.7558 (m-80) REVERT: A 467 LYS cc_start: 0.7887 (mttm) cc_final: 0.7655 (mttp) REVERT: A 685 LYS cc_start: 0.7817 (tttt) cc_final: 0.7556 (tttp) REVERT: B 269 LYS cc_start: 0.8046 (mmmm) cc_final: 0.7371 (mmtt) REVERT: B 467 LYS cc_start: 0.7933 (mttm) cc_final: 0.7586 (mtmm) REVERT: B 685 LYS cc_start: 0.7814 (tttt) cc_final: 0.7490 (ttmm) REVERT: B 747 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7286 (mp0) outliers start: 16 outliers final: 11 residues processed: 180 average time/residue: 1.0210 time to fit residues: 202.8644 Evaluate side-chains 182 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 B residue 320 TRP Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 602 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 674 LEU 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: 0.9990 chunk 78 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 123 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 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 = 0.3442 r_free = 0.3442 target = 0.138260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.118547 restraints weight = 35189.345| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.47 r_work: 0.3107 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2514 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= 0.141 Angle : 0.509 6.138 14596 Z= 0.273 Chirality : 0.039 0.204 1682 Planarity : 0.005 0.044 1804 Dihedral : 10.262 89.903 1634 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.89 % Allowed : 12.12 % Favored : 86.00 % 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: 1.94 (0.22), residues: 1322 helix: 2.46 (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 0.004 0.000 ARG B 260 TYR 0.010 0.001 TYR A 151 PHE 0.016 0.001 PHE B 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 0.00317 / 0.14 (10746) covalent geometry : angle 0.50881 / 0.27 (14596) hydrogen bonds : bond 0.05018 / 3.36 ( 680) hydrogen bonds : angle 4.21096 / 3.04 ( 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 196 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 TYR cc_start: 0.7896 (m-80) cc_final: 0.7535 (m-80) REVERT: A 467 LYS cc_start: 0.7889 (mttm) cc_final: 0.7656 (mttp) REVERT: A 685 LYS cc_start: 0.7793 (tttt) cc_final: 0.7536 (tttp) REVERT: A 747 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: B 269 LYS cc_start: 0.8038 (mmmm) cc_final: 0.7368 (mmtt) REVERT: B 309 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: B 467 LYS cc_start: 0.7944 (mttm) cc_final: 0.7592 (mtmm) REVERT: B 685 LYS cc_start: 0.7798 (tttt) cc_final: 0.7477 (ttmm) REVERT: B 747 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7220 (mp0) outliers start: 21 outliers final: 10 residues processed: 184 average time/residue: 0.8559 time to fit residues: 174.9031 Evaluate side-chains 187 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 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 731 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 747 GLU 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: 2.9990 chunk 76 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.137209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.117667 restraints weight = 35049.650| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.46 r_work: 0.3098 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10746 Z= 0.175 Angle : 0.531 6.514 14596 Z= 0.285 Chirality : 0.040 0.217 1682 Planarity : 0.005 0.044 1804 Dihedral : 10.130 79.482 1634 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.97 % Allowed : 12.39 % Favored : 85.64 % 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: 1.85 (0.22), residues: 1322 helix: 2.38 (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 0.005 0.001 ARG B 260 TYR 0.009 0.001 TYR B 151 PHE 0.014 0.001 PHE B 324 TRP 0.016 0.002 TRP A 519 HIS 0.003 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (10746) covalent geometry : angle 0.53140 / 0.28 (14596) hydrogen bonds : bond 0.05240 / 3.51 ( 680) hydrogen bonds : angle 4.23301 / 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 197 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 TYR cc_start: 0.7934 (m-80) cc_final: 0.7581 (m-80) REVERT: A 467 LYS cc_start: 0.7891 (mttm) cc_final: 0.7656 (mttp) REVERT: A 685 LYS cc_start: 0.7788 (tttt) cc_final: 0.7528 (tttp) REVERT: A 747 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: B 309 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: B 467 LYS cc_start: 0.7918 (mttm) cc_final: 0.7700 (mttp) REVERT: B 685 LYS cc_start: 0.7756 (tttt) cc_final: 0.7437 (ttmm) REVERT: B 747 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7309 (mp0) outliers start: 22 outliers final: 11 residues processed: 184 average time/residue: 0.9034 time to fit residues: 184.0880 Evaluate side-chains 187 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.137618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.118101 restraints weight = 35023.799| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.46 r_work: 0.3098 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10746 Z= 0.156 Angle : 0.524 6.670 14596 Z= 0.280 Chirality : 0.040 0.209 1682 Planarity : 0.005 0.044 1804 Dihedral : 9.917 71.594 1634 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.44 % Allowed : 13.11 % Favored : 85.46 % 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: 1.89 (0.22), residues: 1322 helix: 2.43 (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 0.004 0.000 ARG A 260 TYR 0.011 0.001 TYR A 151 PHE 0.014 0.001 PHE B 324 TRP 0.016 0.001 TRP B 519 HIS 0.003 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (10746) covalent geometry : angle 0.52417 / 0.28 (14596) hydrogen bonds : bond 0.05100 / 3.41 ( 680) hydrogen bonds : angle 4.21131 / 3.04 ( 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 191 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.482 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: 0.5888 (ttmp) cc_final: 0.5530 (ttmp) REVERT: A 401 TYR cc_start: 0.7916 (m-80) cc_final: 0.7557 (m-80) REVERT: A 467 LYS cc_start: 0.7880 (mttm) cc_final: 0.7648 (mttp) REVERT: A 685 LYS cc_start: 0.7774 (tttt) cc_final: 0.7510 (tttp) REVERT: A 747 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: B 266 ARG cc_start: 0.7549 (tpp-160) cc_final: 0.7232 (ttp-170) REVERT: B 309 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: B 467 LYS cc_start: 0.7911 (mttm) cc_final: 0.7690 (mttp) REVERT: B 685 LYS cc_start: 0.7688 (tttt) cc_final: 0.7366 (ttmm) REVERT: B 747 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7278 (mp0) outliers start: 16 outliers final: 12 residues processed: 182 average time/residue: 0.8939 time to fit residues: 180.6960 Evaluate side-chains 185 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 77 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN B 258 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.138714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.119139 restraints weight = 35332.662| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.46 r_work: 0.3110 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2757 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= 0.128 Angle : 0.505 6.685 14596 Z= 0.269 Chirality : 0.039 0.188 1682 Planarity : 0.005 0.044 1804 Dihedral : 9.425 62.401 1634 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.53 % Allowed : 13.20 % 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: 2.06 (0.23), residues: 1322 helix: 2.57 (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 B 260 TYR 0.010 0.001 TYR B 151 PHE 0.014 0.001 PHE B 324 TRP 0.017 0.001 TRP B 519 HIS 0.003 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (10746) covalent geometry : angle 0.50498 / 0.27 (14596) hydrogen bonds : bond 0.04787 / 3.21 ( 680) hydrogen bonds : angle 4.14905 / 3.00 ( 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: 17 poor density : 181 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.5909 (ttmp) cc_final: 0.5547 (ttmp) REVERT: A 401 TYR cc_start: 0.7910 (m-80) cc_final: 0.7550 (m-80) REVERT: A 466 GLU cc_start: 0.8075 (mp0) cc_final: 0.7564 (mp0) REVERT: A 467 LYS cc_start: 0.7870 (mttm) cc_final: 0.7645 (mttp) REVERT: A 685 LYS cc_start: 0.7735 (tttt) cc_final: 0.7471 (tttp) REVERT: A 747 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: B 266 ARG cc_start: 0.7566 (tpp-160) cc_final: 0.7240 (ttp-170) REVERT: B 269 LYS cc_start: 0.8010 (mmmm) cc_final: 0.7337 (mmtt) REVERT: B 309 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: B 401 TYR cc_start: 0.7942 (m-80) cc_final: 0.7730 (m-80) REVERT: B 404 ARG cc_start: 0.6756 (ttt180) cc_final: 0.6232 (ttm-80) REVERT: B 467 LYS cc_start: 0.7898 (mttm) cc_final: 0.7681 (mttp) REVERT: B 685 LYS cc_start: 0.7658 (tttt) cc_final: 0.7325 (ttmm) REVERT: B 747 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7220 (mp0) outliers start: 17 outliers final: 13 residues processed: 188 average time/residue: 0.9084 time to fit residues: 189.7628 Evaluate side-chains 191 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 TRP 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 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 731 ILE 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 92 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.136031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.116280 restraints weight = 35453.875| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.48 r_work: 0.3074 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10746 Z= 0.203 Angle : 0.560 7.035 14596 Z= 0.300 Chirality : 0.041 0.224 1682 Planarity : 0.005 0.044 1804 Dihedral : 9.872 63.947 1634 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.53 % Allowed : 13.55 % Favored : 84.92 % 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: 1.79 (0.23), residues: 1322 helix: 2.34 (0.17), residues: 842 sheet: None (None), residues: 0 loop : -0.97 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 260 TYR 0.010 0.001 TYR B 151 PHE 0.016 0.001 PHE B 324 TRP 0.014 0.002 TRP B 519 HIS 0.005 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (10746) covalent geometry : angle 0.55971 / 0.30 (14596) hydrogen bonds : bond 0.05426 / 3.63 ( 680) hydrogen bonds : angle 4.25170 / 3.06 ( 2022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6309.39 seconds wall clock time: 107 minutes 29.60 seconds (6449.60 seconds total)