Starting phenix.real_space_refine on Fri Jul 3 00:27:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ijx_35502/07_2026/8ijx_35502.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijx_35502/07_2026/8ijx_35502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ijx_35502/07_2026/8ijx_35502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijx_35502/07_2026/8ijx_35502.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ijx_35502/07_2026/8ijx_35502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijx_35502/07_2026/8ijx_35502.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ijx_35502/07_2026/8ijx_35502.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ijx_35502/07_2026/8ijx_35502.cif" } resolution = 2.08 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= -0.002 sd= 0.091 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: 9 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 65 5.16 5 Cl 1 4.86 5 Be 1 3.05 5 C 6573 2.51 5 N 1654 2.21 5 O 2241 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 10545 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7633 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 47, 'TRANS': 935} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "B" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2142 Classifications: {'peptide': 268} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 245} Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 273 Unusual residues: {' MG': 1, 'PCW': 5, 'PZ0': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 124 Unusual residues: {'CLR': 1, 'NAG': 3, 'PCW': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 259 Classifications: {'water': 259} Link IDs: {None: 258} Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Time building chain proxies: 1.73, per 1000 atoms: 0.16 Number of scatterers: 10545 At special positions: 0 Unit cell: (82.72, 94, 174.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Cl 1 17.00 S 65 16.00 P 6 15.00 Mg 1 11.99 F 3 9.00 O 2241 8.00 N 1654 7.00 C 6573 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 152 " distance=2.02 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 262 " distance=2.03 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 Links applied NAG-ASN " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 130 " " NAG B 304 " - " ASN B 161 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 406.8 milliseconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 50.6% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 96 through 105 removed outlier: 3.526A pdb=" N GLN A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 131 Processing helix chain 'A' and resid 135 through 169 removed outlier: 3.952A pdb=" N LEU A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.932A pdb=" N THR A 248 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 291 through 322 Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'A' and resid 344 through 363 removed outlier: 3.711A pdb=" N LYS A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 424 through 437 removed outlier: 3.523A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 459 through 473 Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 519 through 525 Processing helix chain 'A' and resid 542 through 557 Processing helix chain 'A' and resid 607 through 618 Processing helix chain 'A' and resid 629 through 640 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 676 through 681 removed outlier: 3.549A pdb=" N ASP A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 Processing helix chain 'A' and resid 703 through 717 Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 748 through 755 Processing helix chain 'A' and resid 765 through 791 removed outlier: 4.043A pdb=" N LYS A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 805 Proline residue: A 798 - end of helix Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 824 through 831 removed outlier: 3.536A pdb=" N LEU A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 839 through 843 removed outlier: 3.758A pdb=" N LEU A 843 " --> pdb=" O ILE A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 865 through 885 Processing helix chain 'A' and resid 888 through 893 Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 916 through 946 removed outlier: 3.597A pdb=" N ALA A 941 " --> pdb=" O MET A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 957 Processing helix chain 'A' and resid 961 through 981 Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1001 through 1022 Processing helix chain 'A' and resid 1025 through 1032 removed outlier: 3.602A pdb=" N TYR A1032 " --> pdb=" O ASP A1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 66 Processing helix chain 'B' and resid 103 through 118 removed outlier: 4.589A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 155 through 164 removed outlier: 6.733A pdb=" N ASN B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY B 164 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 removed outlier: 4.166A pdb=" N THR B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 190 removed outlier: 11.912A pdb=" N GLN A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N LYS A 203 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N CYS A 258 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A 221 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU A 260 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLY A 219 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA A 217 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN A 264 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP A 211 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 190 removed outlier: 11.912A pdb=" N GLN A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N LYS A 203 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N CYS A 258 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A 221 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU A 260 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLY A 219 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA A 217 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN A 264 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP A 211 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.288A pdb=" N GLY A 740 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU A 759 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA A 742 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 721 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL A 741 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL A 723 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N MET A 743 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLY A 725 " --> pdb=" O MET A 743 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL A 622 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N PHE A 699 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N MET A 624 " --> pdb=" O PHE A 699 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.190A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS A 399 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE A 594 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN A 566 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A 503 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS A 485 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.190A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS A 399 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLY A 596 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 908 Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 85 Processing sheet with id=AA9, first strand: chain 'B' and resid 94 through 99 removed outlier: 4.482A pdb=" N LEU B 94 " --> pdb=" O GLU B 283 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2686 1.33 - 1.45: 1797 1.45 - 1.57: 5803 1.57 - 1.69: 12 1.69 - 1.81: 98 Bond restraints: 10396 Sorted by residual: bond pdb=" F3 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.529 1.765 -0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.535 1.752 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" F1 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.542 1.752 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" CG BFD A 385 " pdb=" OD1 BFD A 385 " ideal model delta sigma weight residual 1.269 1.446 -0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" C11 PCW A1105 " pdb=" O3 PCW A1105 " ideal model delta sigma weight residual 1.326 1.455 -0.129 2.00e-02 2.50e+03 4.16e+01 ... (remaining 10391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.32: 14004 5.32 - 10.64: 65 10.64 - 15.95: 4 15.95 - 21.27: 2 21.27 - 26.59: 3 Bond angle restraints: 14078 Sorted by residual: angle pdb=" C5 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 111.64 85.05 26.59 3.00e+00 1.11e-01 7.86e+01 angle pdb=" C6 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 109.11 86.24 22.87 3.00e+00 1.11e-01 5.81e+01 angle pdb=" C7 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 108.24 86.70 21.54 3.00e+00 1.11e-01 5.16e+01 angle pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " pdb=" F3 BFD A 385 " ideal model delta sigma weight residual 112.60 95.51 17.09 3.00e+00 1.11e-01 3.25e+01 angle pdb=" OD1 BFD A 385 " pdb="BE BFD A 385 " pdb=" F1 BFD A 385 " ideal model delta sigma weight residual 102.38 118.43 -16.05 3.00e+00 1.11e-01 2.86e+01 ... (remaining 14073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6043 35.81 - 71.63: 149 71.63 - 107.44: 14 107.44 - 143.25: 3 143.25 - 179.07: 2 Dihedral angle restraints: 6211 sinusoidal: 2578 harmonic: 3633 Sorted by residual: dihedral pdb=" CA GLY A 131 " pdb=" C GLY A 131 " pdb=" N ASP A 132 " pdb=" CA ASP A 132 " ideal model delta harmonic sigma weight residual 180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 152 " pdb=" CB CYS B 152 " ideal model delta sinusoidal sigma weight residual 93.00 53.65 39.35 1 1.00e+01 1.00e-02 2.18e+01 dihedral pdb=" C33 PCW A1104 " pdb=" C31 PCW A1104 " pdb=" C32 PCW A1104 " pdb=" O2 PCW A1104 " ideal model delta sinusoidal sigma weight residual -168.17 10.90 -179.07 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 6208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1290 0.056 - 0.112: 246 0.112 - 0.169: 23 0.169 - 0.225: 5 0.225 - 0.281: 3 Chirality restraints: 1567 Sorted by residual: chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 99 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C2 PCW A1101 " pdb=" C1 PCW A1101 " pdb=" C3 PCW A1101 " pdb=" O2 PCW A1101 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C13 CLR B 305 " pdb=" C12 CLR B 305 " pdb=" C14 CLR B 305 " pdb=" C17 CLR B 305 " both_signs ideal model delta sigma weight residual False -2.93 -2.70 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1564 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " -0.287 2.00e-02 2.50e+03 2.47e-01 7.62e+02 pdb=" C7 NAG B 303 " 0.061 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " 0.008 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " 0.421 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " -0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " 0.158 2.00e-02 2.50e+03 1.32e-01 2.18e+02 pdb=" C7 NAG B 302 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " 0.116 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " -0.215 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 304 " 0.140 2.00e-02 2.50e+03 1.15e-01 1.65e+02 pdb=" C7 NAG B 304 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG B 304 " 0.105 2.00e-02 2.50e+03 pdb=" N2 NAG B 304 " -0.183 2.00e-02 2.50e+03 pdb=" O7 NAG B 304 " -0.023 2.00e-02 2.50e+03 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 166 2.60 - 3.17: 8932 3.17 - 3.75: 18209 3.75 - 4.32: 25618 4.32 - 4.90: 40020 Nonbonded interactions: 92945 Sorted by model distance: nonbonded pdb=" O THR A 387 " pdb="MG MG A1102 " model vdw 2.024 2.170 nonbonded pdb="MG MG A1102 " pdb=" O HOH A1225 " model vdw 2.089 2.170 nonbonded pdb=" OD2 ASP A 877 " pdb=" O HOH A1201 " model vdw 2.150 3.040 nonbonded pdb=" F1 BFD A 385 " pdb="MG MG A1102 " model vdw 2.170 2.120 nonbonded pdb=" OE2 GLU A 686 " pdb=" O HOH A1202 " model vdw 2.183 3.040 ... (remaining 92940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.030 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.280 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 : 0.007 0.236 10402 Z= 0.344 Angle : 0.927 26.591 14093 Z= 0.374 Chirality : 0.045 0.281 1567 Planarity : 0.008 0.247 1783 Dihedral : 15.129 179.067 3862 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.50 % Allowed : 6.20 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.40 (0.24), residues: 1244 helix: 1.80 (0.22), residues: 578 sheet: 0.28 (0.40), residues: 153 loop : 0.24 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.015 0.001 TYR A 802 PHE 0.017 0.002 PHE B 284 TRP 0.012 0.001 TRP A 915 HIS 0.002 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.34 (10396) covalent geometry : angle 0.92581 / 0.37 (14078) SS BOND : bond 0.00491 / 0.26 ( 3) SS BOND : angle 0.68116 / 0.38 ( 6) hydrogen bonds : bond 0.12352 / 8.19 ( 515) hydrogen bonds : angle 5.53388 / 3.97 ( 1521) link_NAG-ASN : bond 0.00322 / 0.16 ( 3) link_NAG-ASN : angle 1.86541 / 1.71 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 LYS cc_start: 0.8266 (tppt) cc_final: 0.7538 (tmtt) REVERT: A 685 SER cc_start: 0.8093 (m) cc_final: 0.7647 (t) REVERT: B 28 GLN cc_start: 0.6823 (tt0) cc_final: 0.6506 (tt0) REVERT: B 131 CYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6599 (p) REVERT: B 135 LYS cc_start: 0.7551 (mtpp) cc_final: 0.6757 (tptm) outliers start: 16 outliers final: 10 residues processed: 131 average time/residue: 0.6051 time to fit residues: 84.5293 Evaluate side-chains 119 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.0270 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.172978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128944 restraints weight = 8658.717| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.38 r_work: 0.3270 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10402 Z= 0.113 Angle : 0.526 9.920 14093 Z= 0.269 Chirality : 0.043 0.255 1567 Planarity : 0.004 0.048 1783 Dihedral : 13.052 169.651 1582 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.50 % Allowed : 8.27 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.72 (0.24), residues: 1244 helix: 2.00 (0.21), residues: 582 sheet: 0.63 (0.40), residues: 153 loop : 0.41 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 439 TYR 0.014 0.001 TYR A 802 PHE 0.014 0.001 PHE B 284 TRP 0.010 0.001 TRP A 915 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (10396) covalent geometry : angle 0.50893 / 0.26 (14078) SS BOND : bond 0.00320 / 0.16 ( 3) SS BOND : angle 0.66259 / 0.56 ( 6) hydrogen bonds : bond 0.04265 / 2.86 ( 515) hydrogen bonds : angle 4.35377 / 3.14 ( 1521) link_NAG-ASN : bond 0.01269 / 0.61 ( 3) link_NAG-ASN : angle 5.27794 / 2.96 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 250 ASN cc_start: 0.8611 (p0) cc_final: 0.8333 (p0) REVERT: A 358 LYS cc_start: 0.8568 (tppt) cc_final: 0.7991 (tmtt) REVERT: A 477 MET cc_start: 0.6895 (mmt) cc_final: 0.6558 (mpt) REVERT: A 685 SER cc_start: 0.8376 (m) cc_final: 0.8031 (t) REVERT: A 841 MET cc_start: 0.9042 (mmm) cc_final: 0.8831 (mmm) REVERT: B 28 GLN cc_start: 0.6884 (tt0) cc_final: 0.6507 (tt0) REVERT: B 29 MET cc_start: 0.7350 (ttt) cc_final: 0.7036 (ttp) REVERT: B 131 CYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6926 (p) REVERT: B 135 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7154 (tptm) outliers start: 16 outliers final: 9 residues processed: 120 average time/residue: 0.6626 time to fit residues: 84.4686 Evaluate side-chains 118 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 0.3980 chunk 115 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 112 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 55 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.173009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128134 restraints weight = 8678.357| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.46 r_work: 0.3264 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10402 Z= 0.107 Angle : 0.496 6.564 14093 Z= 0.258 Chirality : 0.043 0.260 1567 Planarity : 0.004 0.042 1783 Dihedral : 12.859 168.995 1580 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.79 % Allowed : 8.65 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.80 (0.24), residues: 1244 helix: 2.07 (0.21), residues: 582 sheet: 0.61 (0.38), residues: 163 loop : 0.46 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.014 0.001 TYR A 802 PHE 0.013 0.001 PHE A 970 TRP 0.009 0.001 TRP A 915 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (10396) covalent geometry : angle 0.49337 / 0.26 (14078) SS BOND : bond 0.00391 / 0.20 ( 3) SS BOND : angle 0.55169 / 0.50 ( 6) hydrogen bonds : bond 0.04166 / 2.81 ( 515) hydrogen bonds : angle 4.14988 / 2.99 ( 1521) link_NAG-ASN : bond 0.00457 / 0.23 ( 3) link_NAG-ASN : angle 2.22140 / 1.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 250 ASN cc_start: 0.8541 (p0) cc_final: 0.8331 (p0) REVERT: A 287 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6987 (mm-30) REVERT: A 358 LYS cc_start: 0.8564 (tppt) cc_final: 0.7992 (tmtt) REVERT: A 477 MET cc_start: 0.6842 (mmt) cc_final: 0.6495 (mpt) REVERT: A 686 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7153 (tp30) REVERT: B 29 MET cc_start: 0.7447 (ttt) cc_final: 0.7139 (ttp) REVERT: B 131 CYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6657 (p) REVERT: B 135 LYS cc_start: 0.7913 (mtpp) cc_final: 0.7183 (tptm) outliers start: 19 outliers final: 12 residues processed: 119 average time/residue: 0.6400 time to fit residues: 80.7376 Evaluate side-chains 118 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 289 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.169316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.124612 restraints weight = 8627.312| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.39 r_work: 0.3211 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10402 Z= 0.185 Angle : 0.603 6.930 14093 Z= 0.316 Chirality : 0.047 0.229 1567 Planarity : 0.005 0.046 1783 Dihedral : 13.240 166.309 1578 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.97 % Allowed : 9.30 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.53 (0.24), residues: 1244 helix: 1.79 (0.21), residues: 581 sheet: 0.27 (0.37), residues: 171 loop : 0.50 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 439 TYR 0.020 0.002 TYR A 802 PHE 0.018 0.002 PHE B 284 TRP 0.010 0.002 TRP A 915 HIS 0.006 0.002 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (10396) covalent geometry : angle 0.60065 / 0.32 (14078) SS BOND : bond 0.00542 / 0.26 ( 3) SS BOND : angle 0.93278 / 0.71 ( 6) hydrogen bonds : bond 0.05438 / 3.67 ( 515) hydrogen bonds : angle 4.46399 / 3.22 ( 1521) link_NAG-ASN : bond 0.00298 / 0.15 ( 3) link_NAG-ASN : angle 1.93716 / 1.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.415 Fit side-chains REVERT: A 358 LYS cc_start: 0.8598 (tppt) cc_final: 0.7953 (tmtt) REVERT: A 455 ILE cc_start: 0.7917 (mm) cc_final: 0.7335 (tt) REVERT: B 29 MET cc_start: 0.7356 (ttt) cc_final: 0.7038 (ttp) REVERT: B 135 LYS cc_start: 0.8053 (mtpp) cc_final: 0.7267 (tptm) REVERT: B 160 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7205 (mm-40) outliers start: 21 outliers final: 14 residues processed: 123 average time/residue: 0.6953 time to fit residues: 90.8041 Evaluate side-chains 125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 97 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.170472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126433 restraints weight = 8589.103| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.33 r_work: 0.3243 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10402 Z= 0.138 Angle : 0.551 8.410 14093 Z= 0.286 Chirality : 0.044 0.242 1567 Planarity : 0.004 0.040 1783 Dihedral : 13.085 160.076 1578 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.88 % Allowed : 10.06 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.60 (0.24), residues: 1244 helix: 1.90 (0.21), residues: 581 sheet: 0.22 (0.37), residues: 171 loop : 0.50 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 439 TYR 0.017 0.002 TYR A 802 PHE 0.013 0.002 PHE A 970 TRP 0.011 0.001 TRP A 915 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (10396) covalent geometry : angle 0.53926 / 0.28 (14078) SS BOND : bond 0.00346 / 0.17 ( 3) SS BOND : angle 0.77234 / 0.60 ( 6) hydrogen bonds : bond 0.04742 / 3.19 ( 515) hydrogen bonds : angle 4.25729 / 3.07 ( 1521) link_NAG-ASN : bond 0.01205 / 0.58 ( 3) link_NAG-ASN : angle 4.47073 / 2.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.395 Fit side-chains REVERT: A 358 LYS cc_start: 0.8553 (tppt) cc_final: 0.7962 (tmtt) REVERT: A 477 MET cc_start: 0.6912 (mmt) cc_final: 0.6569 (mpt) REVERT: B 29 MET cc_start: 0.7343 (ttt) cc_final: 0.7029 (ttp) REVERT: B 131 CYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7082 (p) REVERT: B 135 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7238 (tptm) outliers start: 20 outliers final: 14 residues processed: 124 average time/residue: 0.7149 time to fit residues: 94.5582 Evaluate side-chains 127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 38 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 118 optimal weight: 0.0170 chunk 119 optimal weight: 0.7980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.172416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128281 restraints weight = 8724.712| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.33 r_work: 0.3273 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10402 Z= 0.107 Angle : 0.500 7.702 14093 Z= 0.258 Chirality : 0.043 0.251 1567 Planarity : 0.004 0.038 1783 Dihedral : 12.719 161.409 1578 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.88 % Allowed : 10.34 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.71 (0.24), residues: 1244 helix: 2.05 (0.21), residues: 582 sheet: 0.25 (0.37), residues: 171 loop : 0.47 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 439 TYR 0.014 0.001 TYR A 802 PHE 0.014 0.001 PHE A 970 TRP 0.009 0.001 TRP A 915 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (10396) covalent geometry : angle 0.48869 / 0.26 (14078) SS BOND : bond 0.00243 / 0.12 ( 3) SS BOND : angle 0.79401 / 0.54 ( 6) hydrogen bonds : bond 0.04074 / 2.75 ( 515) hydrogen bonds : angle 4.04674 / 2.92 ( 1521) link_NAG-ASN : bond 0.01295 / 0.63 ( 3) link_NAG-ASN : angle 4.21462 / 2.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.442 Fit side-chains REVERT: A 358 LYS cc_start: 0.8553 (tppt) cc_final: 0.7996 (tmtt) REVERT: A 477 MET cc_start: 0.6827 (mmt) cc_final: 0.6565 (mpt) REVERT: A 686 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7074 (tp30) REVERT: B 29 MET cc_start: 0.7403 (ttt) cc_final: 0.7086 (ttp) REVERT: B 131 CYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7083 (p) REVERT: B 135 LYS cc_start: 0.7878 (mtpp) cc_final: 0.7128 (tptm) outliers start: 20 outliers final: 14 residues processed: 125 average time/residue: 0.7401 time to fit residues: 98.3957 Evaluate side-chains 125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.169019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124794 restraints weight = 8515.794| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.39 r_work: 0.3212 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10402 Z= 0.191 Angle : 0.619 8.970 14093 Z= 0.322 Chirality : 0.048 0.263 1567 Planarity : 0.005 0.040 1783 Dihedral : 13.281 165.417 1578 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.97 % Allowed : 10.24 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.47 (0.23), residues: 1244 helix: 1.75 (0.21), residues: 581 sheet: 0.14 (0.37), residues: 171 loop : 0.51 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 439 TYR 0.020 0.002 TYR A 802 PHE 0.017 0.002 PHE A 970 TRP 0.009 0.002 TRP A 915 HIS 0.006 0.002 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (10396) covalent geometry : angle 0.60677 / 0.32 (14078) SS BOND : bond 0.00522 / 0.25 ( 3) SS BOND : angle 0.88913 / 0.65 ( 6) hydrogen bonds : bond 0.05480 / 3.71 ( 515) hydrogen bonds : angle 4.41812 / 3.19 ( 1521) link_NAG-ASN : bond 0.01566 / 0.75 ( 3) link_NAG-ASN : angle 4.77361 / 2.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.409 Fit side-chains REVERT: A 287 GLU cc_start: 0.7439 (mm-30) cc_final: 0.6905 (mm-30) REVERT: A 453 LYS cc_start: 0.8016 (mttp) cc_final: 0.7690 (mtpm) REVERT: B 131 CYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7075 (p) REVERT: B 135 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7271 (tptm) REVERT: B 256 ARG cc_start: 0.8074 (ttm110) cc_final: 0.7843 (ttm-80) outliers start: 21 outliers final: 16 residues processed: 124 average time/residue: 0.7429 time to fit residues: 98.3566 Evaluate side-chains 124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 108 optimal weight: 0.0070 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 121 optimal weight: 0.0980 chunk 78 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.173093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128815 restraints weight = 8623.886| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.41 r_work: 0.3280 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10402 Z= 0.101 Angle : 0.498 9.984 14093 Z= 0.255 Chirality : 0.043 0.263 1567 Planarity : 0.004 0.037 1783 Dihedral : 12.779 167.514 1578 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.69 % Allowed : 10.90 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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 (0.24), residues: 1244 helix: 2.16 (0.21), residues: 571 sheet: 0.39 (0.37), residues: 163 loop : 0.43 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 256 TYR 0.013 0.001 TYR A 802 PHE 0.014 0.001 PHE A 970 TRP 0.009 0.001 TRP A 915 HIS 0.003 0.001 HIS A 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (10396) covalent geometry : angle 0.48196 / 0.25 (14078) SS BOND : bond 0.00277 / 0.14 ( 3) SS BOND : angle 0.79238 / 0.56 ( 6) hydrogen bonds : bond 0.03896 / 2.63 ( 515) hydrogen bonds : angle 3.99012 / 2.87 ( 1521) link_NAG-ASN : bond 0.01171 / 0.56 ( 3) link_NAG-ASN : angle 4.94689 / 2.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.401 Fit side-chains REVERT: A 213 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6390 (tmm-80) REVERT: A 358 LYS cc_start: 0.8517 (tppt) cc_final: 0.7949 (tmtt) REVERT: A 415 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7657 (mm110) REVERT: A 477 MET cc_start: 0.7011 (mmt) cc_final: 0.6517 (mpt) REVERT: A 686 GLU cc_start: 0.8038 (mt-10) cc_final: 0.6838 (tp30) REVERT: B 29 MET cc_start: 0.7467 (ttt) cc_final: 0.7138 (ttp) REVERT: B 131 CYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7005 (p) REVERT: B 135 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7109 (tptm) REVERT: B 256 ARG cc_start: 0.8093 (ttm110) cc_final: 0.7854 (ttm-80) outliers start: 18 outliers final: 14 residues processed: 123 average time/residue: 0.7080 time to fit residues: 92.6142 Evaluate side-chains 123 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 4.9990 chunk 116 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 HIS A 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.171945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127851 restraints weight = 8625.717| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.38 r_work: 0.3261 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10402 Z= 0.115 Angle : 0.522 10.062 14093 Z= 0.268 Chirality : 0.044 0.290 1567 Planarity : 0.004 0.037 1783 Dihedral : 12.709 169.051 1578 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.60 % Allowed : 11.00 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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 (0.24), residues: 1244 helix: 2.06 (0.21), residues: 578 sheet: 0.40 (0.37), residues: 163 loop : 0.51 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 256 TYR 0.015 0.001 TYR A 802 PHE 0.018 0.001 PHE A 970 TRP 0.009 0.001 TRP A 915 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (10396) covalent geometry : angle 0.50585 / 0.26 (14078) SS BOND : bond 0.00318 / 0.16 ( 3) SS BOND : angle 0.62363 / 0.49 ( 6) hydrogen bonds : bond 0.04272 / 2.88 ( 515) hydrogen bonds : angle 4.04925 / 2.92 ( 1521) link_NAG-ASN : bond 0.01161 / 0.56 ( 3) link_NAG-ASN : angle 5.09080 / 2.87 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.395 Fit side-chains REVERT: A 213 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.6402 (tmm-80) REVERT: A 287 GLU cc_start: 0.7411 (pm20) cc_final: 0.6989 (mm-30) REVERT: A 453 LYS cc_start: 0.8008 (mttp) cc_final: 0.7676 (mtpm) REVERT: A 477 MET cc_start: 0.6971 (mmt) cc_final: 0.6519 (mpt) REVERT: B 29 MET cc_start: 0.7471 (ttt) cc_final: 0.7159 (ttp) REVERT: B 131 CYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7014 (p) REVERT: B 135 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7210 (tptm) REVERT: B 256 ARG cc_start: 0.8039 (ttm110) cc_final: 0.7810 (ttm-80) outliers start: 17 outliers final: 14 residues processed: 119 average time/residue: 0.7198 time to fit residues: 91.1331 Evaluate side-chains 121 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 0.0980 chunk 108 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 HIS B 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.171817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127038 restraints weight = 8573.806| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.42 r_work: 0.3256 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10402 Z= 0.117 Angle : 0.525 10.059 14093 Z= 0.270 Chirality : 0.044 0.300 1567 Planarity : 0.004 0.036 1783 Dihedral : 12.673 170.685 1578 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.69 % Allowed : 11.09 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.73 (0.24), residues: 1244 helix: 2.04 (0.21), residues: 578 sheet: 0.34 (0.37), residues: 163 loop : 0.51 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 256 TYR 0.016 0.001 TYR A 802 PHE 0.018 0.001 PHE A 970 TRP 0.009 0.001 TRP A 915 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (10396) covalent geometry : angle 0.50881 / 0.27 (14078) SS BOND : bond 0.00338 / 0.17 ( 3) SS BOND : angle 0.62867 / 0.50 ( 6) hydrogen bonds : bond 0.04334 / 2.92 ( 515) hydrogen bonds : angle 4.06106 / 2.93 ( 1521) link_NAG-ASN : bond 0.01137 / 0.55 ( 3) link_NAG-ASN : angle 5.14319 / 2.89 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.400 Fit side-chains REVERT: A 213 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.6397 (tmm-80) REVERT: A 287 GLU cc_start: 0.7404 (pm20) cc_final: 0.6889 (mm-30) REVERT: A 453 LYS cc_start: 0.8006 (mttp) cc_final: 0.7667 (mtpm) REVERT: A 477 MET cc_start: 0.6972 (mmt) cc_final: 0.6569 (mpt) REVERT: A 686 GLU cc_start: 0.8044 (mt-10) cc_final: 0.6890 (tp30) REVERT: B 29 MET cc_start: 0.7482 (ttt) cc_final: 0.7159 (ttp) REVERT: B 131 CYS cc_start: 0.7375 (OUTLIER) cc_final: 0.7008 (p) REVERT: B 135 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7220 (tptm) REVERT: B 256 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7810 (ttm-80) outliers start: 18 outliers final: 15 residues processed: 118 average time/residue: 0.7365 time to fit residues: 92.2986 Evaluate side-chains 121 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 123 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.171021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127003 restraints weight = 8667.474| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.38 r_work: 0.3251 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10402 Z= 0.124 Angle : 0.535 10.034 14093 Z= 0.276 Chirality : 0.044 0.275 1567 Planarity : 0.004 0.036 1783 Dihedral : 12.708 171.372 1578 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.79 % Allowed : 11.00 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % 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: 1.71 (0.24), residues: 1244 helix: 2.01 (0.21), residues: 578 sheet: 0.34 (0.37), residues: 163 loop : 0.51 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 439 TYR 0.017 0.001 TYR A 802 PHE 0.027 0.002 PHE A 497 TRP 0.009 0.001 TRP A 915 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (10396) covalent geometry : angle 0.51975 / 0.27 (14078) SS BOND : bond 0.00329 / 0.16 ( 3) SS BOND : angle 0.58389 / 0.47 ( 6) hydrogen bonds : bond 0.04491 / 3.03 ( 515) hydrogen bonds : angle 4.09853 / 2.95 ( 1521) link_NAG-ASN : bond 0.01147 / 0.55 ( 3) link_NAG-ASN : angle 5.04721 / 2.84 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5492.16 seconds wall clock time: 94 minutes 0.43 seconds (5640.43 seconds total)