Starting phenix.real_space_refine on Thu Aug 6 05:34:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh9_61476/08_2026/9jh9_61476.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh9_61476/08_2026/9jh9_61476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jh9_61476/08_2026/9jh9_61476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh9_61476/08_2026/9jh9_61476.map" model { file = "/net/cci-nas-00/data/ceres_data/9jh9_61476/08_2026/9jh9_61476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh9_61476/08_2026/9jh9_61476.cif" } resolution = 3.42 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= 0.013 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: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 P 68 5.49 5 S 40 5.16 5 C 8488 2.51 5 N 2236 2.21 5 O 2673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13509 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 357 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "D" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "F" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 358 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.80, per 1000 atoms: 0.21 Number of scatterers: 13509 At special positions: 0 Unit cell: (120.54, 86.1, 101.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 4 24.99 S 40 16.00 P 68 15.00 O 2673 8.00 N 2236 7.00 C 8488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 520.5 milliseconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 24 sheets defined 31.1% alpha, 20.4% beta 11 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.973A pdb=" N LYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 322 through 325 removed outlier: 4.157A pdb=" N ASN A 325 " --> pdb=" O GLU A 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 325' Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 388 through 404 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 474 through 486 Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 506 through 523 Processing helix chain 'A' and resid 583 through 603 Processing helix chain 'A' and resid 620 through 630 removed outlier: 3.595A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 723 through 735 Processing helix chain 'B' and resid 43 through 54 Processing helix chain 'B' and resid 97 through 115 removed outlier: 3.974A pdb=" N LYS B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 281 through 289 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 303 through 319 Processing helix chain 'B' and resid 322 through 325 removed outlier: 4.157A pdb=" N ASN B 325 " --> pdb=" O GLU B 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 322 through 325' Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 388 through 404 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 494 through 503 Processing helix chain 'B' and resid 506 through 523 Processing helix chain 'B' and resid 583 through 603 Processing helix chain 'B' and resid 620 through 630 removed outlier: 3.595A pdb=" N TYR B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 711 Processing helix chain 'B' and resid 723 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.704A pdb=" N ASN A 9 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 11 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.628A pdb=" N LEU A 134 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS A 148 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.628A pdb=" N LEU A 134 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 175 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 172 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 63 removed outlier: 3.521A pdb=" N TYR A 68 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 88 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS A 30 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N PHE A 86 " --> pdb=" O LYS A 30 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA6, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.568A pdb=" N TYR A 271 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 260 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 214 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 346 removed outlier: 5.318A pdb=" N ILE A 690 " --> pdb=" O LYS A 641 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS A 641 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LYS A 692 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU A 639 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N CYS A 539 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N HIS A 612 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL A 541 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA A 614 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU A 543 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 559 " --> pdb=" O GLY A 542 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER A 558 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR A 570 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 560 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359 removed outlier: 4.500A pdb=" N LEU A 352 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 382 through 385 removed outlier: 6.280A pdb=" N VAL A 382 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TYR A 435 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AB4, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.704A pdb=" N ASN B 9 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 11 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.629A pdb=" N LEU B 134 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS B 148 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.629A pdb=" N LEU B 134 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR B 175 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL B 172 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.520A pdb=" N TYR B 68 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B 88 " --> pdb=" O GLN B 28 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS B 30 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N PHE B 86 " --> pdb=" O LYS B 30 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AB9, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AC1, first strand: chain 'B' and resid 268 through 271 removed outlier: 3.568A pdb=" N TYR B 271 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 260 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 214 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 343 through 346 removed outlier: 5.317A pdb=" N ILE B 690 " --> pdb=" O LYS B 641 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS B 641 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LYS B 692 " --> pdb=" O GLU B 639 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU B 639 " --> pdb=" O LYS B 692 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N CYS B 539 " --> pdb=" O VAL B 610 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N HIS B 612 " --> pdb=" O CYS B 539 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL B 541 " --> pdb=" O HIS B 612 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA B 614 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 543 " --> pdb=" O ALA B 614 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 559 " --> pdb=" O GLY B 542 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER B 558 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR B 570 " --> pdb=" O SER B 558 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 560 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 358 through 359 removed outlier: 4.499A pdb=" N LEU B 352 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 382 through 385 removed outlier: 6.280A pdb=" N VAL B 382 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N TYR B 435 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B 384 " --> pdb=" O TYR B 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AC6, first strand: chain 'B' and resid 462 through 463 470 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 1.47 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: 2549 1.33 - 1.44: 3607 1.44 - 1.56: 7564 1.56 - 1.68: 134 1.68 - 1.80: 70 Bond restraints: 13924 Sorted by residual: bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.435 1.373 0.062 1.30e-02 5.92e+03 2.28e+01 bond pdb=" C3' DG D 8 " pdb=" O3' DG D 8 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.23e+01 bond pdb=" C3' DA F 6 " pdb=" O3' DA F 6 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.07e+01 bond pdb=" C3' DA E 6 " pdb=" O3' DA E 6 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.06e+01 bond pdb=" C3' DC E 14 " pdb=" O3' DC E 14 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.78e+01 ... (remaining 13919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 17906 1.92 - 3.84: 1000 3.84 - 5.77: 125 5.77 - 7.69: 24 7.69 - 9.61: 14 Bond angle restraints: 19069 Sorted by residual: angle pdb=" O4' DG D 4 " pdb=" C4' DG D 4 " pdb=" C3' DG D 4 " ideal model delta sigma weight residual 106.00 102.55 3.45 6.00e-01 2.78e+00 3.30e+01 angle pdb=" O4' DG C 4 " pdb=" C4' DG C 4 " pdb=" C3' DG C 4 " ideal model delta sigma weight residual 106.00 102.58 3.42 6.00e-01 2.78e+00 3.25e+01 angle pdb=" C LYS B 63 " pdb=" N ASP B 64 " pdb=" CA ASP B 64 " ideal model delta sigma weight residual 120.82 129.21 -8.39 1.50e+00 4.44e-01 3.13e+01 angle pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 120.82 129.16 -8.34 1.50e+00 4.44e-01 3.09e+01 angle pdb=" N LYS B 63 " pdb=" CA LYS B 63 " pdb=" C LYS B 63 " ideal model delta sigma weight residual 110.14 101.57 8.57 1.55e+00 4.16e-01 3.06e+01 ... (remaining 19064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.72: 7848 28.72 - 57.44: 370 57.44 - 86.15: 30 86.15 - 114.87: 4 114.87 - 143.59: 2 Dihedral angle restraints: 8254 sinusoidal: 3880 harmonic: 4374 Sorted by residual: dihedral pdb=" CA GLU B 470 " pdb=" C GLU B 470 " pdb=" N ILE B 471 " pdb=" CA ILE B 471 " ideal model delta harmonic sigma weight residual -180.00 -136.35 -43.65 0 5.00e+00 4.00e-02 7.62e+01 dihedral pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N ILE A 471 " pdb=" CA ILE A 471 " ideal model delta harmonic sigma weight residual -180.00 -136.43 -43.57 0 5.00e+00 4.00e-02 7.59e+01 dihedral pdb=" CA LYS B 63 " pdb=" C LYS B 63 " pdb=" N ASP B 64 " pdb=" CA ASP B 64 " ideal model delta harmonic sigma weight residual -180.00 -149.35 -30.65 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 8251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1494 0.059 - 0.118: 440 0.118 - 0.177: 123 0.177 - 0.236: 21 0.236 - 0.295: 6 Chirality restraints: 2084 Sorted by residual: chirality pdb=" CB ILE B 44 " pdb=" CA ILE B 44 " pdb=" CG1 ILE B 44 " pdb=" CG2 ILE B 44 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE A 44 " pdb=" CA ILE A 44 " pdb=" CG1 ILE A 44 " pdb=" CG2 ILE A 44 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE A 460 " pdb=" CA ILE A 460 " pdb=" CG1 ILE A 460 " pdb=" CG2 ILE A 460 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2081 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 160 " -0.009 2.00e-02 2.50e+03 1.80e-02 5.68e+00 pdb=" CG PHE B 160 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 160 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE B 160 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 160 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 160 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 160 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 460 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C ILE B 460 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE B 460 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA B 461 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 160 " 0.009 2.00e-02 2.50e+03 1.79e-02 5.62e+00 pdb=" CG PHE A 160 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 160 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 160 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 160 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 160 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 160 " -0.003 2.00e-02 2.50e+03 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 55 2.42 - 3.04: 7529 3.04 - 3.66: 20983 3.66 - 4.28: 32178 4.28 - 4.90: 52433 Nonbonded interactions: 113178 Sorted by model distance: nonbonded pdb=" OD2 ASP A 544 " pdb="MN MN E 801 " model vdw 1.798 2.320 nonbonded pdb=" OD2 ASP B 544 " pdb="MN MN F 801 " model vdw 1.811 2.320 nonbonded pdb=" OP1 DT E 9 " pdb="MN MN E 801 " model vdw 1.827 2.320 nonbonded pdb=" OP1 DT F 9 " pdb="MN MN F 801 " model vdw 1.827 2.320 nonbonded pdb=" OP1 DA D 3 " pdb="MN MN D 801 " model vdw 1.869 2.320 ... (remaining 113173 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 1 through 5 or (resid 6 and (name P or name OP1 or name OP \ 2 or name O5' or name C5' or name C4' or name C3' or name O3' or name C2' or nam \ e C1' or name N9 or name C8 or name N7 or name C5 or name C6 or name N6 or name \ N1 or name C2 or name N3 or name C4 )) or resid 7 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.740 Find NCS groups from input model: 0.140 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: 0.020 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.010 0.075 13924 Z= 0.552 Angle : 0.991 9.612 19069 Z= 0.631 Chirality : 0.062 0.295 2084 Planarity : 0.006 0.044 2180 Dihedral : 15.157 143.591 5466 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.15 % Allowed : 2.54 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -2.74 (0.18), residues: 1486 helix: -2.22 (0.18), residues: 424 sheet: -1.88 (0.28), residues: 264 loop : -1.48 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 721 TYR 0.038 0.003 TYR B 554 PHE 0.039 0.004 PHE B 160 TRP 0.037 0.005 TRP A 623 HIS 0.011 0.002 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00958 / 0.55 (13924) covalent geometry : angle 0.99094 / 0.63 (19069) hydrogen bonds : bond 0.19960 / 12.70 ( 485) hydrogen bonds : angle 8.76866 / 5.94 ( 1400) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 271 time to evaluate : 0.331 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 741 GLN cc_start: 0.8161 (tp40) cc_final: 0.7475 (tp40) REVERT: B 741 GLN cc_start: 0.8191 (tp40) cc_final: 0.7433 (tp40) outliers start: 2 outliers final: 0 residues processed: 271 average time/residue: 0.0919 time to fit residues: 37.0250 Evaluate side-chains 141 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.0570 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 GLN A 55 ASN A 97 ASN A 136 ASN A 155 ASN A 242 ASN ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN A 588 GLN B 28 GLN B 55 ASN B 97 ASN B 136 ASN B 155 ASN B 490 GLN B 513 HIS B 574 ASN B 588 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.060460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.047396 restraints weight = 52571.451| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 4.98 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13924 Z= 0.190 Angle : 0.753 8.725 19069 Z= 0.414 Chirality : 0.051 0.203 2084 Planarity : 0.004 0.033 2180 Dihedral : 18.164 159.081 2388 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.50 % Allowed : 10.40 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.68 (0.20), residues: 1486 helix: -0.66 (0.23), residues: 444 sheet: -1.54 (0.29), residues: 246 loop : -1.17 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 613 TYR 0.025 0.002 TYR B 237 PHE 0.019 0.002 PHE A 388 TRP 0.023 0.004 TRP B 623 HIS 0.010 0.002 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (13924) covalent geometry : angle 0.75315 / 0.41 (19069) hydrogen bonds : bond 0.05800 / 3.77 ( 485) hydrogen bonds : angle 6.35344 / 4.21 ( 1400) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 PHE cc_start: 0.8743 (m-80) cc_final: 0.8281 (m-80) REVERT: A 139 LEU cc_start: 0.9127 (tp) cc_final: 0.8685 (tp) REVERT: A 169 MET cc_start: 0.9319 (tpp) cc_final: 0.9111 (tpp) REVERT: A 191 MET cc_start: 0.9334 (mtt) cc_final: 0.9017 (mtt) REVERT: A 363 MET cc_start: 0.8883 (mmm) cc_final: 0.8514 (tpt) REVERT: A 426 ASN cc_start: 0.9497 (t0) cc_final: 0.9119 (p0) REVERT: A 466 MET cc_start: 0.8627 (ptt) cc_final: 0.8221 (ptp) REVERT: A 472 GLU cc_start: 0.8223 (tp30) cc_final: 0.7974 (tp30) REVERT: A 517 LEU cc_start: 0.9537 (tp) cc_final: 0.9197 (tp) REVERT: A 587 LEU cc_start: 0.9815 (mt) cc_final: 0.9563 (tp) REVERT: A 620 ASP cc_start: 0.9179 (m-30) cc_final: 0.8541 (p0) REVERT: A 705 GLN cc_start: 0.9456 (mt0) cc_final: 0.8929 (mp10) REVERT: A 737 GLU cc_start: 0.8918 (pm20) cc_final: 0.8670 (mm-30) REVERT: A 741 GLN cc_start: 0.8755 (tp40) cc_final: 0.7530 (tp40) REVERT: B 15 PHE cc_start: 0.8726 (m-80) cc_final: 0.8257 (m-80) REVERT: B 132 GLU cc_start: 0.8139 (pm20) cc_final: 0.7932 (pm20) REVERT: B 139 LEU cc_start: 0.9096 (tp) cc_final: 0.8747 (tp) REVERT: B 169 MET cc_start: 0.9259 (tpp) cc_final: 0.9040 (tpp) REVERT: B 191 MET cc_start: 0.9298 (mtt) cc_final: 0.8970 (mtt) REVERT: B 363 MET cc_start: 0.8053 (tpp) cc_final: 0.7124 (tpp) REVERT: B 426 ASN cc_start: 0.9482 (t0) cc_final: 0.9088 (p0) REVERT: B 517 LEU cc_start: 0.9551 (tp) cc_final: 0.9217 (tp) REVERT: B 575 ILE cc_start: 0.8892 (pt) cc_final: 0.8099 (pt) REVERT: B 620 ASP cc_start: 0.9167 (m-30) cc_final: 0.8582 (p0) REVERT: B 705 GLN cc_start: 0.9438 (mt0) cc_final: 0.8923 (mp10) REVERT: B 737 GLU cc_start: 0.8892 (pm20) cc_final: 0.8599 (mm-30) REVERT: B 741 GLN cc_start: 0.8751 (tp40) cc_final: 0.7503 (tp40) outliers start: 20 outliers final: 10 residues processed: 184 average time/residue: 0.0737 time to fit residues: 21.7209 Evaluate side-chains 140 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 539 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 132 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN B 288 ASN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.057285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.044028 restraints weight = 55643.306| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 4.97 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 13924 Z= 0.290 Angle : 0.749 8.374 19069 Z= 0.408 Chirality : 0.048 0.231 2084 Planarity : 0.004 0.038 2180 Dihedral : 18.138 164.106 2388 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.62 % Allowed : 10.70 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.23 (0.20), residues: 1486 helix: -0.10 (0.23), residues: 448 sheet: -1.75 (0.28), residues: 258 loop : -0.82 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 158 TYR 0.026 0.002 TYR B 237 PHE 0.014 0.002 PHE B 61 TRP 0.016 0.002 TRP B 623 HIS 0.005 0.002 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.29 (13924) covalent geometry : angle 0.74900 / 0.41 (19069) hydrogen bonds : bond 0.05016 / 3.27 ( 485) hydrogen bonds : angle 5.77365 / 3.81 ( 1400) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.351 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8137 (pm20) cc_final: 0.7889 (pm20) REVERT: A 169 MET cc_start: 0.9397 (tpp) cc_final: 0.9100 (tpp) REVERT: A 178 CYS cc_start: 0.8225 (p) cc_final: 0.7961 (p) REVERT: A 191 MET cc_start: 0.9363 (mtt) cc_final: 0.8987 (mtt) REVERT: A 298 GLN cc_start: 0.9167 (mp10) cc_final: 0.8781 (mp10) REVERT: A 363 MET cc_start: 0.8842 (mmm) cc_final: 0.8050 (mmm) REVERT: A 403 SER cc_start: 0.9688 (m) cc_final: 0.9483 (p) REVERT: A 426 ASN cc_start: 0.9510 (t0) cc_final: 0.9299 (t0) REVERT: A 512 LEU cc_start: 0.9741 (tp) cc_final: 0.9539 (pp) REVERT: A 545 VAL cc_start: 0.9176 (OUTLIER) cc_final: 0.8839 (m) REVERT: A 585 GLU cc_start: 0.9502 (pt0) cc_final: 0.9168 (pm20) REVERT: A 587 LEU cc_start: 0.9848 (mt) cc_final: 0.9568 (tp) REVERT: A 609 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9100 (mm) REVERT: A 699 MET cc_start: 0.8643 (mmt) cc_final: 0.8264 (mmt) REVERT: A 705 GLN cc_start: 0.9498 (mt0) cc_final: 0.8992 (mp10) REVERT: A 737 GLU cc_start: 0.8946 (pm20) cc_final: 0.8560 (mm-30) REVERT: B 132 GLU cc_start: 0.8214 (pm20) cc_final: 0.8011 (pm20) REVERT: B 169 MET cc_start: 0.9348 (tpp) cc_final: 0.9035 (tpp) REVERT: B 178 CYS cc_start: 0.8214 (p) cc_final: 0.7948 (p) REVERT: B 191 MET cc_start: 0.9346 (mtt) cc_final: 0.8883 (mtt) REVERT: B 298 GLN cc_start: 0.9176 (mp10) cc_final: 0.8776 (mp10) REVERT: B 403 SER cc_start: 0.9663 (m) cc_final: 0.9453 (p) REVERT: B 426 ASN cc_start: 0.9540 (t0) cc_final: 0.9317 (t0) REVERT: B 466 MET cc_start: 0.8822 (ptt) cc_final: 0.8473 (ptp) REVERT: B 491 MET cc_start: 0.9223 (mmp) cc_final: 0.8998 (mmp) REVERT: B 545 VAL cc_start: 0.9180 (OUTLIER) cc_final: 0.8862 (m) REVERT: B 585 GLU cc_start: 0.9495 (pt0) cc_final: 0.9198 (pm20) REVERT: B 587 LEU cc_start: 0.9850 (mt) cc_final: 0.9590 (tp) REVERT: B 699 MET cc_start: 0.8841 (mmt) cc_final: 0.8403 (mmt) REVERT: B 705 GLN cc_start: 0.9495 (mt0) cc_final: 0.8984 (mp10) REVERT: B 737 GLU cc_start: 0.9028 (pm20) cc_final: 0.8594 (mm-30) outliers start: 35 outliers final: 14 residues processed: 175 average time/residue: 0.0823 time to fit residues: 22.5442 Evaluate side-chains 140 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 675 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 134 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** 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 = 0.3141 r_free = 0.3141 target = 0.057204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.043786 restraints weight = 55686.650| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 5.02 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13924 Z= 0.210 Angle : 0.690 9.825 19069 Z= 0.375 Chirality : 0.048 0.250 2084 Planarity : 0.004 0.029 2180 Dihedral : 18.142 164.380 2388 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.62 % Allowed : 10.93 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.86 (0.21), residues: 1486 helix: 0.24 (0.24), residues: 450 sheet: -1.59 (0.29), residues: 262 loop : -0.58 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 307 TYR 0.029 0.002 TYR A 511 PHE 0.017 0.002 PHE A 458 TRP 0.011 0.002 TRP A 623 HIS 0.014 0.002 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 (13924) covalent geometry : angle 0.68960 / 0.37 (19069) hydrogen bonds : bond 0.04337 / 2.84 ( 485) hydrogen bonds : angle 5.41733 / 3.59 ( 1400) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.326 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 132 GLU cc_start: 0.8182 (pm20) cc_final: 0.7926 (pm20) REVERT: A 169 MET cc_start: 0.9377 (tpp) cc_final: 0.9039 (tpp) REVERT: A 178 CYS cc_start: 0.8285 (p) cc_final: 0.7552 (p) REVERT: A 191 MET cc_start: 0.9398 (mtt) cc_final: 0.8992 (mtt) REVERT: A 266 LYS cc_start: 0.7769 (pttt) cc_final: 0.7517 (pptt) REVERT: A 298 GLN cc_start: 0.9145 (mp10) cc_final: 0.8762 (mp10) REVERT: A 363 MET cc_start: 0.8816 (mmm) cc_final: 0.8039 (mmm) REVERT: A 364 GLN cc_start: 0.9466 (mm110) cc_final: 0.9134 (mm-40) REVERT: A 426 ASN cc_start: 0.9530 (t0) cc_final: 0.9328 (t0) REVERT: A 466 MET cc_start: 0.8862 (ptt) cc_final: 0.8515 (ptp) REVERT: A 498 GLU cc_start: 0.9688 (mt-10) cc_final: 0.9417 (mt-10) REVERT: A 545 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8854 (m) REVERT: A 585 GLU cc_start: 0.9531 (pt0) cc_final: 0.9156 (pm20) REVERT: A 587 LEU cc_start: 0.9855 (mt) cc_final: 0.9605 (tp) REVERT: A 609 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9104 (mm) REVERT: A 705 GLN cc_start: 0.9509 (mt0) cc_final: 0.8997 (mp10) REVERT: A 737 GLU cc_start: 0.9033 (pm20) cc_final: 0.8364 (mm-30) REVERT: B 132 GLU cc_start: 0.8233 (pm20) cc_final: 0.7899 (pm20) REVERT: B 169 MET cc_start: 0.9333 (tpp) cc_final: 0.8991 (tpp) REVERT: B 178 CYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7587 (p) REVERT: B 191 MET cc_start: 0.9335 (mtt) cc_final: 0.8882 (mtt) REVERT: B 266 LYS cc_start: 0.7776 (pttt) cc_final: 0.7513 (pptt) REVERT: B 298 GLN cc_start: 0.9164 (mp10) cc_final: 0.8788 (mp10) REVERT: B 426 ASN cc_start: 0.9536 (t0) cc_final: 0.9332 (t0) REVERT: B 466 MET cc_start: 0.8848 (ptt) cc_final: 0.8498 (ptp) REVERT: B 491 MET cc_start: 0.9192 (mmp) cc_final: 0.8959 (mmp) REVERT: B 580 GLU cc_start: 0.8251 (pt0) cc_final: 0.7576 (pm20) REVERT: B 585 GLU cc_start: 0.9519 (pt0) cc_final: 0.9140 (pm20) REVERT: B 705 GLN cc_start: 0.9512 (mt0) cc_final: 0.9012 (mp10) REVERT: B 737 GLU cc_start: 0.9079 (pm20) cc_final: 0.8570 (mm-30) outliers start: 35 outliers final: 25 residues processed: 171 average time/residue: 0.0866 time to fit residues: 22.9585 Evaluate side-chains 148 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 730 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** 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 = 0.3129 r_free = 0.3129 target = 0.056821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.043569 restraints weight = 56068.744| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 4.99 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13924 Z= 0.216 Angle : 0.668 8.894 19069 Z= 0.366 Chirality : 0.047 0.282 2084 Planarity : 0.003 0.028 2180 Dihedral : 18.148 166.722 2388 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.25 % Allowed : 11.98 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.64 (0.22), residues: 1486 helix: 0.37 (0.24), residues: 452 sheet: -1.54 (0.29), residues: 262 loop : -0.38 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 613 TYR 0.025 0.002 TYR B 237 PHE 0.021 0.002 PHE B 561 TRP 0.013 0.002 TRP B 623 HIS 0.011 0.002 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.22 (13924) covalent geometry : angle 0.66812 / 0.37 (19069) hydrogen bonds : bond 0.04133 / 2.70 ( 485) hydrogen bonds : angle 5.26171 / 3.48 ( 1400) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.475 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8225 (pm20) cc_final: 0.7966 (pm20) REVERT: A 169 MET cc_start: 0.9403 (tpp) cc_final: 0.9035 (tpp) REVERT: A 191 MET cc_start: 0.9404 (mtt) cc_final: 0.8890 (mtt) REVERT: A 298 GLN cc_start: 0.9149 (mp10) cc_final: 0.8735 (mp10) REVERT: A 302 MET cc_start: 0.8574 (ttt) cc_final: 0.8211 (ttt) REVERT: A 363 MET cc_start: 0.8855 (mmm) cc_final: 0.8038 (mmm) REVERT: A 364 GLN cc_start: 0.9487 (mm110) cc_final: 0.9144 (mm-40) REVERT: A 498 GLU cc_start: 0.9697 (mt-10) cc_final: 0.9431 (mt-10) REVERT: A 580 GLU cc_start: 0.8421 (pt0) cc_final: 0.7735 (pm20) REVERT: A 585 GLU cc_start: 0.9532 (pt0) cc_final: 0.9173 (pm20) REVERT: A 589 GLU cc_start: 0.9579 (mm-30) cc_final: 0.9367 (tp30) REVERT: A 737 GLU cc_start: 0.9069 (pm20) cc_final: 0.8299 (mm-30) REVERT: B 132 GLU cc_start: 0.8266 (pm20) cc_final: 0.8042 (pm20) REVERT: B 169 MET cc_start: 0.9364 (tpp) cc_final: 0.8996 (tpp) REVERT: B 191 MET cc_start: 0.9348 (mtt) cc_final: 0.8879 (mtt) REVERT: B 298 GLN cc_start: 0.9152 (mp10) cc_final: 0.8738 (mp10) REVERT: B 302 MET cc_start: 0.8549 (ttt) cc_final: 0.8208 (ttt) REVERT: B 512 LEU cc_start: 0.9797 (mt) cc_final: 0.9560 (mt) REVERT: B 585 GLU cc_start: 0.9518 (pt0) cc_final: 0.9148 (pm20) REVERT: B 587 LEU cc_start: 0.9847 (tp) cc_final: 0.9573 (tp) REVERT: B 609 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9094 (mm) REVERT: B 673 MET cc_start: 0.9323 (tpt) cc_final: 0.8873 (tpt) outliers start: 30 outliers final: 19 residues processed: 156 average time/residue: 0.0842 time to fit residues: 20.6928 Evaluate side-chains 140 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 730 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 15 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** 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 = 0.3145 r_free = 0.3145 target = 0.057422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.044136 restraints weight = 55578.451| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 5.02 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13924 Z= 0.161 Angle : 0.632 7.502 19069 Z= 0.347 Chirality : 0.047 0.301 2084 Planarity : 0.003 0.028 2180 Dihedral : 18.145 168.279 2388 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.84 % Allowed : 11.23 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.22), residues: 1486 helix: 0.40 (0.24), residues: 460 sheet: -1.44 (0.30), residues: 242 loop : -0.37 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 548 TYR 0.034 0.002 TYR A 511 PHE 0.022 0.002 PHE A 561 TRP 0.013 0.002 TRP A 623 HIS 0.008 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (13924) covalent geometry : angle 0.63227 / 0.35 (19069) hydrogen bonds : bond 0.03943 / 2.57 ( 485) hydrogen bonds : angle 5.08444 / 3.38 ( 1400) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.591 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8220 (pm20) cc_final: 0.7964 (pm20) REVERT: A 169 MET cc_start: 0.9401 (tpp) cc_final: 0.9016 (tpp) REVERT: A 191 MET cc_start: 0.9362 (mtt) cc_final: 0.8883 (mtt) REVERT: A 298 GLN cc_start: 0.9127 (mp10) cc_final: 0.8732 (mp10) REVERT: A 363 MET cc_start: 0.8842 (mmm) cc_final: 0.8012 (mmm) REVERT: A 364 GLN cc_start: 0.9492 (mm110) cc_final: 0.9146 (mm-40) REVERT: A 512 LEU cc_start: 0.9779 (mt) cc_final: 0.9557 (mt) REVERT: A 517 LEU cc_start: 0.9654 (tp) cc_final: 0.9345 (tp) REVERT: A 554 TYR cc_start: 0.8048 (m-80) cc_final: 0.7746 (m-80) REVERT: A 585 GLU cc_start: 0.9535 (pt0) cc_final: 0.9160 (pm20) REVERT: A 587 LEU cc_start: 0.9850 (tp) cc_final: 0.9615 (tp) REVERT: A 589 GLU cc_start: 0.9560 (mm-30) cc_final: 0.9335 (tp30) REVERT: A 673 MET cc_start: 0.9325 (tpt) cc_final: 0.9016 (tpt) REVERT: A 705 GLN cc_start: 0.9530 (mt0) cc_final: 0.9085 (mt0) REVERT: A 737 GLU cc_start: 0.9085 (pm20) cc_final: 0.8266 (mm-30) REVERT: B 132 GLU cc_start: 0.8254 (pm20) cc_final: 0.7932 (pm20) REVERT: B 169 MET cc_start: 0.9350 (tpp) cc_final: 0.8959 (tpp) REVERT: B 188 ILE cc_start: 0.9799 (mm) cc_final: 0.9530 (mm) REVERT: B 191 MET cc_start: 0.9356 (mtt) cc_final: 0.8875 (mtt) REVERT: B 298 GLN cc_start: 0.9146 (mp10) cc_final: 0.8756 (mp10) REVERT: B 363 MET cc_start: 0.8087 (tpp) cc_final: 0.7728 (tpp) REVERT: B 472 GLU cc_start: 0.8591 (tp30) cc_final: 0.8329 (tp30) REVERT: B 491 MET cc_start: 0.9359 (mmp) cc_final: 0.9050 (mmp) REVERT: B 512 LEU cc_start: 0.9791 (mt) cc_final: 0.9509 (mt) REVERT: B 517 LEU cc_start: 0.9647 (tp) cc_final: 0.9342 (tp) REVERT: B 580 GLU cc_start: 0.8439 (pt0) cc_final: 0.7769 (pm20) REVERT: B 585 GLU cc_start: 0.9515 (pt0) cc_final: 0.9138 (pm20) REVERT: B 587 LEU cc_start: 0.9847 (tp) cc_final: 0.9574 (tp) REVERT: B 737 GLU cc_start: 0.9058 (pm20) cc_final: 0.8289 (mm-30) outliers start: 38 outliers final: 25 residues processed: 166 average time/residue: 0.0914 time to fit residues: 23.8734 Evaluate side-chains 149 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 140 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.055396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.042681 restraints weight = 56172.058| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 4.86 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 13924 Z= 0.275 Angle : 0.689 7.821 19069 Z= 0.376 Chirality : 0.048 0.337 2084 Planarity : 0.004 0.033 2180 Dihedral : 18.206 172.962 2388 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.40 % Allowed : 12.50 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.22), residues: 1486 helix: 0.54 (0.24), residues: 452 sheet: -1.58 (0.30), residues: 258 loop : -0.21 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 667 TYR 0.029 0.002 TYR B 511 PHE 0.024 0.002 PHE A 561 TRP 0.011 0.002 TRP A 623 HIS 0.010 0.002 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.27 (13924) covalent geometry : angle 0.68855 / 0.38 (19069) hydrogen bonds : bond 0.04023 / 2.60 ( 485) hydrogen bonds : angle 5.10874 / 3.39 ( 1400) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.422 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: symmetry clash REVERT: A 132 GLU cc_start: 0.8269 (pm20) cc_final: 0.8014 (pm20) REVERT: A 169 MET cc_start: 0.9427 (tpp) cc_final: 0.9037 (tpp) REVERT: A 191 MET cc_start: 0.9362 (mtt) cc_final: 0.8882 (mtt) REVERT: A 363 MET cc_start: 0.8891 (mmm) cc_final: 0.8002 (mmm) REVERT: A 364 GLN cc_start: 0.9500 (mm110) cc_final: 0.9173 (mm-40) REVERT: A 498 GLU cc_start: 0.9682 (mt-10) cc_final: 0.9413 (mt-10) REVERT: A 512 LEU cc_start: 0.9790 (mt) cc_final: 0.9482 (mt) REVERT: A 585 GLU cc_start: 0.9550 (pt0) cc_final: 0.9235 (pm20) REVERT: A 587 LEU cc_start: 0.9852 (tp) cc_final: 0.9588 (tp) REVERT: A 589 GLU cc_start: 0.9570 (mm-30) cc_final: 0.9358 (tp30) REVERT: A 673 MET cc_start: 0.9393 (tpt) cc_final: 0.9044 (tpt) REVERT: A 737 GLU cc_start: 0.9081 (pm20) cc_final: 0.8320 (mm-30) REVERT: B 132 GLU cc_start: 0.8327 (pm20) cc_final: 0.8096 (pm20) REVERT: B 169 MET cc_start: 0.9412 (tpp) cc_final: 0.9017 (tpp) REVERT: B 188 ILE cc_start: 0.9799 (mm) cc_final: 0.9530 (mm) REVERT: B 191 MET cc_start: 0.9339 (mtt) cc_final: 0.8858 (mtt) REVERT: B 363 MET cc_start: 0.8135 (tpp) cc_final: 0.7747 (tpp) REVERT: B 491 MET cc_start: 0.9392 (mmp) cc_final: 0.9149 (mmp) REVERT: B 512 LEU cc_start: 0.9783 (mt) cc_final: 0.9479 (mt) REVERT: B 580 GLU cc_start: 0.8550 (pt0) cc_final: 0.7889 (pm20) REVERT: B 585 GLU cc_start: 0.9536 (pt0) cc_final: 0.9214 (pm20) REVERT: B 587 LEU cc_start: 0.9858 (tp) cc_final: 0.9577 (tp) REVERT: B 673 MET cc_start: 0.9224 (tpt) cc_final: 0.9005 (tpt) REVERT: B 737 GLU cc_start: 0.9077 (pm20) cc_final: 0.8854 (pm20) outliers start: 32 outliers final: 21 residues processed: 148 average time/residue: 0.0835 time to fit residues: 19.5382 Evaluate side-chains 129 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 730 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** 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 = 0.3120 r_free = 0.3120 target = 0.055619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.042735 restraints weight = 54923.449| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 4.92 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13924 Z= 0.179 Angle : 0.650 9.296 19069 Z= 0.353 Chirality : 0.048 0.350 2084 Planarity : 0.003 0.035 2180 Dihedral : 18.221 174.568 2388 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.65 % Allowed : 13.85 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.22), residues: 1486 helix: 0.62 (0.24), residues: 454 sheet: -1.50 (0.31), residues: 238 loop : -0.26 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 379 TYR 0.025 0.002 TYR B 237 PHE 0.021 0.002 PHE B 561 TRP 0.009 0.001 TRP A 623 HIS 0.006 0.001 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (13924) covalent geometry : angle 0.65009 / 0.35 (19069) hydrogen bonds : bond 0.03816 / 2.48 ( 485) hydrogen bonds : angle 4.98058 / 3.32 ( 1400) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.433 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: symmetry clash REVERT: A 132 GLU cc_start: 0.8236 (pm20) cc_final: 0.7973 (pm20) REVERT: A 169 MET cc_start: 0.9440 (tpp) cc_final: 0.9025 (tpp) REVERT: A 191 MET cc_start: 0.9389 (mtt) cc_final: 0.8913 (mtt) REVERT: A 298 GLN cc_start: 0.9022 (mp10) cc_final: 0.8801 (mp10) REVERT: A 363 MET cc_start: 0.8967 (mmm) cc_final: 0.8020 (mmm) REVERT: A 364 GLN cc_start: 0.9503 (mm110) cc_final: 0.9164 (mm-40) REVERT: A 472 GLU cc_start: 0.8488 (tp30) cc_final: 0.8222 (tp30) REVERT: A 491 MET cc_start: 0.9184 (mmm) cc_final: 0.8963 (mmt) REVERT: A 498 GLU cc_start: 0.9684 (mt-10) cc_final: 0.9397 (mt-10) REVERT: A 512 LEU cc_start: 0.9770 (mt) cc_final: 0.9538 (mt) REVERT: A 517 LEU cc_start: 0.9649 (tp) cc_final: 0.9327 (tp) REVERT: A 585 GLU cc_start: 0.9566 (pt0) cc_final: 0.9191 (pm20) REVERT: A 589 GLU cc_start: 0.9595 (mm-30) cc_final: 0.9350 (tp30) REVERT: A 737 GLU cc_start: 0.9108 (pm20) cc_final: 0.8254 (mm-30) REVERT: B 132 GLU cc_start: 0.8268 (pm20) cc_final: 0.7953 (pm20) REVERT: B 169 MET cc_start: 0.9411 (tpp) cc_final: 0.8996 (tpp) REVERT: B 191 MET cc_start: 0.9373 (mtt) cc_final: 0.8978 (mtt) REVERT: B 298 GLN cc_start: 0.9032 (mp10) cc_final: 0.8790 (mp10) REVERT: B 302 MET cc_start: 0.8329 (ttt) cc_final: 0.8084 (tpt) REVERT: B 472 GLU cc_start: 0.8600 (tp30) cc_final: 0.8328 (tp30) REVERT: B 491 MET cc_start: 0.9351 (mmp) cc_final: 0.9094 (mmp) REVERT: B 512 LEU cc_start: 0.9757 (mt) cc_final: 0.9522 (mt) REVERT: B 517 LEU cc_start: 0.9664 (tp) cc_final: 0.9349 (tp) REVERT: B 580 GLU cc_start: 0.8498 (pt0) cc_final: 0.7793 (pm20) REVERT: B 585 GLU cc_start: 0.9552 (pt0) cc_final: 0.9218 (pm20) REVERT: B 587 LEU cc_start: 0.9838 (tp) cc_final: 0.9628 (tp) REVERT: B 737 GLU cc_start: 0.9100 (pm20) cc_final: 0.8240 (mm-30) outliers start: 22 outliers final: 15 residues processed: 139 average time/residue: 0.0834 time to fit residues: 18.7564 Evaluate side-chains 129 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 676 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** 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 = 0.3107 r_free = 0.3107 target = 0.054730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.041890 restraints weight = 56005.566| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 4.93 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13924 Z= 0.210 Angle : 0.658 9.340 19069 Z= 0.357 Chirality : 0.047 0.363 2084 Planarity : 0.003 0.039 2180 Dihedral : 18.251 177.667 2388 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.50 % Allowed : 13.92 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.22), residues: 1486 helix: 0.72 (0.24), residues: 454 sheet: -1.53 (0.31), residues: 238 loop : -0.21 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 379 TYR 0.026 0.002 TYR B 237 PHE 0.022 0.002 PHE A 561 TRP 0.022 0.002 TRP A 623 HIS 0.006 0.001 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (13924) covalent geometry : angle 0.65833 / 0.36 (19069) hydrogen bonds : bond 0.03880 / 2.50 ( 485) hydrogen bonds : angle 4.97083 / 3.31 ( 1400) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.335 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: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8264 (pm20) cc_final: 0.8008 (pm20) REVERT: A 169 MET cc_start: 0.9451 (tpp) cc_final: 0.9051 (tpp) REVERT: A 191 MET cc_start: 0.9391 (mtt) cc_final: 0.8943 (mtt) REVERT: A 298 GLN cc_start: 0.9037 (mp10) cc_final: 0.8798 (mp10) REVERT: A 363 MET cc_start: 0.8973 (mmm) cc_final: 0.8046 (mmm) REVERT: A 491 MET cc_start: 0.9159 (mmm) cc_final: 0.8852 (mmp) REVERT: A 512 LEU cc_start: 0.9758 (mt) cc_final: 0.9504 (mt) REVERT: A 517 LEU cc_start: 0.9664 (tp) cc_final: 0.9342 (tp) REVERT: A 533 MET cc_start: 0.8998 (tpp) cc_final: 0.8598 (ttm) REVERT: A 585 GLU cc_start: 0.9558 (pt0) cc_final: 0.9216 (pm20) REVERT: A 589 GLU cc_start: 0.9593 (mm-30) cc_final: 0.9386 (tp30) REVERT: A 673 MET cc_start: 0.9369 (tpt) cc_final: 0.9064 (tpt) REVERT: A 737 GLU cc_start: 0.9109 (pm20) cc_final: 0.8238 (mm-30) REVERT: B 132 GLU cc_start: 0.8307 (pm20) cc_final: 0.7992 (pm20) REVERT: B 169 MET cc_start: 0.9428 (tpp) cc_final: 0.9025 (tpp) REVERT: B 191 MET cc_start: 0.9391 (mtt) cc_final: 0.8924 (mtt) REVERT: B 298 GLN cc_start: 0.9072 (mp10) cc_final: 0.8828 (mp10) REVERT: B 353 MET cc_start: 0.9074 (mmm) cc_final: 0.8648 (mmm) REVERT: B 363 MET cc_start: 0.8029 (tpp) cc_final: 0.7238 (tpp) REVERT: B 472 GLU cc_start: 0.8632 (tp30) cc_final: 0.8362 (tp30) REVERT: B 491 MET cc_start: 0.9338 (mmp) cc_final: 0.9111 (mmp) REVERT: B 512 LEU cc_start: 0.9752 (mt) cc_final: 0.9503 (mt) REVERT: B 517 LEU cc_start: 0.9677 (tp) cc_final: 0.9368 (tp) REVERT: B 533 MET cc_start: 0.9066 (tpp) cc_final: 0.8610 (ttm) REVERT: B 585 GLU cc_start: 0.9556 (pt0) cc_final: 0.9217 (pm20) REVERT: B 587 LEU cc_start: 0.9840 (tp) cc_final: 0.9630 (tp) outliers start: 20 outliers final: 18 residues processed: 130 average time/residue: 0.0829 time to fit residues: 17.1013 Evaluate side-chains 131 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 730 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 46 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** 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 = 0.3082 r_free = 0.3082 target = 0.053862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.041146 restraints weight = 56446.249| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 4.88 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 13924 Z= 0.266 Angle : 0.694 9.896 19069 Z= 0.373 Chirality : 0.048 0.376 2084 Planarity : 0.004 0.040 2180 Dihedral : 18.343 178.113 2388 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.57 % Allowed : 13.92 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.22), residues: 1486 helix: 0.77 (0.24), residues: 448 sheet: -1.49 (0.32), residues: 240 loop : -0.20 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 379 TYR 0.027 0.002 TYR B 237 PHE 0.026 0.002 PHE B 561 TRP 0.033 0.002 TRP A 623 HIS 0.008 0.002 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.27 (13924) covalent geometry : angle 0.69350 / 0.37 (19069) hydrogen bonds : bond 0.03962 / 2.54 ( 485) hydrogen bonds : angle 5.05177 / 3.38 ( 1400) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.365 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: symmetry clash REVERT: A 132 GLU cc_start: 0.8307 (pm20) cc_final: 0.8066 (pm20) REVERT: A 169 MET cc_start: 0.9441 (tpp) cc_final: 0.9030 (tpp) REVERT: A 191 MET cc_start: 0.9380 (mtt) cc_final: 0.8924 (mtt) REVERT: A 491 MET cc_start: 0.9222 (mmm) cc_final: 0.8982 (mmt) REVERT: A 512 LEU cc_start: 0.9759 (mt) cc_final: 0.9502 (mt) REVERT: A 533 MET cc_start: 0.9042 (tpp) cc_final: 0.8680 (ttm) REVERT: A 585 GLU cc_start: 0.9543 (pt0) cc_final: 0.9206 (pm20) REVERT: A 589 GLU cc_start: 0.9620 (mm-30) cc_final: 0.9407 (tp30) REVERT: A 737 GLU cc_start: 0.9131 (pm20) cc_final: 0.8792 (pm20) REVERT: B 132 GLU cc_start: 0.8355 (pm20) cc_final: 0.8047 (pm20) REVERT: B 169 MET cc_start: 0.9446 (tpp) cc_final: 0.9041 (tpp) REVERT: B 191 MET cc_start: 0.9382 (mtt) cc_final: 0.8918 (mtt) REVERT: B 363 MET cc_start: 0.8095 (tpp) cc_final: 0.7333 (tpp) REVERT: B 364 GLN cc_start: 0.9563 (mm110) cc_final: 0.9237 (mm-40) REVERT: B 472 GLU cc_start: 0.8646 (tp30) cc_final: 0.8372 (tp30) REVERT: B 491 MET cc_start: 0.9356 (mmp) cc_final: 0.9135 (mmp) REVERT: B 512 LEU cc_start: 0.9758 (mt) cc_final: 0.9418 (mt) REVERT: B 585 GLU cc_start: 0.9554 (pt0) cc_final: 0.9254 (pm20) REVERT: B 587 LEU cc_start: 0.9843 (tp) cc_final: 0.9642 (tp) REVERT: B 737 GLU cc_start: 0.9090 (pm20) cc_final: 0.8280 (mm-30) outliers start: 21 outliers final: 21 residues processed: 126 average time/residue: 0.0874 time to fit residues: 17.4699 Evaluate side-chains 127 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 673 MET Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 730 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 95 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 131 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** 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 = 0.3105 r_free = 0.3105 target = 0.054740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.041982 restraints weight = 55896.958| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 4.90 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13924 Z= 0.192 Angle : 0.656 9.895 19069 Z= 0.354 Chirality : 0.047 0.375 2084 Planarity : 0.003 0.042 2180 Dihedral : 18.399 176.822 2388 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.65 % Allowed : 13.55 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.22), residues: 1486 helix: 0.76 (0.24), residues: 456 sheet: -1.42 (0.32), residues: 240 loop : -0.18 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 379 TYR 0.025 0.002 TYR B 237 PHE 0.021 0.002 PHE A 561 TRP 0.022 0.002 TRP A 623 HIS 0.005 0.001 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (13924) covalent geometry : angle 0.65611 / 0.35 (19069) hydrogen bonds : bond 0.03821 / 2.44 ( 485) hydrogen bonds : angle 4.94113 / 3.31 ( 1400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1694.13 seconds wall clock time: 30 minutes 24.45 seconds (1824.45 seconds total)