Starting phenix.real_space_refine on Fri Jul 3 10:51:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh9_61476/07_2026/9jh9_61476.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh9_61476/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jh9_61476/07_2026/9jh9_61476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh9_61476/07_2026/9jh9_61476.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jh9_61476/07_2026/9jh9_61476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh9_61476/07_2026/9jh9_61476.map" } 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-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 3.33, per 1000 atoms: 0.25 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: 1.06 Conformation dependent library (CDL) restraints added in 540.9 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: 1.56 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: 2.78 Time building geometry restraints manager: 1.45 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: 17904 1.92 - 3.84: 1004 3.84 - 5.77: 123 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 3.060 nonbonded pdb=" OD2 ASP B 544 " pdb="MN MN F 801 " model vdw 1.811 3.060 nonbonded pdb=" OP1 DT E 9 " pdb="MN MN E 801 " model vdw 1.827 3.060 nonbonded pdb=" OP1 DT F 9 " pdb="MN MN F 801 " model vdw 1.827 3.060 nonbonded pdb=" OP1 DA D 3 " pdb="MN MN D 801 " model vdw 1.869 3.060 ... (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: 0.010 Normalize map: mean=0, sd=1: 1.210 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.600 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- 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= 0.551 Angle : 0.991 9.612 19069 Z= 0.630 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 0.99110 / 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 : 0.493 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: 0.7474 (tp40) REVERT: B 741 GLN cc_start: 0.8191 (tp40) cc_final: 0.7431 (tp40) outliers start: 2 outliers final: 0 residues processed: 271 average time/residue: 0.1145 time to fit residues: 45.9963 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 : 0.651 ------------------------------------------------------------------------------- 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: 0.9980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 GLN ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN A 136 ASN A 242 ASN A 490 GLN ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN A 588 GLN B 28 GLN ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.059839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.046808 restraints weight = 53202.648| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 5.06 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13924 Z= 0.190 Angle : 0.755 8.904 19069 Z= 0.416 Chirality : 0.051 0.194 2084 Planarity : 0.004 0.033 2180 Dihedral : 18.162 159.859 2388 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.31 % Favored : 95.56 % Rotamer: Outliers : 1.57 % Allowed : 10.93 % Favored : 87.50 % 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: -1.64 (0.20), residues: 1486 helix: -0.62 (0.23), residues: 444 sheet: -1.55 (0.29), residues: 246 loop : -1.14 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 263 TYR 0.028 0.002 TYR B 237 PHE 0.021 0.002 PHE A 388 TRP 0.022 0.003 TRP B 623 HIS 0.011 0.002 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (13924) covalent geometry : angle 0.75501 / 0.42 (19069) hydrogen bonds : bond 0.05696 / 3.68 ( 485) hydrogen bonds : angle 6.30225 / 4.17 ( 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 191 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 PHE cc_start: 0.8771 (m-80) cc_final: 0.8274 (m-80) REVERT: A 139 LEU cc_start: 0.9133 (tp) cc_final: 0.8698 (tp) REVERT: A 169 MET cc_start: 0.9333 (tpp) cc_final: 0.9122 (tpp) REVERT: A 191 MET cc_start: 0.9333 (mtt) cc_final: 0.9020 (mtt) REVERT: A 266 LYS cc_start: 0.7711 (pttt) cc_final: 0.7509 (pptt) REVERT: A 363 MET cc_start: 0.8882 (mmm) cc_final: 0.8474 (tpt) REVERT: A 426 ASN cc_start: 0.9512 (t0) cc_final: 0.9151 (p0) REVERT: A 466 MET cc_start: 0.8630 (ptt) cc_final: 0.8223 (ptp) REVERT: A 587 LEU cc_start: 0.9814 (mt) cc_final: 0.9568 (tp) REVERT: A 620 ASP cc_start: 0.9180 (m-30) cc_final: 0.8530 (p0) REVERT: A 699 MET cc_start: 0.8597 (mmt) cc_final: 0.8268 (mmt) REVERT: A 705 GLN cc_start: 0.9455 (mt0) cc_final: 0.8942 (mp10) REVERT: A 741 GLN cc_start: 0.8721 (tp40) cc_final: 0.7515 (tp40) REVERT: B 15 PHE cc_start: 0.8751 (m-80) cc_final: 0.8254 (m-80) REVERT: B 132 GLU cc_start: 0.8131 (pm20) cc_final: 0.7926 (pm20) REVERT: B 139 LEU cc_start: 0.9096 (tp) cc_final: 0.8745 (tp) REVERT: B 169 MET cc_start: 0.9270 (tpp) cc_final: 0.9046 (tpp) REVERT: B 191 MET cc_start: 0.9307 (mtt) cc_final: 0.8982 (mtt) REVERT: B 426 ASN cc_start: 0.9498 (t0) cc_final: 0.9095 (p0) REVERT: B 517 LEU cc_start: 0.9554 (tp) cc_final: 0.9220 (tp) REVERT: B 620 ASP cc_start: 0.9178 (m-30) cc_final: 0.8582 (p0) REVERT: B 705 GLN cc_start: 0.9442 (mt0) cc_final: 0.8925 (mp10) REVERT: B 737 GLU cc_start: 0.8926 (pm20) cc_final: 0.8644 (mm-30) REVERT: B 741 GLN cc_start: 0.8738 (tp40) cc_final: 0.7498 (tp40) outliers start: 21 outliers final: 10 residues processed: 182 average time/residue: 0.0892 time to fit residues: 26.0041 Evaluate side-chains 141 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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: 5.9990 chunk 45 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 ASN A 155 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 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 = 0.3172 r_free = 0.3172 target = 0.059142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.046077 restraints weight = 54692.973| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 5.03 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13924 Z= 0.195 Angle : 0.690 8.869 19069 Z= 0.378 Chirality : 0.047 0.231 2084 Planarity : 0.004 0.054 2180 Dihedral : 18.190 163.453 2388 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.40 % Allowed : 11.00 % Favored : 86.60 % 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: -1.25 (0.20), residues: 1486 helix: -0.16 (0.24), residues: 448 sheet: -1.56 (0.30), residues: 242 loop : -0.90 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 307 TYR 0.024 0.002 TYR B 237 PHE 0.013 0.001 PHE A 388 TRP 0.015 0.002 TRP B 623 HIS 0.004 0.001 HIS B 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (13924) covalent geometry : angle 0.68988 / 0.38 (19069) hydrogen bonds : bond 0.04862 / 3.18 ( 485) hydrogen bonds : angle 5.66868 / 3.73 ( 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 174 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.501 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: 0.8094 (pm20) cc_final: 0.7819 (pm20) REVERT: A 169 MET cc_start: 0.9371 (tpp) cc_final: 0.9066 (tpp) REVERT: A 178 CYS cc_start: 0.8119 (p) cc_final: 0.7842 (p) REVERT: A 191 MET cc_start: 0.9375 (mtt) cc_final: 0.8981 (mtt) REVERT: A 298 GLN cc_start: 0.9139 (mp10) cc_final: 0.8745 (mp10) REVERT: A 363 MET cc_start: 0.8798 (mmm) cc_final: 0.7945 (mmm) REVERT: A 426 ASN cc_start: 0.9508 (t0) cc_final: 0.9295 (t0) REVERT: A 466 MET cc_start: 0.8700 (ptt) cc_final: 0.8322 (ptp) REVERT: A 585 GLU cc_start: 0.9496 (pt0) cc_final: 0.9131 (pm20) REVERT: A 587 LEU cc_start: 0.9838 (mt) cc_final: 0.9549 (tp) REVERT: A 620 ASP cc_start: 0.9248 (m-30) cc_final: 0.8598 (p0) REVERT: A 705 GLN cc_start: 0.9464 (mt0) cc_final: 0.8952 (mp10) REVERT: B 132 GLU cc_start: 0.8191 (pm20) cc_final: 0.7976 (pm20) REVERT: B 169 MET cc_start: 0.9330 (tpp) cc_final: 0.9016 (tpp) REVERT: B 178 CYS cc_start: 0.8123 (p) cc_final: 0.7471 (p) REVERT: B 191 MET cc_start: 0.9341 (mtt) cc_final: 0.8929 (mtt) REVERT: B 298 GLN cc_start: 0.9153 (mp10) cc_final: 0.8768 (mp10) REVERT: B 426 ASN cc_start: 0.9534 (t0) cc_final: 0.9306 (t0) REVERT: B 466 MET cc_start: 0.8767 (ptt) cc_final: 0.8375 (ptp) REVERT: B 585 GLU cc_start: 0.9503 (pt0) cc_final: 0.9147 (pm20) REVERT: B 587 LEU cc_start: 0.9845 (mt) cc_final: 0.9592 (tp) REVERT: B 620 ASP cc_start: 0.9237 (m-30) cc_final: 0.8680 (p0) REVERT: B 699 MET cc_start: 0.8711 (mmt) cc_final: 0.8506 (mmt) REVERT: B 705 GLN cc_start: 0.9487 (mt0) cc_final: 0.8980 (mp10) REVERT: B 737 GLU cc_start: 0.9021 (pm20) cc_final: 0.8563 (mm-30) outliers start: 32 outliers final: 16 residues processed: 170 average time/residue: 0.1005 time to fit residues: 26.7234 Evaluate side-chains 142 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP 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 675 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 482 TRP Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 134 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN B 288 ASN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.054950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.041991 restraints weight = 57933.632| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 4.98 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 13924 Z= 0.368 Angle : 0.793 8.713 19069 Z= 0.429 Chirality : 0.049 0.251 2084 Planarity : 0.004 0.038 2180 Dihedral : 18.239 167.722 2388 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.77 % Allowed : 11.30 % Favored : 85.93 % 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: -0.85 (0.21), residues: 1486 helix: 0.17 (0.24), residues: 452 sheet: -1.62 (0.29), residues: 258 loop : -0.51 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 548 TYR 0.032 0.003 TYR A 511 PHE 0.020 0.002 PHE B 458 TRP 0.013 0.002 TRP A 623 HIS 0.017 0.003 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00767 / 0.37 (13924) covalent geometry : angle 0.79277 / 0.43 (19069) hydrogen bonds : bond 0.04648 / 3.02 ( 485) hydrogen bonds : angle 5.54446 / 3.66 ( 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 174 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.490 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: 0.8201 (pm20) cc_final: 0.7962 (pm20) REVERT: A 169 MET cc_start: 0.9442 (tpp) cc_final: 0.9100 (tpp) REVERT: A 178 CYS cc_start: 0.8456 (p) cc_final: 0.7737 (p) REVERT: A 191 MET cc_start: 0.9379 (mtt) cc_final: 0.8915 (mtt) REVERT: A 266 LYS cc_start: 0.7749 (pttt) cc_final: 0.7504 (pptt) REVERT: A 363 MET cc_start: 0.8833 (mmm) cc_final: 0.7973 (mmm) REVERT: A 364 GLN cc_start: 0.9510 (mm110) cc_final: 0.9164 (mm-40) REVERT: A 403 SER cc_start: 0.9698 (m) cc_final: 0.9496 (p) REVERT: A 426 ASN cc_start: 0.9523 (t0) cc_final: 0.9319 (t0) REVERT: A 580 GLU cc_start: 0.8382 (pt0) cc_final: 0.7819 (pm20) REVERT: A 585 GLU cc_start: 0.9530 (pt0) cc_final: 0.9206 (pm20) REVERT: A 587 LEU cc_start: 0.9854 (mt) cc_final: 0.9572 (tp) REVERT: A 705 GLN cc_start: 0.9530 (mt0) cc_final: 0.9028 (mp10) REVERT: B 132 GLU cc_start: 0.8292 (pm20) cc_final: 0.8082 (pm20) REVERT: B 169 MET cc_start: 0.9404 (tpp) cc_final: 0.9066 (tpp) REVERT: B 191 MET cc_start: 0.9362 (mtt) cc_final: 0.8869 (mtt) REVERT: B 266 LYS cc_start: 0.7786 (pttt) cc_final: 0.7547 (pptt) REVERT: B 298 GLN cc_start: 0.9192 (mp10) cc_final: 0.8803 (mp10) REVERT: B 302 MET cc_start: 0.8534 (ttt) cc_final: 0.8304 (ttt) REVERT: B 363 MET cc_start: 0.8231 (tpp) cc_final: 0.7854 (tpp) REVERT: B 580 GLU cc_start: 0.8424 (pt0) cc_final: 0.7864 (pm20) REVERT: B 585 GLU cc_start: 0.9522 (pt0) cc_final: 0.9259 (pm20) REVERT: B 587 LEU cc_start: 0.9860 (mt) cc_final: 0.9540 (tp) REVERT: B 705 GLN cc_start: 0.9535 (mt0) cc_final: 0.9090 (mp10) outliers start: 37 outliers final: 22 residues processed: 169 average time/residue: 0.0903 time to fit residues: 24.5049 Evaluate side-chains 135 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 109 ILE 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 262 VAL 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 454 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain B residue 109 ILE 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 675 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3128 r_free = 0.3128 target = 0.056995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.043743 restraints weight = 56568.412| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 5.04 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13924 Z= 0.178 Angle : 0.658 7.450 19069 Z= 0.361 Chirality : 0.047 0.266 2084 Planarity : 0.003 0.033 2180 Dihedral : 18.222 168.040 2388 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.65 % Allowed : 12.87 % Favored : 85.48 % 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: -0.60 (0.22), residues: 1486 helix: 0.44 (0.24), residues: 452 sheet: -1.56 (0.29), residues: 258 loop : -0.37 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 613 TYR 0.024 0.002 TYR B 237 PHE 0.019 0.002 PHE B 750 TRP 0.009 0.002 TRP B 623 HIS 0.009 0.002 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (13924) covalent geometry : angle 0.65808 / 0.36 (19069) hydrogen bonds : bond 0.04108 / 2.70 ( 485) hydrogen bonds : angle 5.23380 / 3.47 ( 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 151 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.563 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: 0.8255 (pm20) cc_final: 0.7999 (pm20) REVERT: A 169 MET cc_start: 0.9395 (tpp) cc_final: 0.9014 (tpp) REVERT: A 191 MET cc_start: 0.9364 (mtt) cc_final: 0.8892 (mtt) REVERT: A 298 GLN cc_start: 0.9064 (mp10) cc_final: 0.8757 (mp10) REVERT: A 302 MET cc_start: 0.8509 (ttt) cc_final: 0.8225 (ttt) REVERT: A 363 MET cc_start: 0.8869 (mmm) cc_final: 0.8020 (mmm) REVERT: A 512 LEU cc_start: 0.9791 (mt) cc_final: 0.9511 (mt) REVERT: A 585 GLU cc_start: 0.9531 (pt0) cc_final: 0.9154 (pm20) REVERT: A 737 GLU cc_start: 0.7520 (mm-30) cc_final: 0.6918 (mm-30) REVERT: B 132 GLU cc_start: 0.8279 (pm20) cc_final: 0.7960 (pm20) REVERT: B 169 MET cc_start: 0.9367 (tpp) cc_final: 0.8984 (tpp) REVERT: B 191 MET cc_start: 0.9337 (mtt) cc_final: 0.8842 (mtt) REVERT: B 298 GLN cc_start: 0.9168 (mp10) cc_final: 0.8780 (mp10) REVERT: B 363 MET cc_start: 0.8175 (tpp) cc_final: 0.7911 (tpp) REVERT: B 512 LEU cc_start: 0.9799 (mt) cc_final: 0.9518 (mt) REVERT: B 517 LEU cc_start: 0.9646 (tp) cc_final: 0.9357 (tp) REVERT: B 580 GLU cc_start: 0.8360 (pt0) cc_final: 0.7795 (pm20) REVERT: B 585 GLU cc_start: 0.9528 (pt0) cc_final: 0.9170 (pm20) REVERT: B 705 GLN cc_start: 0.9546 (mt0) cc_final: 0.9062 (mp10) outliers start: 22 outliers final: 15 residues processed: 150 average time/residue: 0.1091 time to fit residues: 25.2812 Evaluate side-chains 134 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 262 VAL 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 454 ASN Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 620 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: 10.0000 chunk 50 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 126 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- 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 = 0.3089 r_free = 0.3089 target = 0.055106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.041984 restraints weight = 58056.075| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 5.00 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 13924 Z= 0.280 Angle : 0.701 7.772 19069 Z= 0.381 Chirality : 0.047 0.299 2084 Planarity : 0.004 0.034 2180 Dihedral : 18.299 172.605 2388 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.54 % Allowed : 12.57 % Favored : 84.88 % 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: -0.53 (0.22), residues: 1486 helix: 0.51 (0.24), residues: 452 sheet: -1.62 (0.29), residues: 258 loop : -0.29 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 613 TYR 0.027 0.002 TYR B 237 PHE 0.023 0.002 PHE B 561 TRP 0.015 0.002 TRP A 623 HIS 0.011 0.002 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.28 (13924) covalent geometry : angle 0.70057 / 0.38 (19069) hydrogen bonds : bond 0.04111 / 2.67 ( 485) hydrogen bonds : angle 5.21875 / 3.46 ( 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 152 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.518 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: 0.8279 (pm20) cc_final: 0.8036 (pm20) REVERT: A 169 MET cc_start: 0.9448 (tpp) cc_final: 0.9055 (tpp) REVERT: A 191 MET cc_start: 0.9359 (mtt) cc_final: 0.8879 (mtt) REVERT: A 363 MET cc_start: 0.8894 (mmm) cc_final: 0.7938 (mmm) REVERT: A 364 GLN cc_start: 0.9523 (mm110) cc_final: 0.9163 (mm-40) REVERT: A 498 GLU cc_start: 0.9691 (mt-10) cc_final: 0.9330 (mp0) REVERT: A 512 LEU cc_start: 0.9799 (mt) cc_final: 0.9490 (mt) REVERT: A 585 GLU cc_start: 0.9541 (pt0) cc_final: 0.9210 (pm20) REVERT: B 132 GLU cc_start: 0.8344 (pm20) cc_final: 0.8048 (pm20) REVERT: B 169 MET cc_start: 0.9425 (tpp) cc_final: 0.9035 (tpp) REVERT: B 191 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.8843 (mtt) REVERT: B 298 GLN cc_start: 0.9154 (mp10) cc_final: 0.8772 (mp10) REVERT: B 512 LEU cc_start: 0.9795 (mt) cc_final: 0.9487 (mt) REVERT: B 580 GLU cc_start: 0.8395 (pt0) cc_final: 0.7805 (pm20) REVERT: B 585 GLU cc_start: 0.9529 (pt0) cc_final: 0.9216 (pm20) REVERT: B 587 LEU cc_start: 0.9853 (tp) cc_final: 0.9593 (tp) REVERT: B 737 GLU cc_start: 0.9113 (pm20) cc_final: 0.8434 (mm-30) outliers start: 34 outliers final: 23 residues processed: 148 average time/residue: 0.0944 time to fit residues: 21.8827 Evaluate side-chains 135 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 262 VAL 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 454 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 262 VAL 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 454 ASN Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 676 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 140 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.3106 r_free = 0.3106 target = 0.055512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.042431 restraints weight = 56935.591| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 4.96 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3644 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= 0.211 Angle : 0.670 9.003 19069 Z= 0.364 Chirality : 0.047 0.318 2084 Planarity : 0.004 0.036 2180 Dihedral : 18.333 175.408 2388 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.25 % Allowed : 12.87 % Favored : 84.88 % 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: -0.47 (0.22), residues: 1486 helix: 0.57 (0.24), residues: 452 sheet: -1.59 (0.30), residues: 258 loop : -0.26 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 379 TYR 0.027 0.002 TYR A 511 PHE 0.025 0.002 PHE B 561 TRP 0.020 0.002 TRP A 623 HIS 0.008 0.002 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (13924) covalent geometry : angle 0.66988 / 0.36 (19069) hydrogen bonds : bond 0.03926 / 2.55 ( 485) hydrogen bonds : angle 5.09405 / 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 147 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.517 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: 0.8266 (pm20) cc_final: 0.8021 (pm20) REVERT: A 169 MET cc_start: 0.9441 (tpp) cc_final: 0.9041 (tpp) REVERT: A 191 MET cc_start: 0.9373 (mtt) cc_final: 0.8888 (mtt) REVERT: A 363 MET cc_start: 0.8918 (mmm) cc_final: 0.8013 (mmm) REVERT: A 491 MET cc_start: 0.8828 (mmt) cc_final: 0.8364 (mmm) REVERT: A 512 LEU cc_start: 0.9775 (mt) cc_final: 0.9547 (mt) REVERT: A 585 GLU cc_start: 0.9530 (pt0) cc_final: 0.9157 (pm20) REVERT: B 132 GLU cc_start: 0.8334 (pm20) cc_final: 0.8027 (pm20) REVERT: B 169 MET cc_start: 0.9395 (tpp) cc_final: 0.8983 (tpp) REVERT: B 191 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.8957 (mtt) REVERT: B 281 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9154 (p) REVERT: B 298 GLN cc_start: 0.9153 (mp10) cc_final: 0.8780 (mp10) REVERT: B 472 GLU cc_start: 0.8608 (tp30) cc_final: 0.8336 (tp30) REVERT: B 512 LEU cc_start: 0.9772 (mt) cc_final: 0.9548 (mt) REVERT: B 580 GLU cc_start: 0.8387 (pt0) cc_final: 0.7800 (pm20) REVERT: B 585 GLU cc_start: 0.9531 (pt0) cc_final: 0.9198 (pm20) REVERT: B 673 MET cc_start: 0.9171 (tpt) cc_final: 0.8860 (tpt) REVERT: B 737 GLU cc_start: 0.9104 (pm20) cc_final: 0.8281 (mm-30) outliers start: 30 outliers final: 19 residues processed: 144 average time/residue: 0.0856 time to fit residues: 19.8548 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 : 0.434 ------------------------------------------------------------------------------- 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 181 ASP 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 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 21 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 359 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3110 r_free = 0.3110 target = 0.055651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.042582 restraints weight = 56526.970| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 4.98 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13924 Z= 0.192 Angle : 0.657 8.959 19069 Z= 0.354 Chirality : 0.048 0.330 2084 Planarity : 0.003 0.036 2180 Dihedral : 18.367 178.535 2388 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.32 % Allowed : 12.95 % Favored : 84.73 % 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: -0.43 (0.22), residues: 1486 helix: 0.61 (0.24), residues: 454 sheet: -1.57 (0.31), residues: 238 loop : -0.28 (0.23), residues: 794 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 0.022 0.002 PHE A 561 TRP 0.017 0.002 TRP B 623 HIS 0.006 0.001 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (13924) covalent geometry : angle 0.65700 / 0.35 (19069) hydrogen bonds : bond 0.03870 / 2.51 ( 485) hydrogen bonds : angle 5.00656 / 3.34 ( 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 146 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.470 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: 0.8293 (pm20) cc_final: 0.8036 (pm20) REVERT: A 169 MET cc_start: 0.9427 (tpp) cc_final: 0.9024 (tpp) REVERT: A 191 MET cc_start: 0.9395 (mtt) cc_final: 0.9003 (mtt) REVERT: A 363 MET cc_start: 0.8923 (mmm) cc_final: 0.7994 (mmm) REVERT: A 472 GLU cc_start: 0.8569 (tp30) cc_final: 0.8276 (tp30) REVERT: A 512 LEU cc_start: 0.9762 (mt) cc_final: 0.9502 (mt) REVERT: A 580 GLU cc_start: 0.8665 (pt0) cc_final: 0.8085 (pm20) REVERT: A 585 GLU cc_start: 0.9527 (pt0) cc_final: 0.9148 (pm20) REVERT: B 132 GLU cc_start: 0.8343 (pm20) cc_final: 0.8037 (pm20) REVERT: B 169 MET cc_start: 0.9401 (tpp) cc_final: 0.8991 (tpp) REVERT: B 191 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.8984 (mtt) REVERT: B 298 GLN cc_start: 0.9149 (mp10) cc_final: 0.8773 (mp10) REVERT: B 472 GLU cc_start: 0.8630 (tp30) cc_final: 0.8350 (tp30) REVERT: B 512 LEU cc_start: 0.9756 (mt) cc_final: 0.9499 (mt) REVERT: B 580 GLU cc_start: 0.8346 (pt0) cc_final: 0.7793 (pm20) REVERT: B 585 GLU cc_start: 0.9532 (pt0) cc_final: 0.9155 (pm20) REVERT: B 673 MET cc_start: 0.9227 (tpt) cc_final: 0.9001 (tpt) REVERT: B 737 GLU cc_start: 0.9115 (pm20) cc_final: 0.8285 (mm-30) outliers start: 31 outliers final: 22 residues processed: 139 average time/residue: 0.0895 time to fit residues: 20.1496 Evaluate side-chains 135 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 181 ASP 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 463 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 234 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 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: 1.9990 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 240 ASN ** 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 = 0.3140 r_free = 0.3140 target = 0.056918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.044146 restraints weight = 56163.340| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.98 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13924 Z= 0.147 Angle : 0.643 9.366 19069 Z= 0.345 Chirality : 0.047 0.332 2084 Planarity : 0.003 0.033 2180 Dihedral : 18.371 179.954 2388 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.02 % Allowed : 13.25 % Favored : 84.73 % 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: -0.35 (0.22), residues: 1486 helix: 0.64 (0.24), residues: 458 sheet: -1.46 (0.32), residues: 238 loop : -0.25 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 379 TYR 0.024 0.001 TYR B 237 PHE 0.018 0.002 PHE B 561 TRP 0.019 0.002 TRP B 623 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (13924) covalent geometry : angle 0.64295 / 0.34 (19069) hydrogen bonds : bond 0.03801 / 2.44 ( 485) hydrogen bonds : angle 4.89998 / 3.28 ( 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 146 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8252 (pm20) cc_final: 0.7981 (pm20) REVERT: A 169 MET cc_start: 0.9403 (tpp) cc_final: 0.8963 (tpp) REVERT: A 191 MET cc_start: 0.9437 (mtt) cc_final: 0.8987 (mtt) REVERT: A 207 TRP cc_start: 0.8784 (m-10) cc_final: 0.8506 (m-10) REVERT: A 363 MET cc_start: 0.8910 (mmm) cc_final: 0.7949 (mmm) REVERT: A 512 LEU cc_start: 0.9742 (mt) cc_final: 0.9499 (mt) REVERT: A 580 GLU cc_start: 0.8605 (pt0) cc_final: 0.7904 (pm20) REVERT: A 585 GLU cc_start: 0.9527 (pt0) cc_final: 0.9159 (pm20) REVERT: A 673 MET cc_start: 0.9293 (tpt) cc_final: 0.8988 (tpt) REVERT: B 132 GLU cc_start: 0.8325 (pm20) cc_final: 0.8012 (pm20) REVERT: B 169 MET cc_start: 0.9397 (tpp) cc_final: 0.8974 (tpp) REVERT: B 191 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.8981 (mtt) REVERT: B 298 GLN cc_start: 0.9132 (mp10) cc_final: 0.8881 (mp10) REVERT: B 363 MET cc_start: 0.7975 (tpp) cc_final: 0.7656 (tpp) REVERT: B 364 GLN cc_start: 0.9552 (mm110) cc_final: 0.9231 (mm-40) REVERT: B 472 GLU cc_start: 0.8626 (tp30) cc_final: 0.8339 (tp30) REVERT: B 512 LEU cc_start: 0.9740 (mt) cc_final: 0.9503 (mt) REVERT: B 580 GLU cc_start: 0.8342 (pt0) cc_final: 0.7831 (pm20) REVERT: B 585 GLU cc_start: 0.9526 (pt0) cc_final: 0.9151 (pm20) REVERT: B 737 GLU cc_start: 0.9099 (pm20) cc_final: 0.8209 (mm-30) outliers start: 27 outliers final: 18 residues processed: 138 average time/residue: 0.0867 time to fit residues: 19.3236 Evaluate side-chains 127 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 237 TYR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 378 VAL 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 688 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 234 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 432 PHE Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 675 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 46 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 88 optimal weight: 0.0670 chunk 139 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 overall best weight: 4.3924 ------------------------------------------------------------------------------- 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 = 0.3094 r_free = 0.3094 target = 0.054353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.041462 restraints weight = 57662.689| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 4.97 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13924 Z= 0.258 Angle : 0.693 9.925 19069 Z= 0.370 Chirality : 0.047 0.335 2084 Planarity : 0.004 0.035 2180 Dihedral : 18.399 175.872 2388 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.95 % Allowed : 14.07 % Favored : 83.98 % 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: -0.29 (0.22), residues: 1486 helix: 0.69 (0.24), residues: 462 sheet: -1.47 (0.32), residues: 244 loop : -0.17 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 379 TYR 0.027 0.002 TYR B 237 PHE 0.027 0.002 PHE B 561 TRP 0.017 0.002 TRP B 207 HIS 0.007 0.002 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.26 (13924) covalent geometry : angle 0.69282 / 0.37 (19069) hydrogen bonds : bond 0.03970 / 2.54 ( 485) hydrogen bonds : angle 4.99900 / 3.33 ( 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 131 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.561 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: 0.8331 (pm20) cc_final: 0.8085 (pm20) REVERT: A 169 MET cc_start: 0.9424 (tpp) cc_final: 0.8994 (tpp) REVERT: A 191 MET cc_start: 0.9405 (mtt) cc_final: 0.8938 (mtt) REVERT: A 512 LEU cc_start: 0.9749 (mt) cc_final: 0.9498 (mt) REVERT: A 533 MET cc_start: 0.9079 (tpp) cc_final: 0.8752 (ttm) REVERT: A 580 GLU cc_start: 0.8626 (pt0) cc_final: 0.7885 (pm20) REVERT: A 585 GLU cc_start: 0.9537 (pt0) cc_final: 0.9117 (pm20) REVERT: A 673 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.8949 (tpt) REVERT: B 132 GLU cc_start: 0.8396 (pm20) cc_final: 0.8092 (pm20) REVERT: B 169 MET cc_start: 0.9427 (tpp) cc_final: 0.9016 (tpp) REVERT: B 191 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.8985 (mtt) REVERT: B 364 GLN cc_start: 0.9560 (mm110) cc_final: 0.9235 (mm-40) REVERT: B 472 GLU cc_start: 0.8675 (tp30) cc_final: 0.8384 (tp30) REVERT: B 512 LEU cc_start: 0.9749 (mt) cc_final: 0.9478 (mt) REVERT: B 580 GLU cc_start: 0.8344 (pt0) cc_final: 0.7797 (pm20) REVERT: B 585 GLU cc_start: 0.9525 (pt0) cc_final: 0.9145 (pm20) REVERT: B 737 GLU cc_start: 0.9120 (pm20) cc_final: 0.8254 (mm-30) outliers start: 26 outliers final: 20 residues processed: 123 average time/residue: 0.1045 time to fit residues: 20.6015 Evaluate side-chains 126 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 237 TYR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 234 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 432 PHE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 676 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 95 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3117 r_free = 0.3117 target = 0.055563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.042854 restraints weight = 56533.503| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 4.98 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13924 Z= 0.177 Angle : 0.657 9.550 19069 Z= 0.352 Chirality : 0.047 0.334 2084 Planarity : 0.004 0.048 2180 Dihedral : 18.413 174.686 2388 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.57 % Allowed : 14.45 % Favored : 83.98 % 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: -0.23 (0.22), residues: 1486 helix: 0.76 (0.24), residues: 462 sheet: -1.40 (0.32), residues: 238 loop : -0.17 (0.24), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 379 TYR 0.025 0.002 TYR B 237 PHE 0.022 0.002 PHE A 561 TRP 0.018 0.002 TRP B 207 HIS 0.005 0.001 HIS B 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (13924) covalent geometry : angle 0.65713 / 0.35 (19069) hydrogen bonds : bond 0.03793 / 2.44 ( 485) hydrogen bonds : angle 4.95583 / 3.32 ( 1400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1903.70 seconds wall clock time: 34 minutes 10.70 seconds (2050.70 seconds total)