Starting phenix.real_space_refine on Thu Sep 18 03:43:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh9_61476/09_2025/9jh9_61476.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh9_61476/09_2025/9jh9_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_61476/09_2025/9jh9_61476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh9_61476/09_2025/9jh9_61476.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jh9_61476/09_2025/9jh9_61476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh9_61476/09_2025/9jh9_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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13509 Number of models: 1 Model: "" Number of chains: 6 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: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'DNA': 1} Modifications used: {'5*END': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, D, F Time building chain proxies: 5.91, per 1000 atoms: 0.44 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: 1.07 Conformation dependent library (CDL) restraints added in 580.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.85 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: 2.67 Time building geometry restraints manager: 1.46 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: 3606 1.44 - 1.56: 7563 1.56 - 1.68: 134 1.68 - 1.80: 70 Bond restraints: 13922 Sorted by residual: bond pdb=" C ARG B 721 " pdb=" N LEU B 722 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.47e-02 4.63e+03 7.65e+00 bond pdb=" N ASP B 64 " pdb=" CA ASP B 64 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.23e-02 6.61e+03 7.44e+00 bond pdb=" C ARG A 721 " pdb=" N LEU A 722 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.47e-02 4.63e+03 7.44e+00 bond pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.23e-02 6.61e+03 7.13e+00 bond pdb=" CB ILE A 300 " pdb=" CG2 ILE A 300 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.22e+00 ... (remaining 13917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 18004 1.92 - 3.84: 901 3.84 - 5.77: 121 5.77 - 7.69: 24 7.69 - 9.61: 14 Bond angle restraints: 19064 Sorted by residual: 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 angle pdb=" N LYS A 63 " pdb=" CA LYS A 63 " pdb=" C LYS A 63 " ideal model delta sigma weight residual 110.14 101.64 8.50 1.55e+00 4.16e-01 3.01e+01 angle pdb=" C ASP A 468 " pdb=" N GLU A 469 " pdb=" CA GLU A 469 " ideal model delta sigma weight residual 120.63 127.66 -7.03 1.61e+00 3.86e-01 1.90e+01 ... (remaining 19059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.72: 7847 28.72 - 57.44: 367 57.44 - 86.15: 30 86.15 - 114.87: 4 114.87 - 143.59: 2 Dihedral angle restraints: 8250 sinusoidal: 3876 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 8247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1508 0.059 - 0.118: 461 0.118 - 0.177: 105 0.177 - 0.236: 4 0.236 - 0.295: 4 Chirality restraints: 2082 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 2079 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: 1.41 - 2.11: 12 2.11 - 2.80: 3782 2.80 - 3.50: 17691 3.50 - 4.20: 34104 4.20 - 4.90: 57596 Nonbonded interactions: 113185 Sorted by model distance: nonbonded pdb=" O4' DA F 6 " pdb=" C1' DA F 6 " model vdw 1.407 3.470 nonbonded pdb=" C4' DA F 6 " pdb=" O4' DA F 6 " model vdw 1.451 3.470 nonbonded pdb=" OD2 ASP A 544 " pdb="MN MN E 801 " model vdw 1.798 2.320 nonbonded pdb=" OD2 ASP B 544 " pdb="MN MN F 801 " model vdw 1.811 2.320 nonbonded pdb=" OP1 DT E 9 " pdb="MN MN E 801 " model vdw 1.827 2.320 ... (remaining 113180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 1 through 5 or (resid 6 and (name P or name OP1 or name OP \ 2 or name O5' or name C5' or name C4' or name C3' or name O3' or name C2' or nam \ e C1' or name N9 or name C8 or name N7 or name C5 or name C6 or name N6 or name \ N1 or name C2 or name N3 or name C4 )) or resid 7 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.660 Find NCS groups from input model: 0.170 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.009 0.075 13922 Z= 0.397 Angle : 0.962 9.612 19064 Z= 0.534 Chirality : 0.058 0.295 2082 Planarity : 0.006 0.044 2180 Dihedral : 15.128 143.591 5462 Min Nonbonded Distance : 1.407 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 aren 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 covalent geometry : bond 0.00940 (13922) covalent geometry : angle 0.96245 (19064) hydrogen bonds : bond 0.19960 ( 485) hydrogen bonds : angle 8.76866 ( 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 : 0.452 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: 0.1157 time to fit residues: 46.1369 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 : 0.459 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 55 ASN A 97 ASN A 136 ASN A 155 ASN A 242 ASN A 490 GLN A 574 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN B 55 ASN B 97 ASN B 136 ASN B 155 ASN B 490 GLN B 513 HIS B 574 ASN ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.060606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.047717 restraints weight = 52439.282| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 4.94 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13922 Z= 0.160 Angle : 0.688 8.729 19064 Z= 0.372 Chirality : 0.047 0.203 2082 Planarity : 0.004 0.037 2180 Dihedral : 18.291 163.980 2384 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.20 % Allowed : 10.78 % Favored : 88.02 % 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 aren not related in a simple way. whole: -1.49 (0.19), residues: 1486 helix: -0.43 (0.23), residues: 444 sheet: -1.29 (0.29), residues: 236 loop : -1.17 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.022 0.002 TYR B 237 PHE 0.018 0.002 PHE A 61 TRP 0.023 0.003 TRP B 623 HIS 0.006 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00358 (13922) covalent geometry : angle 0.68780 (19064) hydrogen bonds : bond 0.04818 ( 485) hydrogen bonds : angle 5.79138 ( 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 201 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.398 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 113 LEU cc_start: 0.9616 (mm) cc_final: 0.9378 (tp) REVERT: A 132 GLU cc_start: 0.8178 (pm20) cc_final: 0.7875 (pm20) REVERT: A 139 LEU cc_start: 0.9157 (tp) cc_final: 0.8761 (tp) REVERT: A 169 MET cc_start: 0.9400 (tpp) cc_final: 0.9145 (tpp) REVERT: A 191 MET cc_start: 0.9415 (mtt) cc_final: 0.9034 (mtt) REVERT: A 298 GLN cc_start: 0.9134 (mp10) cc_final: 0.8778 (mp10) REVERT: A 466 MET cc_start: 0.8680 (ptt) cc_final: 0.8281 (ptp) REVERT: A 587 LEU cc_start: 0.9834 (mt) cc_final: 0.9538 (tp) REVERT: A 588 GLN cc_start: 0.8778 (tp-100) cc_final: 0.8356 (tp-100) REVERT: A 620 ASP cc_start: 0.9235 (m-30) cc_final: 0.8639 (p0) REVERT: A 674 VAL cc_start: 0.9479 (t) cc_final: 0.9256 (p) REVERT: A 699 MET cc_start: 0.8455 (mmt) cc_final: 0.8239 (mmt) REVERT: A 705 GLN cc_start: 0.9373 (mt0) cc_final: 0.8855 (mp10) REVERT: A 737 GLU cc_start: 0.8926 (pm20) cc_final: 0.8542 (mm-30) REVERT: B 132 GLU cc_start: 0.8179 (pm20) cc_final: 0.7874 (pm20) REVERT: B 139 LEU cc_start: 0.9124 (tp) cc_final: 0.8753 (tp) REVERT: B 169 MET cc_start: 0.9346 (tpp) cc_final: 0.9076 (tpp) REVERT: B 191 MET cc_start: 0.9380 (mtt) cc_final: 0.8907 (mtt) REVERT: B 266 LYS cc_start: 0.7697 (pttt) cc_final: 0.7496 (pptt) REVERT: B 298 GLN cc_start: 0.9187 (mp10) cc_final: 0.8810 (mp10) REVERT: B 363 MET cc_start: 0.8049 (tpp) cc_final: 0.7190 (tpp) REVERT: B 426 ASN cc_start: 0.9503 (t0) cc_final: 0.9293 (t0) REVERT: B 466 MET cc_start: 0.8748 (ptt) cc_final: 0.8355 (ptp) REVERT: B 587 LEU cc_start: 0.9828 (mt) cc_final: 0.9549 (tp) REVERT: B 588 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8430 (tp-100) REVERT: B 620 ASP cc_start: 0.9221 (m-30) cc_final: 0.8680 (p0) REVERT: B 705 GLN cc_start: 0.9369 (mt0) cc_final: 0.8884 (mp10) REVERT: B 737 GLU cc_start: 0.8932 (pm20) cc_final: 0.8354 (mm-30) outliers start: 16 outliers final: 8 residues processed: 197 average time/residue: 0.1019 time to fit residues: 31.3079 Evaluate side-chains 138 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL 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 B residue 21 VAL Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 574 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 132 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3153 r_free = 0.3153 target = 0.057760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.044775 restraints weight = 54845.011| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 4.94 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13922 Z= 0.205 Angle : 0.648 7.274 19064 Z= 0.351 Chirality : 0.046 0.189 2082 Planarity : 0.004 0.032 2180 Dihedral : 18.264 164.975 2384 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.99 % Allowed : 10.25 % Favored : 86.75 % 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 aren not related in a simple way. whole: -0.78 (0.20), residues: 1486 helix: 0.27 (0.24), residues: 450 sheet: -1.31 (0.30), residues: 238 loop : -0.64 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 548 TYR 0.026 0.002 TYR A 511 PHE 0.019 0.002 PHE A 458 TRP 0.015 0.002 TRP B 623 HIS 0.005 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00457 (13922) covalent geometry : angle 0.64777 (19064) hydrogen bonds : bond 0.04076 ( 485) hydrogen bonds : angle 5.12579 ( 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 187 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.488 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 113 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9336 (tp) REVERT: A 132 GLU cc_start: 0.8240 (pm20) cc_final: 0.7924 (pm20) REVERT: A 169 MET cc_start: 0.9448 (tpp) cc_final: 0.9078 (tpp) REVERT: A 191 MET cc_start: 0.9409 (mtt) cc_final: 0.8921 (mtt) REVERT: A 363 MET cc_start: 0.8810 (mmm) cc_final: 0.7973 (mmm) REVERT: A 364 GLN cc_start: 0.9431 (mm110) cc_final: 0.9093 (mm-40) REVERT: A 466 MET cc_start: 0.8830 (ptt) cc_final: 0.8470 (ptp) REVERT: A 580 GLU cc_start: 0.8186 (pt0) cc_final: 0.7572 (pm20) REVERT: A 585 GLU cc_start: 0.9542 (pt0) cc_final: 0.9238 (pm20) REVERT: A 588 GLN cc_start: 0.8826 (tp-100) cc_final: 0.8335 (tp-100) REVERT: A 620 ASP cc_start: 0.9333 (m-30) cc_final: 0.8747 (p0) REVERT: A 737 GLU cc_start: 0.9017 (pm20) cc_final: 0.8394 (mm-30) REVERT: B 132 GLU cc_start: 0.8237 (pm20) cc_final: 0.7932 (pm20) REVERT: B 169 MET cc_start: 0.9379 (tpp) cc_final: 0.8992 (tpp) REVERT: B 191 MET cc_start: 0.9361 (mtt) cc_final: 0.8912 (mtt) REVERT: B 298 GLN cc_start: 0.9202 (mp10) cc_final: 0.8732 (mp10) REVERT: B 363 MET cc_start: 0.8219 (tpp) cc_final: 0.7295 (tpp) REVERT: B 426 ASN cc_start: 0.9510 (t0) cc_final: 0.9296 (t0) REVERT: B 433 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8785 (mm-30) REVERT: B 466 MET cc_start: 0.8815 (ptt) cc_final: 0.8458 (ptp) REVERT: B 517 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9443 (tp) REVERT: B 585 GLU cc_start: 0.9543 (pt0) cc_final: 0.9206 (pm20) REVERT: B 588 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8313 (tp-100) REVERT: B 620 ASP cc_start: 0.9302 (m-30) cc_final: 0.8727 (p0) REVERT: B 705 GLN cc_start: 0.9313 (mt0) cc_final: 0.9071 (mt0) outliers start: 40 outliers final: 21 residues processed: 178 average time/residue: 0.0942 time to fit residues: 25.9806 Evaluate side-chains 150 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 138 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 463 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 675 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 134 optimal weight: 0.7980 chunk 128 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 28 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS B 574 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.058802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.045820 restraints weight = 54499.120| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 5.01 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13922 Z= 0.133 Angle : 0.607 11.378 19064 Z= 0.325 Chirality : 0.045 0.172 2082 Planarity : 0.003 0.035 2180 Dihedral : 18.328 167.549 2384 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.32 % Allowed : 10.78 % Favored : 86.90 % 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 aren not related in a simple way. whole: -0.39 (0.21), residues: 1486 helix: 0.54 (0.24), residues: 450 sheet: -0.99 (0.30), residues: 256 loop : -0.36 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 548 TYR 0.023 0.001 TYR B 237 PHE 0.015 0.001 PHE A 61 TRP 0.021 0.002 TRP A 623 HIS 0.008 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00298 (13922) covalent geometry : angle 0.60654 (19064) hydrogen bonds : bond 0.03719 ( 485) hydrogen bonds : angle 4.77394 ( 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 172 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8143 (pm20) cc_final: 0.7809 (pm20) REVERT: A 169 MET cc_start: 0.9445 (tpp) cc_final: 0.9021 (tpp) REVERT: A 191 MET cc_start: 0.9423 (mtt) cc_final: 0.8995 (mtt) REVERT: A 363 MET cc_start: 0.8833 (mmm) cc_final: 0.7983 (mmm) REVERT: A 466 MET cc_start: 0.8763 (ptt) cc_final: 0.8377 (ptp) REVERT: A 517 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9416 (tp) REVERT: A 545 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8835 (m) REVERT: A 585 GLU cc_start: 0.9526 (pt0) cc_final: 0.9179 (pm20) REVERT: A 589 GLU cc_start: 0.9634 (mm-30) cc_final: 0.9416 (tp30) REVERT: A 620 ASP cc_start: 0.9300 (m-30) cc_final: 0.8707 (p0) REVERT: A 737 GLU cc_start: 0.9086 (pm20) cc_final: 0.8234 (mm-30) REVERT: B 132 GLU cc_start: 0.8202 (pm20) cc_final: 0.7855 (pm20) REVERT: B 169 MET cc_start: 0.9393 (tpp) cc_final: 0.8946 (tpp) REVERT: B 191 MET cc_start: 0.9408 (mtt) cc_final: 0.9011 (mtt) REVERT: B 363 MET cc_start: 0.8402 (tpp) cc_final: 0.7439 (tpp) REVERT: B 426 ASN cc_start: 0.9526 (t0) cc_final: 0.9309 (t0) REVERT: B 466 MET cc_start: 0.8738 (ptt) cc_final: 0.8365 (ptp) REVERT: B 472 GLU cc_start: 0.8738 (tp30) cc_final: 0.8473 (tp30) REVERT: B 517 LEU cc_start: 0.9628 (tp) cc_final: 0.9281 (tp) REVERT: B 581 LYS cc_start: 0.9339 (tttt) cc_final: 0.9091 (tmtt) REVERT: B 585 GLU cc_start: 0.9542 (pt0) cc_final: 0.9183 (pm20) REVERT: B 587 LEU cc_start: 0.9822 (tp) cc_final: 0.9566 (tp) REVERT: B 589 GLU cc_start: 0.9618 (mm-30) cc_final: 0.9393 (tp30) REVERT: B 620 ASP cc_start: 0.9300 (m-30) cc_final: 0.8806 (p0) REVERT: B 705 GLN cc_start: 0.9349 (mt0) cc_final: 0.9045 (mt0) REVERT: B 737 GLU cc_start: 0.9085 (pm20) cc_final: 0.8192 (mm-30) REVERT: B 751 LEU cc_start: 0.8529 (tt) cc_final: 0.8293 (tt) outliers start: 31 outliers final: 19 residues processed: 165 average time/residue: 0.0918 time to fit residues: 24.0387 Evaluate side-chains 139 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 539 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 136 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.042586 restraints weight = 55876.309| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 4.89 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13922 Z= 0.241 Angle : 0.643 10.839 19064 Z= 0.346 Chirality : 0.045 0.157 2082 Planarity : 0.004 0.030 2180 Dihedral : 18.631 174.432 2384 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.54 % Allowed : 11.90 % Favored : 85.55 % 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 aren not related in a simple way. whole: -0.17 (0.22), residues: 1486 helix: 0.63 (0.24), residues: 458 sheet: -0.96 (0.31), residues: 242 loop : -0.16 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 667 TYR 0.035 0.002 TYR B 306 PHE 0.017 0.002 PHE A 366 TRP 0.027 0.002 TRP B 207 HIS 0.011 0.002 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00532 (13922) covalent geometry : angle 0.64337 (19064) hydrogen bonds : bond 0.03770 ( 485) hydrogen bonds : angle 4.80929 ( 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 149 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.512 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 132 GLU cc_start: 0.8347 (pm20) cc_final: 0.8069 (pm20) REVERT: A 169 MET cc_start: 0.9482 (tpp) cc_final: 0.9020 (tpp) REVERT: A 188 ILE cc_start: 0.9791 (mm) cc_final: 0.9551 (mm) REVERT: A 191 MET cc_start: 0.9397 (mtt) cc_final: 0.8969 (mtt) REVERT: A 363 MET cc_start: 0.8907 (mmm) cc_final: 0.8030 (mmm) REVERT: A 472 GLU cc_start: 0.8597 (tp30) cc_final: 0.8349 (tp30) REVERT: A 545 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8972 (m) REVERT: A 585 GLU cc_start: 0.9545 (pt0) cc_final: 0.9225 (pm20) REVERT: A 589 GLU cc_start: 0.9657 (mm-30) cc_final: 0.9345 (tp30) REVERT: A 699 MET cc_start: 0.9188 (mmt) cc_final: 0.8898 (mmt) REVERT: A 737 GLU cc_start: 0.9133 (pm20) cc_final: 0.8896 (pm20) REVERT: B 113 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9379 (tp) REVERT: B 132 GLU cc_start: 0.8327 (pm20) cc_final: 0.8022 (pm20) REVERT: B 169 MET cc_start: 0.9469 (tpp) cc_final: 0.9016 (tpp) REVERT: B 191 MET cc_start: 0.9417 (mtt) cc_final: 0.8954 (mtt) REVERT: B 353 MET cc_start: 0.9195 (mmm) cc_final: 0.8993 (mmm) REVERT: B 363 MET cc_start: 0.8433 (tpp) cc_final: 0.7442 (tpp) REVERT: B 426 ASN cc_start: 0.9533 (t0) cc_final: 0.9303 (t0) REVERT: B 472 GLU cc_start: 0.8746 (tp30) cc_final: 0.8479 (tp30) REVERT: B 517 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9442 (tp) REVERT: B 580 GLU cc_start: 0.8026 (pt0) cc_final: 0.7796 (pm20) REVERT: B 585 GLU cc_start: 0.9562 (pt0) cc_final: 0.9244 (pm20) REVERT: B 589 GLU cc_start: 0.9646 (mm-30) cc_final: 0.9426 (tp30) REVERT: B 737 GLU cc_start: 0.9179 (pm20) cc_final: 0.8190 (mm-30) outliers start: 34 outliers final: 19 residues processed: 145 average time/residue: 0.0900 time to fit residues: 20.7805 Evaluate side-chains 124 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 359 ILE 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 A residue 545 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 730 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 15 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 107 optimal weight: 0.0670 chunk 126 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.056790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.044041 restraints weight = 55137.339| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 4.87 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13922 Z= 0.150 Angle : 0.600 9.850 19064 Z= 0.317 Chirality : 0.045 0.154 2082 Planarity : 0.003 0.067 2180 Dihedral : 18.749 173.652 2384 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.17 % Allowed : 12.43 % Favored : 85.40 % 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 aren not related in a simple way. whole: 0.01 (0.22), residues: 1486 helix: 0.80 (0.24), residues: 460 sheet: -0.88 (0.31), residues: 262 loop : -0.02 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 379 TYR 0.033 0.001 TYR B 306 PHE 0.015 0.002 PHE A 458 TRP 0.016 0.002 TRP B 207 HIS 0.008 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00340 (13922) covalent geometry : angle 0.60045 (19064) hydrogen bonds : bond 0.03504 ( 485) hydrogen bonds : angle 4.65217 ( 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 145 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.459 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: 0.8365 (pm20) cc_final: 0.8053 (pm20) REVERT: A 169 MET cc_start: 0.9460 (tpp) cc_final: 0.8980 (tpp) REVERT: A 191 MET cc_start: 0.9421 (mtt) cc_final: 0.9044 (mtt) REVERT: A 207 TRP cc_start: 0.8748 (m-10) cc_final: 0.8515 (m-10) REVERT: A 363 MET cc_start: 0.8824 (mmm) cc_final: 0.8023 (mmm) REVERT: A 513 HIS cc_start: 0.8467 (m-70) cc_final: 0.8133 (m-70) REVERT: A 517 LEU cc_start: 0.9670 (tp) cc_final: 0.9426 (tp) REVERT: A 545 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8897 (m) REVERT: A 585 GLU cc_start: 0.9514 (pt0) cc_final: 0.9134 (pm20) REVERT: A 589 GLU cc_start: 0.9643 (mm-30) cc_final: 0.9309 (tp30) REVERT: A 699 MET cc_start: 0.9170 (mmt) cc_final: 0.8942 (mmt) REVERT: A 737 GLU cc_start: 0.9134 (pm20) cc_final: 0.8887 (pm20) REVERT: B 113 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9339 (tp) REVERT: B 132 GLU cc_start: 0.8338 (pm20) cc_final: 0.8021 (pm20) REVERT: B 169 MET cc_start: 0.9435 (tpp) cc_final: 0.8946 (tpp) REVERT: B 191 MET cc_start: 0.9412 (mtt) cc_final: 0.8968 (mtt) REVERT: B 363 MET cc_start: 0.8481 (tpp) cc_final: 0.7579 (tpp) REVERT: B 426 ASN cc_start: 0.9522 (t0) cc_final: 0.9304 (t0) REVERT: B 433 GLU cc_start: 0.8876 (mm-30) cc_final: 0.7992 (tt0) REVERT: B 472 GLU cc_start: 0.8780 (tp30) cc_final: 0.8493 (tp30) REVERT: B 491 MET cc_start: 0.9317 (mmm) cc_final: 0.8660 (mmp) REVERT: B 517 LEU cc_start: 0.9648 (tp) cc_final: 0.9419 (tp) REVERT: B 581 LYS cc_start: 0.9238 (tttt) cc_final: 0.9014 (tttm) REVERT: B 585 GLU cc_start: 0.9548 (pt0) cc_final: 0.9232 (pm20) REVERT: B 587 LEU cc_start: 0.9842 (tp) cc_final: 0.9564 (tp) REVERT: B 589 GLU cc_start: 0.9629 (mm-30) cc_final: 0.9390 (tp30) REVERT: B 737 GLU cc_start: 0.9160 (pm20) cc_final: 0.8183 (mm-30) outliers start: 29 outliers final: 16 residues processed: 140 average time/residue: 0.1023 time to fit residues: 22.3419 Evaluate side-chains 125 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 113 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 448 LEU Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 113 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 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: 9.9990 chunk 33 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** 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 = 0.3052 r_free = 0.3052 target = 0.052670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.039892 restraints weight = 58018.841| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 4.81 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 13922 Z= 0.366 Angle : 0.733 8.580 19064 Z= 0.393 Chirality : 0.048 0.159 2082 Planarity : 0.004 0.034 2180 Dihedral : 19.102 178.856 2384 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.17 % Allowed : 12.72 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.22), residues: 1486 helix: 0.67 (0.23), residues: 452 sheet: -1.14 (0.32), residues: 240 loop : -0.06 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 379 TYR 0.039 0.002 TYR B 306 PHE 0.024 0.002 PHE A 561 TRP 0.011 0.002 TRP B 528 HIS 0.009 0.002 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00796 (13922) covalent geometry : angle 0.73290 (19064) hydrogen bonds : bond 0.04075 ( 485) hydrogen bonds : angle 5.12231 ( 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 137 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.407 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: 0.8479 (pm20) cc_final: 0.8212 (pm20) REVERT: A 169 MET cc_start: 0.9470 (tpp) cc_final: 0.8990 (tpp) REVERT: A 191 MET cc_start: 0.9402 (mtt) cc_final: 0.8972 (mtt) REVERT: A 517 LEU cc_start: 0.9708 (tp) cc_final: 0.9505 (tp) REVERT: A 545 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8936 (m) REVERT: A 580 GLU cc_start: 0.8142 (pt0) cc_final: 0.7786 (pm20) REVERT: A 585 GLU cc_start: 0.9530 (pt0) cc_final: 0.9199 (pm20) REVERT: A 589 GLU cc_start: 0.9627 (mm-30) cc_final: 0.9313 (tp30) REVERT: A 737 GLU cc_start: 0.9192 (pm20) cc_final: 0.8983 (pm20) REVERT: B 132 GLU cc_start: 0.8478 (pm20) cc_final: 0.8205 (pm20) REVERT: B 169 MET cc_start: 0.9476 (tpp) cc_final: 0.9026 (tpp) REVERT: B 191 MET cc_start: 0.9389 (mtt) cc_final: 0.8980 (mtt) REVERT: B 353 MET cc_start: 0.9102 (mmm) cc_final: 0.8773 (mmm) REVERT: B 363 MET cc_start: 0.8512 (tpp) cc_final: 0.7590 (tpp) REVERT: B 472 GLU cc_start: 0.8763 (tp30) cc_final: 0.8457 (tp30) REVERT: B 585 GLU cc_start: 0.9539 (pt0) cc_final: 0.9218 (pm20) REVERT: B 589 GLU cc_start: 0.9620 (mm-30) cc_final: 0.9412 (tp30) REVERT: B 737 GLU cc_start: 0.9205 (pm20) cc_final: 0.8923 (pm20) outliers start: 29 outliers final: 22 residues processed: 134 average time/residue: 0.1005 time to fit residues: 20.7637 Evaluate side-chains 118 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 575 ILE 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 113 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 666 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 730 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** 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 = 0.3148 r_free = 0.3148 target = 0.056113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.043522 restraints weight = 54564.934| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 4.87 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13922 Z= 0.138 Angle : 0.614 11.221 19064 Z= 0.323 Chirality : 0.045 0.159 2082 Planarity : 0.003 0.032 2180 Dihedral : 19.005 177.371 2384 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.80 % Allowed : 13.32 % 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 aren not related in a simple way. whole: 0.10 (0.22), residues: 1486 helix: 0.86 (0.24), residues: 458 sheet: -0.87 (0.32), residues: 256 loop : 0.05 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 379 TYR 0.035 0.002 TYR B 306 PHE 0.016 0.002 PHE A 366 TRP 0.014 0.002 TRP B 207 HIS 0.010 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00313 (13922) covalent geometry : angle 0.61403 (19064) hydrogen bonds : bond 0.03559 ( 485) hydrogen bonds : angle 4.69298 ( 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 143 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.526 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: 0.8431 (pm20) cc_final: 0.8138 (pm20) REVERT: A 169 MET cc_start: 0.9425 (tpp) cc_final: 0.8918 (tpp) REVERT: A 191 MET cc_start: 0.9439 (mtt) cc_final: 0.9012 (mtt) REVERT: A 363 MET cc_start: 0.8772 (mmm) cc_final: 0.8138 (mmm) REVERT: A 491 MET cc_start: 0.9145 (mmp) cc_final: 0.8933 (mmp) REVERT: A 513 HIS cc_start: 0.8440 (m170) cc_final: 0.8151 (m-70) REVERT: A 517 LEU cc_start: 0.9679 (tp) cc_final: 0.9449 (tp) REVERT: A 585 GLU cc_start: 0.9509 (pt0) cc_final: 0.9171 (pm20) REVERT: A 589 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9317 (tp30) REVERT: A 737 GLU cc_start: 0.9174 (pm20) cc_final: 0.8938 (pm20) REVERT: B 132 GLU cc_start: 0.8390 (pm20) cc_final: 0.8096 (pm20) REVERT: B 169 MET cc_start: 0.9451 (tpp) cc_final: 0.8993 (tpp) REVERT: B 181 ASP cc_start: 0.9032 (t0) cc_final: 0.8637 (m-30) REVERT: B 363 MET cc_start: 0.8509 (tpp) cc_final: 0.7592 (tpp) REVERT: B 426 ASN cc_start: 0.9531 (t0) cc_final: 0.9330 (t0) REVERT: B 472 GLU cc_start: 0.8795 (tp30) cc_final: 0.8505 (tp30) REVERT: B 491 MET cc_start: 0.9225 (mmm) cc_final: 0.8796 (mmm) REVERT: B 517 LEU cc_start: 0.9681 (tp) cc_final: 0.9326 (tp) REVERT: B 581 LYS cc_start: 0.9281 (tttt) cc_final: 0.9005 (tttm) REVERT: B 585 GLU cc_start: 0.9559 (pt0) cc_final: 0.9265 (pm20) REVERT: B 587 LEU cc_start: 0.9853 (tp) cc_final: 0.9627 (tp) REVERT: B 589 GLU cc_start: 0.9636 (mm-30) cc_final: 0.9409 (tp30) REVERT: B 737 GLU cc_start: 0.9161 (pm20) cc_final: 0.8888 (pm20) outliers start: 24 outliers final: 20 residues processed: 137 average time/residue: 0.0958 time to fit residues: 20.7456 Evaluate side-chains 124 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 113 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 539 CYS Chi-restraints excluded: chain A residue 575 ILE 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 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 448 LEU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 675 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: 9.9990 chunk 131 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.053327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.040816 restraints weight = 56959.732| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 4.81 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13922 Z= 0.269 Angle : 0.678 10.674 19064 Z= 0.362 Chirality : 0.046 0.161 2082 Planarity : 0.004 0.033 2180 Dihedral : 19.118 178.114 2384 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.02 % Allowed : 14.15 % Favored : 83.83 % 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 aren not related in a simple way. whole: -0.03 (0.23), residues: 1486 helix: 0.79 (0.23), residues: 468 sheet: -1.23 (0.28), residues: 322 loop : 0.22 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 548 TYR 0.045 0.002 TYR B 306 PHE 0.016 0.002 PHE A 61 TRP 0.013 0.002 TRP A 528 HIS 0.007 0.002 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00593 (13922) covalent geometry : angle 0.67797 (19064) hydrogen bonds : bond 0.03710 ( 485) hydrogen bonds : angle 4.85543 ( 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 131 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.507 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: 0.8487 (pm20) cc_final: 0.8212 (pm20) REVERT: A 169 MET cc_start: 0.9453 (tpp) cc_final: 0.8975 (tpp) REVERT: A 191 MET cc_start: 0.9428 (mtt) cc_final: 0.8965 (mtt) REVERT: A 363 MET cc_start: 0.8820 (mmm) cc_final: 0.8049 (mmm) REVERT: A 491 MET cc_start: 0.9339 (mmp) cc_final: 0.9114 (mmp) REVERT: A 517 LEU cc_start: 0.9717 (tp) cc_final: 0.9498 (tp) REVERT: A 581 LYS cc_start: 0.9081 (tttt) cc_final: 0.8860 (tttm) REVERT: A 585 GLU cc_start: 0.9544 (pt0) cc_final: 0.9228 (pm20) REVERT: A 589 GLU cc_start: 0.9632 (mm-30) cc_final: 0.9334 (tp30) REVERT: A 737 GLU cc_start: 0.9183 (pm20) cc_final: 0.8931 (pm20) REVERT: B 132 GLU cc_start: 0.8459 (pm20) cc_final: 0.8179 (pm20) REVERT: B 169 MET cc_start: 0.9496 (tpp) cc_final: 0.9067 (tpp) REVERT: B 191 MET cc_start: 0.9396 (mtt) cc_final: 0.8957 (mtt) REVERT: B 363 MET cc_start: 0.8602 (tpp) cc_final: 0.7679 (tpp) REVERT: B 426 ASN cc_start: 0.9500 (t0) cc_final: 0.9291 (t0) REVERT: B 472 GLU cc_start: 0.8802 (tp30) cc_final: 0.8502 (tp30) REVERT: B 491 MET cc_start: 0.9367 (mmm) cc_final: 0.9041 (mmm) REVERT: B 517 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9517 (tp) REVERT: B 549 GLU cc_start: 0.8956 (pm20) cc_final: 0.8697 (pm20) REVERT: B 581 LYS cc_start: 0.9197 (tttt) cc_final: 0.8967 (tttm) REVERT: B 585 GLU cc_start: 0.9554 (pt0) cc_final: 0.9256 (pm20) REVERT: B 589 GLU cc_start: 0.9651 (mm-30) cc_final: 0.9440 (tp30) REVERT: B 737 GLU cc_start: 0.9189 (pm20) cc_final: 0.8859 (pm20) outliers start: 27 outliers final: 24 residues processed: 126 average time/residue: 0.1060 time to fit residues: 20.6474 Evaluate side-chains 125 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 575 ILE 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 113 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 448 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 730 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 46 optimal weight: 10.0000 chunk 132 optimal weight: 0.0980 chunk 88 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 2 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 103 optimal weight: 0.0470 overall best weight: 2.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.054889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.042359 restraints weight = 55737.619| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 4.84 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13922 Z= 0.183 Angle : 0.641 10.230 19064 Z= 0.339 Chirality : 0.045 0.220 2082 Planarity : 0.003 0.041 2180 Dihedral : 19.105 178.893 2384 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.25 % Allowed : 13.92 % Favored : 83.83 % 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 aren not related in a simple way. whole: 0.08 (0.23), residues: 1486 helix: 0.95 (0.23), residues: 464 sheet: -1.21 (0.28), residues: 324 loop : 0.28 (0.27), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 548 TYR 0.033 0.002 TYR B 306 PHE 0.016 0.002 PHE B 591 TRP 0.024 0.002 TRP A 207 HIS 0.006 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00411 (13922) covalent geometry : angle 0.64090 (19064) hydrogen bonds : bond 0.03574 ( 485) hydrogen bonds : angle 4.74057 ( 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 135 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.423 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: 0.8471 (pm20) cc_final: 0.8189 (pm20) REVERT: A 169 MET cc_start: 0.9458 (tpp) cc_final: 0.8972 (tpp) REVERT: A 191 MET cc_start: 0.9435 (mtt) cc_final: 0.9000 (mtt) REVERT: A 363 MET cc_start: 0.8815 (mmm) cc_final: 0.8032 (mmm) REVERT: A 517 LEU cc_start: 0.9713 (tp) cc_final: 0.9468 (tp) REVERT: A 533 MET cc_start: 0.9164 (tpp) cc_final: 0.8795 (ttm) REVERT: A 581 LYS cc_start: 0.9046 (tttt) cc_final: 0.8712 (tttm) REVERT: A 585 GLU cc_start: 0.9523 (pt0) cc_final: 0.9164 (pm20) REVERT: A 589 GLU cc_start: 0.9639 (mm-30) cc_final: 0.9341 (tp30) REVERT: A 737 GLU cc_start: 0.9176 (pm20) cc_final: 0.8881 (pm20) REVERT: B 132 GLU cc_start: 0.8420 (pm20) cc_final: 0.8135 (pm20) REVERT: B 169 MET cc_start: 0.9493 (tpp) cc_final: 0.9056 (tpp) REVERT: B 181 ASP cc_start: 0.9072 (t0) cc_final: 0.8672 (m-30) REVERT: B 302 MET cc_start: 0.8325 (tpp) cc_final: 0.7892 (tpp) REVERT: B 353 MET cc_start: 0.9085 (mmm) cc_final: 0.8595 (mmm) REVERT: B 363 MET cc_start: 0.8550 (tpp) cc_final: 0.7618 (tpp) REVERT: B 426 ASN cc_start: 0.9523 (t0) cc_final: 0.9321 (t0) REVERT: B 472 GLU cc_start: 0.8800 (tp30) cc_final: 0.8511 (tp30) REVERT: B 491 MET cc_start: 0.9290 (mmm) cc_final: 0.8940 (mmm) REVERT: B 517 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9498 (tp) REVERT: B 549 GLU cc_start: 0.9049 (pm20) cc_final: 0.8708 (pm20) REVERT: B 581 LYS cc_start: 0.9105 (tttt) cc_final: 0.8799 (tmtm) REVERT: B 585 GLU cc_start: 0.9551 (pt0) cc_final: 0.9232 (pm20) REVERT: B 589 GLU cc_start: 0.9663 (mm-30) cc_final: 0.9455 (tp30) REVERT: B 737 GLU cc_start: 0.9210 (pm20) cc_final: 0.8984 (pm20) outliers start: 30 outliers final: 24 residues processed: 126 average time/residue: 0.0974 time to fit residues: 18.9755 Evaluate side-chains 127 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 539 CYS 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 113 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 448 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 730 ASP Chi-restraints excluded: chain B residue 736 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 95 optimal weight: 8.9990 chunk 8 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** 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 = 0.3132 r_free = 0.3132 target = 0.055323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.042823 restraints weight = 55760.252| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 4.89 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13922 Z= 0.166 Angle : 0.630 10.213 19064 Z= 0.331 Chirality : 0.045 0.213 2082 Planarity : 0.003 0.047 2180 Dihedral : 18.991 175.438 2384 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.87 % Allowed : 14.45 % Favored : 83.68 % 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 aren not related in a simple way. whole: 0.09 (0.23), residues: 1486 helix: 0.92 (0.23), residues: 464 sheet: -1.14 (0.29), residues: 324 loop : 0.28 (0.27), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 548 TYR 0.034 0.002 TYR B 306 PHE 0.015 0.002 PHE A 749 TRP 0.019 0.002 TRP A 207 HIS 0.005 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00375 (13922) covalent geometry : angle 0.63050 (19064) hydrogen bonds : bond 0.03536 ( 485) hydrogen bonds : angle 4.63316 ( 1400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.71 seconds wall clock time: 35 minutes 0.87 seconds (2100.87 seconds total)