Starting phenix.real_space_refine on Wed Feb 4 23:03:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh9_61476/02_2026/9jh9_61476.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh9_61476/02_2026/9jh9_61476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jh9_61476/02_2026/9jh9_61476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh9_61476/02_2026/9jh9_61476.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jh9_61476/02_2026/9jh9_61476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh9_61476/02_2026/9jh9_61476.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 P 68 5.49 5 S 40 5.16 5 C 8488 2.51 5 N 2236 2.21 5 O 2673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13509 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 357 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "D" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "F" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 358 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.26, per 1000 atoms: 0.24 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: 1.28 Conformation dependent library (CDL) restraints added in 472.6 milliseconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 24 sheets defined 31.1% alpha, 20.4% beta 11 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 2.06 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: 2.64 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2549 1.33 - 1.44: 3607 1.44 - 1.56: 7564 1.56 - 1.68: 134 1.68 - 1.80: 70 Bond restraints: 13924 Sorted by residual: bond pdb=" 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 13919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 18009 1.92 - 3.84: 901 3.84 - 5.77: 121 5.77 - 7.69: 24 7.69 - 9.61: 14 Bond angle restraints: 19069 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 19064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.72: 7848 28.72 - 57.44: 370 57.44 - 86.15: 30 86.15 - 114.87: 4 114.87 - 143.59: 2 Dihedral angle restraints: 8254 sinusoidal: 3880 harmonic: 4374 Sorted by residual: dihedral pdb=" CA GLU B 470 " pdb=" C GLU B 470 " pdb=" N ILE B 471 " pdb=" CA ILE B 471 " ideal model delta harmonic sigma weight residual -180.00 -136.35 -43.65 0 5.00e+00 4.00e-02 7.62e+01 dihedral pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N ILE A 471 " pdb=" CA ILE A 471 " ideal model delta harmonic sigma weight residual -180.00 -136.43 -43.57 0 5.00e+00 4.00e-02 7.59e+01 dihedral pdb=" CA LYS B 63 " pdb=" C LYS B 63 " pdb=" N ASP B 64 " pdb=" CA ASP B 64 " ideal model delta harmonic sigma weight residual -180.00 -149.35 -30.65 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 8251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1510 0.059 - 0.118: 461 0.118 - 0.177: 105 0.177 - 0.236: 4 0.236 - 0.295: 4 Chirality restraints: 2084 Sorted by residual: chirality pdb=" CB ILE B 44 " pdb=" CA ILE B 44 " pdb=" CG1 ILE B 44 " pdb=" CG2 ILE B 44 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE A 44 " pdb=" CA ILE A 44 " pdb=" CG1 ILE A 44 " pdb=" CG2 ILE A 44 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE A 460 " pdb=" CA ILE A 460 " pdb=" CG1 ILE A 460 " pdb=" CG2 ILE A 460 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2081 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 160 " -0.009 2.00e-02 2.50e+03 1.80e-02 5.68e+00 pdb=" CG PHE B 160 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 160 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE B 160 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 160 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 160 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 160 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 460 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C ILE B 460 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE B 460 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA B 461 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 160 " 0.009 2.00e-02 2.50e+03 1.79e-02 5.62e+00 pdb=" CG PHE A 160 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 160 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 160 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 160 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 160 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 160 " -0.003 2.00e-02 2.50e+03 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 55 2.42 - 3.04: 7529 3.04 - 3.66: 20983 3.66 - 4.28: 32178 4.28 - 4.90: 52433 Nonbonded interactions: 113178 Sorted by model distance: nonbonded pdb=" OD2 ASP A 544 " pdb="MN MN E 801 " model vdw 1.798 2.320 nonbonded pdb=" OD2 ASP B 544 " pdb="MN MN F 801 " model vdw 1.811 2.320 nonbonded pdb=" OP1 DT E 9 " pdb="MN MN E 801 " model vdw 1.827 2.320 nonbonded pdb=" OP1 DT F 9 " pdb="MN MN F 801 " model vdw 1.827 2.320 nonbonded pdb=" OP1 DA D 3 " pdb="MN MN D 801 " model vdw 1.869 2.320 ... (remaining 113173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 1 through 5 or (resid 6 and (name P or name OP1 or name OP \ 2 or name O5' or name C5' or name C4' or name C3' or name O3' or name C2' or nam \ e C1' or name N9 or name C8 or name N7 or name C5 or name C6 or name N6 or name \ N1 or name C2 or name N3 or name C4 )) or resid 7 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.690 Find NCS groups from input model: 0.160 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.960 ------------------------------------------------------------------------------- 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 13924 Z= 0.397 Angle : 0.962 9.612 19069 Z= 0.534 Chirality : 0.058 0.295 2084 Planarity : 0.006 0.044 2180 Dihedral : 15.157 143.591 5466 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.15 % Allowed : 2.54 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.18), residues: 1486 helix: -2.22 (0.18), residues: 424 sheet: -1.88 (0.28), residues: 264 loop : -1.48 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 721 TYR 0.038 0.003 TYR B 554 PHE 0.039 0.004 PHE B 160 TRP 0.037 0.005 TRP A 623 HIS 0.011 0.002 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00940 (13924) covalent geometry : angle 0.96234 (19069) 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 : 0.524 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: 0.1212 time to fit residues: 48.4040 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 : 0.528 ------------------------------------------------------------------------------- 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 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3203 r_free = 0.3203 target = 0.060604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.047661 restraints weight = 52580.267| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 4.96 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13924 Z= 0.159 Angle : 0.687 8.563 19069 Z= 0.371 Chirality : 0.047 0.202 2084 Planarity : 0.004 0.037 2180 Dihedral : 18.326 164.757 2388 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.20 % Allowed : 10.85 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.19), residues: 1486 helix: -0.44 (0.23), residues: 444 sheet: -1.27 (0.29), residues: 236 loop : -1.15 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 263 TYR 0.022 0.002 TYR B 237 PHE 0.017 0.002 PHE A 61 TRP 0.024 0.003 TRP B 623 HIS 0.006 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00360 (13924) covalent geometry : angle 0.68653 (19069) hydrogen bonds : bond 0.04809 ( 485) hydrogen bonds : angle 5.75881 ( 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 199 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9616 (mm) cc_final: 0.9380 (tp) REVERT: A 132 GLU cc_start: 0.8156 (pm20) cc_final: 0.7854 (pm20) REVERT: A 139 LEU cc_start: 0.9171 (tp) cc_final: 0.8766 (tp) REVERT: A 169 MET cc_start: 0.9408 (tpp) cc_final: 0.9145 (tpp) REVERT: A 191 MET cc_start: 0.9429 (mtt) cc_final: 0.9056 (mtt) REVERT: A 426 ASN cc_start: 0.9523 (t0) cc_final: 0.9200 (p0) REVERT: A 466 MET cc_start: 0.8678 (ptt) cc_final: 0.8285 (ptp) REVERT: A 517 LEU cc_start: 0.9631 (tp) cc_final: 0.9323 (tp) REVERT: A 583 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8009 (p0) REVERT: A 587 LEU cc_start: 0.9833 (mt) cc_final: 0.9553 (tp) REVERT: A 620 ASP cc_start: 0.9240 (m-30) cc_final: 0.8651 (p0) REVERT: A 674 VAL cc_start: 0.9465 (t) cc_final: 0.9244 (p) REVERT: A 737 GLU cc_start: 0.8926 (pm20) cc_final: 0.8518 (mm-30) REVERT: B 132 GLU cc_start: 0.8174 (pm20) cc_final: 0.7861 (pm20) REVERT: B 139 LEU cc_start: 0.9125 (tp) cc_final: 0.8752 (tp) REVERT: B 169 MET cc_start: 0.9348 (tpp) cc_final: 0.9072 (tpp) REVERT: B 191 MET cc_start: 0.9393 (mtt) cc_final: 0.8933 (mtt) REVERT: B 298 GLN cc_start: 0.9198 (mp10) cc_final: 0.8816 (mp10) REVERT: B 363 MET cc_start: 0.8131 (tpp) cc_final: 0.7278 (tpp) REVERT: B 426 ASN cc_start: 0.9523 (t0) cc_final: 0.9320 (t0) REVERT: B 466 MET cc_start: 0.8739 (ptt) cc_final: 0.8349 (ptp) REVERT: B 517 LEU cc_start: 0.9649 (tp) cc_final: 0.9341 (tp) REVERT: B 587 LEU cc_start: 0.9836 (mt) cc_final: 0.9557 (tp) REVERT: B 588 GLN cc_start: 0.8776 (tp-100) cc_final: 0.8404 (tp-100) REVERT: B 620 ASP cc_start: 0.9220 (m-30) cc_final: 0.8692 (p0) REVERT: B 705 GLN cc_start: 0.9363 (mt0) cc_final: 0.8873 (mp10) REVERT: B 737 GLU cc_start: 0.8950 (pm20) cc_final: 0.8325 (mm-30) outliers start: 16 outliers final: 8 residues processed: 193 average time/residue: 0.1017 time to fit residues: 30.9592 Evaluate side-chains 142 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 A residue 583 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: 8.9990 chunk 45 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 0.0040 chunk 116 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.8796 ------------------------------------------------------------------------------- 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** A 588 GLN B 288 ASN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS B 574 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.059333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.045974 restraints weight = 54804.403| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 5.02 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13924 Z= 0.169 Angle : 0.630 7.620 19069 Z= 0.340 Chirality : 0.045 0.190 2084 Planarity : 0.003 0.034 2180 Dihedral : 18.258 164.313 2388 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.99 % Allowed : 10.40 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1486 helix: 0.25 (0.24), residues: 450 sheet: -1.33 (0.30), residues: 242 loop : -0.70 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 548 TYR 0.025 0.002 TYR A 511 PHE 0.017 0.002 PHE A 458 TRP 0.015 0.002 TRP B 623 HIS 0.004 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00380 (13924) covalent geometry : angle 0.62956 (19069) hydrogen bonds : bond 0.04022 ( 485) hydrogen bonds : angle 5.10195 ( 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 186 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.502 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 113 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9308 (tp) REVERT: A 132 GLU cc_start: 0.8215 (pm20) cc_final: 0.7892 (pm20) REVERT: A 169 MET cc_start: 0.9440 (tpp) cc_final: 0.9081 (tpp) REVERT: A 191 MET cc_start: 0.9443 (mtt) cc_final: 0.8997 (mtt) REVERT: A 363 MET cc_start: 0.8843 (mmm) cc_final: 0.7991 (mmm) REVERT: A 403 SER cc_start: 0.9619 (m) cc_final: 0.9413 (p) REVERT: A 426 ASN cc_start: 0.9530 (t0) cc_final: 0.9330 (t0) REVERT: A 466 MET cc_start: 0.8770 (ptt) cc_final: 0.8398 (ptp) REVERT: A 498 GLU cc_start: 0.9670 (mt-10) cc_final: 0.9385 (mt-10) REVERT: A 548 ARG cc_start: 0.8659 (tpp80) cc_final: 0.8349 (tpp80) REVERT: A 583 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8252 (p0) REVERT: A 620 ASP cc_start: 0.9304 (m-30) cc_final: 0.8771 (p0) REVERT: A 703 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9446 (mm) REVERT: A 737 GLU cc_start: 0.8992 (pm20) cc_final: 0.8447 (mm-30) REVERT: B 132 GLU cc_start: 0.8227 (pm20) cc_final: 0.7882 (pm20) REVERT: B 169 MET cc_start: 0.9368 (tpp) cc_final: 0.8988 (tpp) REVERT: B 191 MET cc_start: 0.9369 (mtt) cc_final: 0.8933 (mtt) REVERT: B 298 GLN cc_start: 0.9203 (mp10) cc_final: 0.8728 (mp10) REVERT: B 363 MET cc_start: 0.8264 (tpp) cc_final: 0.7330 (tpp) REVERT: B 426 ASN cc_start: 0.9529 (t0) cc_final: 0.9323 (t0) REVERT: B 433 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8765 (mm-30) REVERT: B 466 MET cc_start: 0.8789 (ptt) cc_final: 0.8424 (ptp) REVERT: B 581 LYS cc_start: 0.9327 (tttt) cc_final: 0.9125 (tmtt) REVERT: B 585 GLU cc_start: 0.9542 (pt0) cc_final: 0.9198 (pm20) REVERT: B 588 GLN cc_start: 0.8772 (tp-100) cc_final: 0.8342 (tp-100) REVERT: B 620 ASP cc_start: 0.9268 (m-30) cc_final: 0.8837 (p0) REVERT: B 705 GLN cc_start: 0.9335 (mt0) cc_final: 0.9085 (mt0) REVERT: B 737 GLU cc_start: 0.9102 (pm20) cc_final: 0.8456 (mm-30) outliers start: 40 outliers final: 21 residues processed: 177 average time/residue: 0.1057 time to fit residues: 29.0186 Evaluate side-chains 151 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 583 ASN Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 674 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 134 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 30.0000 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3117 r_free = 0.3117 target = 0.056102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.043321 restraints weight = 56383.206| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 4.91 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13924 Z= 0.245 Angle : 0.654 9.204 19069 Z= 0.354 Chirality : 0.046 0.186 2084 Planarity : 0.004 0.031 2180 Dihedral : 18.506 170.761 2388 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.14 % Allowed : 10.48 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1486 helix: 0.45 (0.24), residues: 460 sheet: -1.15 (0.30), residues: 242 loop : -0.36 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 548 TYR 0.031 0.002 TYR B 306 PHE 0.018 0.002 PHE A 61 TRP 0.021 0.002 TRP A 623 HIS 0.012 0.002 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00543 (13924) covalent geometry : angle 0.65425 (19069) hydrogen bonds : bond 0.03870 ( 485) hydrogen bonds : angle 4.96247 ( 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 158 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9332 (tp) REVERT: A 132 GLU cc_start: 0.8266 (pm20) cc_final: 0.7971 (pm20) REVERT: A 169 MET cc_start: 0.9450 (tpp) cc_final: 0.9035 (tpp) REVERT: A 191 MET cc_start: 0.9391 (mtt) cc_final: 0.8940 (mtt) REVERT: A 363 MET cc_start: 0.8807 (mmm) cc_final: 0.7885 (mmm) REVERT: A 426 ASN cc_start: 0.9522 (t0) cc_final: 0.9302 (t0) REVERT: A 517 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9381 (tp) REVERT: A 545 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8978 (m) REVERT: A 737 GLU cc_start: 0.9105 (pm20) cc_final: 0.8307 (mm-30) REVERT: B 132 GLU cc_start: 0.8287 (pm20) cc_final: 0.7986 (pm20) REVERT: B 169 MET cc_start: 0.9438 (tpp) cc_final: 0.9015 (tpp) REVERT: B 191 MET cc_start: 0.9377 (mtt) cc_final: 0.8989 (mtt) REVERT: B 302 MET cc_start: 0.8469 (ttm) cc_final: 0.7828 (ttt) REVERT: B 363 MET cc_start: 0.8343 (tpp) cc_final: 0.7450 (tpp) REVERT: B 426 ASN cc_start: 0.9520 (t0) cc_final: 0.9280 (t0) REVERT: B 433 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8826 (mm-30) REVERT: B 517 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9432 (tp) REVERT: B 585 GLU cc_start: 0.9559 (pt0) cc_final: 0.9216 (pm20) REVERT: B 589 GLU cc_start: 0.9627 (mm-30) cc_final: 0.9417 (tp30) REVERT: B 737 GLU cc_start: 0.9143 (pm20) cc_final: 0.8424 (mm-30) outliers start: 42 outliers final: 26 residues processed: 151 average time/residue: 0.1010 time to fit residues: 24.1529 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 : 0.420 ------------------------------------------------------------------------------- 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 432 PHE 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 675 THR Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 730 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** 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 = 0.056112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.043076 restraints weight = 56547.755| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 4.93 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13924 Z= 0.220 Angle : 0.630 7.550 19069 Z= 0.340 Chirality : 0.045 0.187 2084 Planarity : 0.004 0.063 2180 Dihedral : 18.713 173.482 2388 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.54 % Allowed : 12.05 % 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 are not related in a simple way. whole: -0.25 (0.22), residues: 1486 helix: 0.55 (0.23), residues: 460 sheet: -1.06 (0.31), residues: 244 loop : -0.17 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 379 TYR 0.027 0.002 TYR B 306 PHE 0.017 0.002 PHE A 458 TRP 0.010 0.001 TRP B 623 HIS 0.010 0.002 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00489 (13924) covalent geometry : angle 0.63045 (19069) hydrogen bonds : bond 0.03665 ( 485) hydrogen bonds : angle 4.82483 ( 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 150 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.534 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: 0.8384 (pm20) cc_final: 0.8103 (pm20) REVERT: A 169 MET cc_start: 0.9434 (tpp) cc_final: 0.8978 (tpp) REVERT: A 188 ILE cc_start: 0.9803 (mm) cc_final: 0.9563 (mm) REVERT: A 191 MET cc_start: 0.9398 (mtt) cc_final: 0.8964 (mtt) REVERT: A 363 MET cc_start: 0.8832 (mmm) cc_final: 0.7934 (mmm) REVERT: A 426 ASN cc_start: 0.9526 (t0) cc_final: 0.9318 (t0) REVERT: A 500 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.9104 (m-80) REVERT: A 512 LEU cc_start: 0.9770 (tp) cc_final: 0.9457 (pp) REVERT: A 545 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.9006 (m) REVERT: A 737 GLU cc_start: 0.9128 (pm20) cc_final: 0.8310 (mm-30) REVERT: B 113 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9345 (tp) REVERT: B 132 GLU cc_start: 0.8393 (pm20) cc_final: 0.8101 (pm20) REVERT: B 169 MET cc_start: 0.9437 (tpp) cc_final: 0.8990 (tpp) REVERT: B 191 MET cc_start: 0.9413 (mtt) cc_final: 0.8980 (mtt) REVERT: B 302 MET cc_start: 0.8357 (ttm) cc_final: 0.7824 (ttt) REVERT: B 363 MET cc_start: 0.8395 (tpp) cc_final: 0.7504 (tpp) REVERT: B 426 ASN cc_start: 0.9533 (t0) cc_final: 0.9309 (t0) REVERT: B 472 GLU cc_start: 0.8749 (tp30) cc_final: 0.8453 (tp30) REVERT: B 517 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9420 (tp) REVERT: B 585 GLU cc_start: 0.9537 (pt0) cc_final: 0.9220 (pm20) REVERT: B 589 GLU cc_start: 0.9603 (mm-30) cc_final: 0.9371 (tp30) REVERT: B 737 GLU cc_start: 0.9149 (pm20) cc_final: 0.8406 (mm-30) outliers start: 34 outliers final: 21 residues processed: 145 average time/residue: 0.1043 time to fit residues: 24.0298 Evaluate side-chains 124 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 262 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL 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 138 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 730 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 15 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 126 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.057362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.044566 restraints weight = 55352.891| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 4.93 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13924 Z= 0.137 Angle : 0.598 8.092 19069 Z= 0.318 Chirality : 0.045 0.182 2084 Planarity : 0.003 0.060 2180 Dihedral : 18.867 174.164 2388 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.62 % Allowed : 12.50 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.22), residues: 1486 helix: 0.81 (0.24), residues: 458 sheet: -0.73 (0.33), residues: 226 loop : -0.20 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 379 TYR 0.024 0.001 TYR A 306 PHE 0.018 0.002 PHE A 561 TRP 0.030 0.002 TRP B 207 HIS 0.006 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00311 (13924) covalent geometry : angle 0.59754 (19069) hydrogen bonds : bond 0.03519 ( 485) hydrogen bonds : angle 4.62365 ( 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 159 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8381 (pm20) cc_final: 0.8065 (pm20) REVERT: A 169 MET cc_start: 0.9443 (tpp) cc_final: 0.8961 (tpp) REVERT: A 191 MET cc_start: 0.9409 (mtt) cc_final: 0.9011 (mtt) REVERT: A 207 TRP cc_start: 0.8725 (m-10) cc_final: 0.8401 (m-10) REVERT: A 426 ASN cc_start: 0.9544 (t0) cc_final: 0.9339 (t0) REVERT: A 500 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.9089 (m-80) REVERT: A 517 LEU cc_start: 0.9665 (tp) cc_final: 0.9337 (tp) REVERT: A 545 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8920 (m) REVERT: A 737 GLU cc_start: 0.9108 (pm20) cc_final: 0.8188 (mm-30) REVERT: B 113 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9324 (tp) REVERT: B 132 GLU cc_start: 0.8386 (pm20) cc_final: 0.8066 (pm20) REVERT: B 169 MET cc_start: 0.9427 (tpp) cc_final: 0.8957 (tpp) REVERT: B 191 MET cc_start: 0.9413 (mtt) cc_final: 0.8973 (mtt) REVERT: B 302 MET cc_start: 0.8383 (ttm) cc_final: 0.7772 (ttt) REVERT: B 363 MET cc_start: 0.8459 (tpp) cc_final: 0.7582 (tpp) REVERT: B 426 ASN cc_start: 0.9526 (t0) cc_final: 0.9309 (t0) REVERT: B 472 GLU cc_start: 0.8780 (tp30) cc_final: 0.8483 (tp30) REVERT: B 517 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9418 (tp) REVERT: B 581 LYS cc_start: 0.9391 (tttt) cc_final: 0.9050 (tttm) REVERT: B 585 GLU cc_start: 0.9552 (pt0) cc_final: 0.9224 (pm20) REVERT: B 589 GLU cc_start: 0.9630 (mm-30) cc_final: 0.9386 (tp30) REVERT: B 737 GLU cc_start: 0.9163 (pm20) cc_final: 0.8369 (mm-30) outliers start: 35 outliers final: 17 residues processed: 150 average time/residue: 0.1038 time to fit residues: 24.4035 Evaluate side-chains 129 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 359 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL 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 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 448 LEU Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 517 LEU 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: 10.0000 chunk 25 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 overall best weight: 6.9788 ------------------------------------------------------------------------------- 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 232 GLN B 240 ASN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.052303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.039489 restraints weight = 58326.071| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 4.81 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 13924 Z= 0.389 Angle : 0.758 9.090 19069 Z= 0.406 Chirality : 0.049 0.177 2084 Planarity : 0.004 0.047 2180 Dihedral : 19.188 177.827 2388 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.54 % Allowed : 13.02 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1486 helix: 0.69 (0.23), residues: 450 sheet: -1.26 (0.32), residues: 240 loop : -0.13 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 379 TYR 0.028 0.002 TYR B 237 PHE 0.038 0.003 PHE A 561 TRP 0.018 0.003 TRP B 207 HIS 0.012 0.003 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00845 (13924) covalent geometry : angle 0.75781 (19069) hydrogen bonds : bond 0.04184 ( 485) hydrogen bonds : angle 5.16926 ( 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: 34 poor density : 103 time to evaluate : 0.537 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: 0.8497 (pm20) cc_final: 0.8240 (pm20) REVERT: A 169 MET cc_start: 0.9470 (tpp) cc_final: 0.9012 (tpp) REVERT: A 191 MET cc_start: 0.9405 (mtt) cc_final: 0.8985 (mtt) REVERT: A 353 MET cc_start: 0.9093 (mmm) cc_final: 0.8734 (mmm) REVERT: A 363 MET cc_start: 0.8874 (mmm) cc_final: 0.8140 (mmm) REVERT: A 484 GLU cc_start: 0.9297 (tm-30) cc_final: 0.8892 (tm-30) REVERT: A 491 MET cc_start: 0.8642 (mpp) cc_final: 0.8337 (mpp) REVERT: A 500 PHE cc_start: 0.9470 (OUTLIER) cc_final: 0.9163 (m-80) REVERT: A 512 LEU cc_start: 0.9745 (tp) cc_final: 0.9435 (pp) REVERT: A 545 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9000 (m) REVERT: A 580 GLU cc_start: 0.8220 (pt0) cc_final: 0.7784 (pm20) REVERT: A 652 ASN cc_start: 0.9046 (t0) cc_final: 0.8825 (t0) REVERT: B 132 GLU cc_start: 0.8508 (pm20) cc_final: 0.8248 (pm20) REVERT: B 169 MET cc_start: 0.9462 (tpp) cc_final: 0.9008 (tpp) REVERT: B 191 MET cc_start: 0.9389 (mtt) cc_final: 0.8988 (mtt) REVERT: B 302 MET cc_start: 0.8494 (ttm) cc_final: 0.7931 (ttt) REVERT: B 353 MET cc_start: 0.9086 (mmm) cc_final: 0.8712 (mmm) REVERT: B 363 MET cc_start: 0.8457 (tpp) cc_final: 0.7546 (tpp) REVERT: B 472 GLU cc_start: 0.8780 (tp30) cc_final: 0.8469 (tp30) REVERT: B 491 MET cc_start: 0.9353 (mmm) cc_final: 0.8725 (mmp) REVERT: B 580 GLU cc_start: 0.8703 (tt0) cc_final: 0.8198 (mp0) REVERT: B 581 LYS cc_start: 0.9384 (tttt) cc_final: 0.9092 (tttm) REVERT: B 585 GLU cc_start: 0.9544 (pt0) cc_final: 0.9184 (pm20) REVERT: B 589 GLU cc_start: 0.9611 (mm-30) cc_final: 0.9310 (tp30) REVERT: B 652 ASN cc_start: 0.9075 (t0) cc_final: 0.8854 (t0) REVERT: B 737 GLU cc_start: 0.9175 (pm20) cc_final: 0.8910 (pm20) outliers start: 34 outliers final: 23 residues processed: 134 average time/residue: 0.0972 time to fit residues: 20.4033 Evaluate side-chains 118 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 359 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 730 ASP 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 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 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: 8.9990 chunk 83 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 232 GLN B 240 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.055341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.042396 restraints weight = 55846.112| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 4.90 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13924 Z= 0.154 Angle : 0.622 8.966 19069 Z= 0.330 Chirality : 0.045 0.216 2084 Planarity : 0.003 0.036 2180 Dihedral : 19.108 179.733 2388 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.65 % Allowed : 13.70 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.22), residues: 1486 helix: 0.93 (0.24), residues: 458 sheet: -1.11 (0.32), residues: 244 loop : -0.10 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 379 TYR 0.024 0.001 TYR B 237 PHE 0.022 0.002 PHE B 561 TRP 0.017 0.002 TRP B 207 HIS 0.008 0.002 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00349 (13924) covalent geometry : angle 0.62194 (19069) hydrogen bonds : bond 0.03539 ( 485) hydrogen bonds : angle 4.73544 ( 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 133 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.494 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: 0.9701 (OUTLIER) cc_final: 0.9394 (tp) REVERT: A 132 GLU cc_start: 0.8445 (pm20) cc_final: 0.8164 (pm20) REVERT: A 169 MET cc_start: 0.9425 (tpp) cc_final: 0.8928 (tpp) REVERT: A 191 MET cc_start: 0.9426 (mtt) cc_final: 0.9008 (mtt) REVERT: A 363 MET cc_start: 0.8803 (mmm) cc_final: 0.8062 (mmm) REVERT: A 500 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.9136 (m-80) REVERT: A 517 LEU cc_start: 0.9675 (tp) cc_final: 0.9346 (tp) REVERT: A 737 GLU cc_start: 0.9135 (pm20) cc_final: 0.8890 (pm20) REVERT: B 132 GLU cc_start: 0.8441 (pm20) cc_final: 0.8155 (pm20) REVERT: B 169 MET cc_start: 0.9427 (tpp) cc_final: 0.8936 (tpp) REVERT: B 302 MET cc_start: 0.8398 (ttm) cc_final: 0.7802 (ttt) REVERT: B 353 MET cc_start: 0.9103 (mmm) cc_final: 0.8838 (mmm) REVERT: B 363 MET cc_start: 0.8451 (tpp) cc_final: 0.7558 (tpp) REVERT: B 472 GLU cc_start: 0.8800 (tp30) cc_final: 0.8496 (tp30) REVERT: B 517 LEU cc_start: 0.9651 (tp) cc_final: 0.9446 (tp) REVERT: B 581 LYS cc_start: 0.9417 (tttt) cc_final: 0.9102 (tttm) REVERT: B 585 GLU cc_start: 0.9549 (pt0) cc_final: 0.9156 (pm20) REVERT: B 589 GLU cc_start: 0.9608 (mm-30) cc_final: 0.9281 (tp30) REVERT: B 737 GLU cc_start: 0.9157 (pm20) cc_final: 0.8383 (mm-30) outliers start: 22 outliers final: 17 residues processed: 127 average time/residue: 0.1080 time to fit residues: 21.4520 Evaluate side-chains 118 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 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 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 432 PHE Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 539 CYS 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 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 448 LEU Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 666 LEU 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: 5.9990 chunk 131 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3063 r_free = 0.3063 target = 0.052907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.040129 restraints weight = 57899.525| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 4.84 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 13924 Z= 0.318 Angle : 0.706 9.904 19069 Z= 0.377 Chirality : 0.047 0.188 2084 Planarity : 0.004 0.041 2180 Dihedral : 19.246 176.062 2388 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.95 % Allowed : 14.30 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1486 helix: 0.85 (0.24), residues: 450 sheet: -1.37 (0.28), residues: 324 loop : 0.10 (0.26), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 379 TYR 0.028 0.002 TYR B 237 PHE 0.028 0.002 PHE A 561 TRP 0.014 0.002 TRP B 207 HIS 0.009 0.003 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00697 (13924) covalent geometry : angle 0.70579 (19069) hydrogen bonds : bond 0.03838 ( 485) hydrogen bonds : angle 5.00972 ( 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 125 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8504 (pm20) cc_final: 0.8229 (pm20) REVERT: A 169 MET cc_start: 0.9452 (tpp) cc_final: 0.8977 (tpp) REVERT: A 191 MET cc_start: 0.9413 (mtt) cc_final: 0.8954 (mtt) REVERT: A 363 MET cc_start: 0.8822 (mmm) cc_final: 0.8028 (mmm) REVERT: A 484 GLU cc_start: 0.9270 (tm-30) cc_final: 0.8836 (tm-30) REVERT: A 500 PHE cc_start: 0.9448 (OUTLIER) cc_final: 0.9165 (m-80) REVERT: A 512 LEU cc_start: 0.9742 (tp) cc_final: 0.9451 (pp) REVERT: A 580 GLU cc_start: 0.8085 (pt0) cc_final: 0.7812 (pm20) REVERT: A 589 GLU cc_start: 0.9578 (tp30) cc_final: 0.9050 (tm-30) REVERT: A 652 ASN cc_start: 0.9042 (t0) cc_final: 0.8834 (t0) REVERT: B 132 GLU cc_start: 0.8511 (pm20) cc_final: 0.8232 (pm20) REVERT: B 169 MET cc_start: 0.9453 (tpp) cc_final: 0.8989 (tpp) REVERT: B 191 MET cc_start: 0.9388 (mtt) cc_final: 0.8957 (mtt) REVERT: B 363 MET cc_start: 0.8507 (tpp) cc_final: 0.7585 (tpp) REVERT: B 472 GLU cc_start: 0.8798 (tp30) cc_final: 0.8475 (tp30) REVERT: B 533 MET cc_start: 0.9224 (tpp) cc_final: 0.8831 (ttm) REVERT: B 585 GLU cc_start: 0.9541 (pt0) cc_final: 0.9170 (pm20) REVERT: B 589 GLU cc_start: 0.9618 (mm-30) cc_final: 0.9316 (tp30) REVERT: B 652 ASN cc_start: 0.9096 (t0) cc_final: 0.8892 (t0) outliers start: 26 outliers final: 23 residues processed: 120 average time/residue: 0.1042 time to fit residues: 19.8255 Evaluate side-chains 116 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 432 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 730 ASP 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 237 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 676 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 46 optimal weight: 10.0000 chunk 132 optimal weight: 0.0570 chunk 88 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 62 optimal weight: 0.0770 chunk 2 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.6058 ------------------------------------------------------------------------------- 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 574 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 = 0.3130 r_free = 0.3130 target = 0.055123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.042513 restraints weight = 55826.980| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 4.93 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13924 Z= 0.150 Angle : 0.643 12.896 19069 Z= 0.337 Chirality : 0.046 0.355 2084 Planarity : 0.003 0.044 2180 Dihedral : 19.130 179.060 2388 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.50 % Allowed : 15.12 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.23), residues: 1486 helix: 0.96 (0.24), residues: 458 sheet: -1.19 (0.29), residues: 322 loop : 0.09 (0.26), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 379 TYR 0.028 0.001 TYR B 306 PHE 0.018 0.002 PHE A 561 TRP 0.015 0.002 TRP B 207 HIS 0.007 0.002 HIS B 553 Details of bonding type rmsd covalent geometry : bond 0.00343 (13924) covalent geometry : angle 0.64295 (19069) hydrogen bonds : bond 0.03507 ( 485) hydrogen bonds : angle 4.71062 ( 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 129 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.537 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: 0.8437 (pm20) cc_final: 0.8146 (pm20) REVERT: A 169 MET cc_start: 0.9446 (tpp) cc_final: 0.8954 (tpp) REVERT: A 191 MET cc_start: 0.9437 (mtt) cc_final: 0.9007 (mtt) REVERT: A 353 MET cc_start: 0.9062 (mmm) cc_final: 0.8607 (mmm) REVERT: A 363 MET cc_start: 0.8811 (mmm) cc_final: 0.8029 (mmm) REVERT: A 484 GLU cc_start: 0.9250 (tm-30) cc_final: 0.8794 (tm-30) REVERT: A 500 PHE cc_start: 0.9375 (OUTLIER) cc_final: 0.9155 (m-80) REVERT: A 512 LEU cc_start: 0.9739 (tp) cc_final: 0.9444 (pp) REVERT: A 517 LEU cc_start: 0.9673 (tp) cc_final: 0.9354 (tp) REVERT: A 699 MET cc_start: 0.8777 (mmt) cc_final: 0.8411 (mmt) REVERT: A 737 GLU cc_start: 0.9117 (pm20) cc_final: 0.8861 (pm20) REVERT: B 132 GLU cc_start: 0.8424 (pm20) cc_final: 0.8137 (pm20) REVERT: B 169 MET cc_start: 0.9474 (tpp) cc_final: 0.8991 (tpp) REVERT: B 302 MET cc_start: 0.8090 (ttm) cc_final: 0.7738 (ttm) REVERT: B 363 MET cc_start: 0.8498 (tpp) cc_final: 0.7568 (tpp) REVERT: B 472 GLU cc_start: 0.8789 (tp30) cc_final: 0.8490 (tp30) REVERT: B 491 MET cc_start: 0.9226 (mmm) cc_final: 0.8785 (mmm) REVERT: B 533 MET cc_start: 0.9151 (tpp) cc_final: 0.8710 (ttm) REVERT: B 585 GLU cc_start: 0.9556 (pt0) cc_final: 0.9194 (pm20) REVERT: B 589 GLU cc_start: 0.9634 (mm-30) cc_final: 0.9316 (tp30) REVERT: B 737 GLU cc_start: 0.9083 (pm20) cc_final: 0.8136 (mm-30) outliers start: 20 outliers final: 18 residues processed: 124 average time/residue: 0.1022 time to fit residues: 20.1645 Evaluate side-chains 117 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 432 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 539 CYS 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 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 539 CYS Chi-restraints excluded: chain B residue 666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 95 optimal weight: 7.9990 chunk 8 optimal weight: 0.0170 chunk 131 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- 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 574 ASN ** B 577 GLN ** 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 = 0.3123 r_free = 0.3123 target = 0.055152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.042627 restraints weight = 56457.571| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.89 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13924 Z= 0.181 Angle : 0.660 12.356 19069 Z= 0.344 Chirality : 0.046 0.322 2084 Planarity : 0.004 0.051 2180 Dihedral : 19.109 179.623 2388 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.87 % Allowed : 14.97 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.23), residues: 1486 helix: 0.85 (0.24), residues: 458 sheet: -1.14 (0.29), residues: 322 loop : 0.10 (0.26), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 379 TYR 0.034 0.002 TYR A 306 PHE 0.019 0.002 PHE A 561 TRP 0.023 0.002 TRP A 207 HIS 0.008 0.002 HIS B 553 Details of bonding type rmsd covalent geometry : bond 0.00411 (13924) covalent geometry : angle 0.65962 (19069) hydrogen bonds : bond 0.03537 ( 485) hydrogen bonds : angle 4.68535 ( 1400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2034.92 seconds wall clock time: 36 minutes 23.73 seconds (2183.73 seconds total)