Starting phenix.real_space_refine on Thu Feb 15 12:58:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qp6_4611/02_2024/6qp6_4611_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qp6_4611/02_2024/6qp6_4611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qp6_4611/02_2024/6qp6_4611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qp6_4611/02_2024/6qp6_4611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qp6_4611/02_2024/6qp6_4611_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qp6_4611/02_2024/6qp6_4611_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.011 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 Ca 6 9.91 5 P 2 5.49 5 S 80 5.16 5 C 8100 2.51 5 N 1978 2.21 5 O 2164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ASP 66": "OD1" <-> "OD2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 583": "OD1" <-> "OD2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ASP 721": "OD1" <-> "OD2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A ASP 767": "OD1" <-> "OD2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 810": "NH1" <-> "NH2" Residue "A ASP 811": "OD1" <-> "OD2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B ASP 259": "OD1" <-> "OD2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 277": "NH1" <-> "NH2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B ASP 327": "OD1" <-> "OD2" Residue "B ASP 329": "OD1" <-> "OD2" Residue "B ASP 353": "OD1" <-> "OD2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "B GLU 539": "OE1" <-> "OE2" Residue "B GLU 548": "OE1" <-> "OE2" Residue "B PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B GLU 595": "OE1" <-> "OE2" Residue "B ASP 597": "OD1" <-> "OD2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B ASP 721": "OD1" <-> "OD2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "B ASP 767": "OD1" <-> "OD2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 810": "NH1" <-> "NH2" Residue "B ASP 811": "OD1" <-> "OD2" Residue "B ARG 870": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12330 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6124 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 9 Chain: "B" Number of atoms: 6124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6124 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 9 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' CA': 3, 'P1O': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' CA': 3, 'P1O': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.68, per 1000 atoms: 0.54 Number of scatterers: 12330 At special positions: 0 Unit cell: (88.044, 123.464, 112.332, 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) Ca 6 19.99 S 80 16.00 P 2 15.00 O 2164 8.00 N 1978 7.00 C 8100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.02 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.01 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.02 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.01 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.02 Conformation dependent library (CDL) restraints added in 2.2 seconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 6 sheets defined 58.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 90 through 108 removed outlier: 3.701A pdb=" N GLN A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 206 through 219 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 294 through 326 removed outlier: 3.514A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 361 through 374 removed outlier: 5.046A pdb=" N GLU A 366 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 407 removed outlier: 4.069A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.624A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 487 removed outlier: 3.531A pdb=" N ILE A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 538 removed outlier: 3.827A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 572 removed outlier: 5.194A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 638 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 688 through 709 removed outlier: 4.033A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.909A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 759 Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 798 through 801 No H-bonds generated for 'chain 'A' and resid 798 through 801' Processing helix chain 'A' and resid 826 through 856 Processing helix chain 'A' and resid 862 through 874 Processing helix chain 'B' and resid 90 through 108 removed outlier: 3.699A pdb=" N GLN B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 206 through 219 Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 294 through 326 removed outlier: 3.513A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 361 through 374 removed outlier: 5.046A pdb=" N GLU B 366 " --> pdb=" O ILE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 407 removed outlier: 4.069A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 426 removed outlier: 3.625A pdb=" N GLN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 487 removed outlier: 3.532A pdb=" N ILE B 451 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 538 removed outlier: 3.827A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 572 removed outlier: 5.194A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 649 through 654 Processing helix chain 'B' and resid 665 through 679 Processing helix chain 'B' and resid 688 through 709 removed outlier: 4.033A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.909A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 759 Processing helix chain 'B' and resid 776 through 780 Processing helix chain 'B' and resid 798 through 801 No H-bonds generated for 'chain 'B' and resid 798 through 801' Processing helix chain 'B' and resid 826 through 856 Processing helix chain 'B' and resid 862 through 874 Processing sheet with id= A, first strand: chain 'A' and resid 244 through 246 Processing sheet with id= B, first strand: chain 'A' and resid 146 through 148 removed outlier: 3.671A pdb=" N SER A 190 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 782 through 785 Processing sheet with id= D, first strand: chain 'B' and resid 244 through 246 Processing sheet with id= E, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.671A pdb=" N SER B 190 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 782 through 785 668 hydrogen bonds defined for protein. 1914 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1923 1.32 - 1.44: 3666 1.44 - 1.56: 6926 1.56 - 1.69: 15 1.69 - 1.81: 122 Bond restraints: 12652 Sorted by residual: bond pdb=" O3 P1O B1003 " pdb=" P1 P1O B1003 " ideal model delta sigma weight residual 1.648 1.776 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" O3 P1O A1003 " pdb=" P1 P1O A1003 " ideal model delta sigma weight residual 1.648 1.776 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C19 P1O B1003 " pdb=" C20 P1O B1003 " ideal model delta sigma weight residual 1.502 1.583 -0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C19 P1O A1003 " pdb=" C20 P1O A1003 " ideal model delta sigma weight residual 1.502 1.583 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C19 P1O A1003 " pdb=" O7 P1O A1003 " ideal model delta sigma weight residual 1.331 1.409 -0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 12647 not shown) Histogram of bond angle deviations from ideal: 97.50 - 104.87: 235 104.87 - 112.25: 5960 112.25 - 119.62: 4549 119.62 - 126.99: 6228 126.99 - 134.36: 154 Bond angle restraints: 17126 Sorted by residual: angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 117.09 -6.39 1.22e+00 6.72e-01 2.74e+01 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 117.04 -6.34 1.22e+00 6.72e-01 2.70e+01 angle pdb=" C ARG A 191 " pdb=" N MET A 192 " pdb=" CA MET A 192 " ideal model delta sigma weight residual 121.54 130.92 -9.38 1.91e+00 2.74e-01 2.41e+01 angle pdb=" C ARG B 191 " pdb=" N MET B 192 " pdb=" CA MET B 192 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 angle pdb=" CB GLU A 871 " pdb=" CG GLU A 871 " pdb=" CD GLU A 871 " ideal model delta sigma weight residual 112.60 119.60 -7.00 1.70e+00 3.46e-01 1.70e+01 ... (remaining 17121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.22: 7180 29.22 - 58.44: 278 58.44 - 87.66: 30 87.66 - 116.88: 0 116.88 - 146.10: 2 Dihedral angle restraints: 7490 sinusoidal: 3108 harmonic: 4382 Sorted by residual: dihedral pdb=" CB CYS B 596 " pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " pdb=" CB CYS B 601 " ideal model delta sinusoidal sigma weight residual 93.00 151.43 -58.43 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 151.39 -58.39 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CA ARG A 191 " pdb=" C ARG A 191 " pdb=" N MET A 192 " pdb=" CA MET A 192 " ideal model delta harmonic sigma weight residual -180.00 -150.41 -29.59 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 7487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.022: 1852 1.022 - 2.044: 0 2.044 - 3.066: 0 3.066 - 4.087: 0 4.087 - 5.109: 2 Chirality restraints: 1854 Sorted by residual: chirality pdb=" C7 P1O B1003 " pdb=" C6 P1O B1003 " pdb=" C8 P1O B1003 " pdb=" O7 P1O B1003 " both_signs ideal model delta sigma weight residual False -2.35 2.76 -5.11 2.00e-01 2.50e+01 6.53e+02 chirality pdb=" C7 P1O A1003 " pdb=" C6 P1O A1003 " pdb=" C8 P1O A1003 " pdb=" O7 P1O A1003 " both_signs ideal model delta sigma weight residual False -2.35 2.76 -5.11 2.00e-01 2.50e+01 6.52e+02 chirality pdb=" CG LEU B 465 " pdb=" CB LEU B 465 " pdb=" CD1 LEU B 465 " pdb=" CD2 LEU B 465 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1851 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 597 " 0.059 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO B 598 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 598 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 598 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 597 " -0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO A 598 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 364 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C THR A 364 " 0.054 2.00e-02 2.50e+03 pdb=" O THR A 364 " -0.020 2.00e-02 2.50e+03 pdb=" N CYS A 365 " -0.018 2.00e-02 2.50e+03 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 119 2.56 - 3.14: 9456 3.14 - 3.73: 19724 3.73 - 4.31: 27267 4.31 - 4.90: 45733 Nonbonded interactions: 102299 Sorted by model distance: nonbonded pdb=" OH TYR A 406 " pdb=" OE2 GLU A 871 " model vdw 1.975 2.440 nonbonded pdb=" OH TYR B 406 " pdb=" OE2 GLU B 871 " model vdw 1.975 2.440 nonbonded pdb=" OG SER A 190 " pdb=" OD2 ASP A 194 " model vdw 2.228 2.440 nonbonded pdb=" OG SER B 190 " pdb=" OD2 ASP B 194 " model vdw 2.228 2.440 nonbonded pdb=" OG SER B 782 " pdb=" O ASP B 811 " model vdw 2.269 2.440 ... (remaining 102294 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.490 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: 2.960 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 35.200 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.128 12652 Z= 0.644 Angle : 1.061 10.069 17126 Z= 0.590 Chirality : 0.178 5.109 1854 Planarity : 0.010 0.089 2120 Dihedral : 15.828 146.103 4642 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.45 % Allowed : 8.83 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.18), residues: 1442 helix: -1.53 (0.14), residues: 902 sheet: -1.24 (0.55), residues: 54 loop : -2.15 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 397 HIS 0.011 0.002 HIS A 830 PHE 0.038 0.003 PHE B 685 TYR 0.023 0.003 TYR B 580 ARG 0.007 0.001 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 222 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 138 TYR cc_start: 0.7579 (m-80) cc_final: 0.7176 (m-80) REVERT: A 191 ARG cc_start: 0.6878 (mpp-170) cc_final: 0.6628 (mpp-170) REVERT: A 215 PHE cc_start: 0.8395 (t80) cc_final: 0.8166 (t80) REVERT: A 221 LYS cc_start: 0.7205 (mtmt) cc_final: 0.5959 (mmtt) REVERT: A 270 TYR cc_start: 0.8493 (t80) cc_final: 0.8281 (t80) REVERT: A 611 ILE cc_start: 0.8934 (mm) cc_final: 0.8723 (mm) REVERT: A 619 TRP cc_start: 0.7215 (t60) cc_final: 0.6977 (t-100) REVERT: B 108 HIS cc_start: 0.6240 (m90) cc_final: 0.6029 (m90) REVERT: B 138 TYR cc_start: 0.7468 (m-80) cc_final: 0.7038 (m-80) REVERT: B 221 LYS cc_start: 0.7356 (mtmt) cc_final: 0.6061 (mptt) REVERT: B 270 TYR cc_start: 0.8582 (t80) cc_final: 0.8327 (t80) REVERT: B 366 GLU cc_start: 0.7724 (tp30) cc_final: 0.7342 (mm-30) REVERT: B 542 ARG cc_start: 0.7312 (ptm-80) cc_final: 0.7100 (ptm-80) REVERT: B 594 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6955 (mt-10) REVERT: B 611 ILE cc_start: 0.8898 (mm) cc_final: 0.8681 (mm) REVERT: B 619 TRP cc_start: 0.7251 (t60) cc_final: 0.7049 (t-100) REVERT: B 760 PHE cc_start: 0.8351 (m-80) cc_final: 0.8129 (m-80) REVERT: B 773 MET cc_start: 0.8756 (mmm) cc_final: 0.8369 (mmt) outliers start: 6 outliers final: 2 residues processed: 226 average time/residue: 0.2608 time to fit residues: 83.4920 Evaluate side-chains 172 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain B residue 536 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 223 GLN A 283 GLN A 328 GLN A 549 ASN A 632 ASN A 655 HIS A 730 GLN A 814 ASN B 99 GLN B 143 HIS B 223 GLN B 283 GLN B 549 ASN B 632 ASN B 655 HIS B 730 GLN B 814 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12652 Z= 0.185 Angle : 0.577 7.674 17126 Z= 0.312 Chirality : 0.040 0.146 1854 Planarity : 0.006 0.062 2120 Dihedral : 9.216 141.674 1696 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.72 % Allowed : 10.85 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.20), residues: 1442 helix: -0.07 (0.15), residues: 910 sheet: -1.08 (0.60), residues: 52 loop : -1.79 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 397 HIS 0.011 0.001 HIS B 655 PHE 0.015 0.001 PHE B 556 TYR 0.022 0.001 TYR A 406 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 1.553 Fit side-chains revert: symmetry clash REVERT: A 138 TYR cc_start: 0.7485 (m-80) cc_final: 0.7045 (m-80) REVERT: A 215 PHE cc_start: 0.8322 (t80) cc_final: 0.8053 (t80) REVERT: A 235 ARG cc_start: 0.7637 (ttt180) cc_final: 0.7282 (mtp180) REVERT: A 619 TRP cc_start: 0.7183 (t60) cc_final: 0.6977 (t-100) REVERT: B 138 TYR cc_start: 0.7346 (m-80) cc_final: 0.7051 (m-80) REVERT: B 142 MET cc_start: 0.7262 (ptm) cc_final: 0.7034 (ptm) REVERT: B 221 LYS cc_start: 0.7046 (mtmt) cc_final: 0.5688 (mptt) REVERT: B 270 TYR cc_start: 0.8538 (t80) cc_final: 0.8303 (t80) REVERT: B 366 GLU cc_start: 0.7689 (tp30) cc_final: 0.7283 (mm-30) REVERT: B 594 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6731 (mt-10) REVERT: B 717 GLU cc_start: 0.7241 (mp0) cc_final: 0.7039 (mp0) REVERT: B 760 PHE cc_start: 0.8235 (m-80) cc_final: 0.8028 (m-80) REVERT: B 773 MET cc_start: 0.8731 (mmm) cc_final: 0.8309 (mmt) outliers start: 23 outliers final: 11 residues processed: 183 average time/residue: 0.2482 time to fit residues: 66.1095 Evaluate side-chains 162 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 650 TRP Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 650 TRP Chi-restraints excluded: chain B residue 769 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12652 Z= 0.367 Angle : 0.648 9.959 17126 Z= 0.345 Chirality : 0.044 0.137 1854 Planarity : 0.006 0.059 2120 Dihedral : 9.248 139.888 1694 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.07 % Allowed : 13.92 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1442 helix: 0.42 (0.16), residues: 912 sheet: -1.01 (0.64), residues: 52 loop : -1.87 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 397 HIS 0.006 0.001 HIS B 830 PHE 0.027 0.002 PHE B 685 TYR 0.046 0.002 TYR B 528 ARG 0.005 0.001 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 1.505 Fit side-chains REVERT: A 122 LYS cc_start: 0.7387 (ptpt) cc_final: 0.7094 (pttt) REVERT: A 138 TYR cc_start: 0.7663 (m-80) cc_final: 0.7233 (m-80) REVERT: A 221 LYS cc_start: 0.7004 (mtmt) cc_final: 0.6449 (pttm) REVERT: A 235 ARG cc_start: 0.7576 (ttt180) cc_final: 0.7306 (mtp180) REVERT: A 619 TRP cc_start: 0.7245 (t60) cc_final: 0.6984 (t-100) REVERT: A 661 LYS cc_start: 0.7308 (pttt) cc_final: 0.7004 (ptmm) REVERT: B 138 TYR cc_start: 0.7371 (m-80) cc_final: 0.6988 (m-80) REVERT: B 221 LYS cc_start: 0.6996 (mtmt) cc_final: 0.5707 (mptt) REVERT: B 406 TYR cc_start: 0.7984 (t80) cc_final: 0.7552 (t80) REVERT: B 407 GLU cc_start: 0.7435 (tt0) cc_final: 0.7060 (mt-10) REVERT: B 528 TYR cc_start: 0.8031 (t80) cc_final: 0.7745 (t80) REVERT: B 760 PHE cc_start: 0.8287 (m-80) cc_final: 0.8060 (m-80) outliers start: 41 outliers final: 32 residues processed: 184 average time/residue: 0.2387 time to fit residues: 64.8615 Evaluate side-chains 183 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 38 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12652 Z= 0.153 Angle : 0.517 8.121 17126 Z= 0.278 Chirality : 0.039 0.136 1854 Planarity : 0.005 0.049 2120 Dihedral : 8.859 137.503 1694 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.02 % Allowed : 15.57 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1442 helix: 0.87 (0.17), residues: 916 sheet: -0.72 (0.67), residues: 52 loop : -1.66 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 397 HIS 0.002 0.001 HIS A 655 PHE 0.012 0.001 PHE B 558 TYR 0.039 0.001 TYR B 528 ARG 0.004 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.502 Fit side-chains REVERT: A 122 LYS cc_start: 0.7280 (ptpt) cc_final: 0.6987 (pttt) REVERT: A 138 TYR cc_start: 0.7645 (m-80) cc_final: 0.7060 (m-80) REVERT: A 194 ASP cc_start: 0.6985 (m-30) cc_final: 0.6601 (m-30) REVERT: A 221 LYS cc_start: 0.6869 (mtmt) cc_final: 0.6419 (pttm) REVERT: A 268 LEU cc_start: 0.8919 (tt) cc_final: 0.8562 (pp) REVERT: A 365 CYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6153 (t) REVERT: A 594 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6554 (mt-10) REVERT: A 619 TRP cc_start: 0.7120 (t60) cc_final: 0.6900 (t-100) REVERT: A 661 LYS cc_start: 0.7276 (pttt) cc_final: 0.6924 (ptmt) REVERT: B 142 MET cc_start: 0.7159 (ptm) cc_final: 0.6922 (ptm) REVERT: B 221 LYS cc_start: 0.6789 (mtmt) cc_final: 0.6314 (pttm) REVERT: B 365 CYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6404 (t) REVERT: B 407 GLU cc_start: 0.7351 (tt0) cc_final: 0.7058 (mt-10) REVERT: B 517 SER cc_start: 0.9008 (p) cc_final: 0.8654 (p) REVERT: B 528 TYR cc_start: 0.8041 (t80) cc_final: 0.7529 (t80) REVERT: B 594 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6694 (mt-10) outliers start: 27 outliers final: 18 residues processed: 176 average time/residue: 0.2355 time to fit residues: 61.0921 Evaluate side-chains 171 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 721 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 98 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 128 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 655 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12652 Z= 0.214 Angle : 0.544 9.679 17126 Z= 0.289 Chirality : 0.040 0.133 1854 Planarity : 0.005 0.048 2120 Dihedral : 8.730 136.401 1694 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.77 % Allowed : 15.79 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1442 helix: 1.06 (0.17), residues: 916 sheet: -0.50 (0.67), residues: 52 loop : -1.60 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 397 HIS 0.006 0.001 HIS A 655 PHE 0.015 0.001 PHE A 685 TYR 0.034 0.002 TYR B 528 ARG 0.004 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.7418 (ptpt) cc_final: 0.7109 (pttt) REVERT: A 142 MET cc_start: 0.6748 (ptt) cc_final: 0.6226 (ptt) REVERT: A 194 ASP cc_start: 0.6817 (m-30) cc_final: 0.6475 (m-30) REVERT: A 215 PHE cc_start: 0.8205 (t80) cc_final: 0.7861 (t80) REVERT: A 221 LYS cc_start: 0.6865 (mtmt) cc_final: 0.6360 (pttm) REVERT: A 346 ILE cc_start: 0.8613 (mm) cc_final: 0.8285 (mt) REVERT: A 365 CYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6259 (t) REVERT: A 661 LYS cc_start: 0.7302 (pttt) cc_final: 0.6983 (ptmm) REVERT: B 122 LYS cc_start: 0.7548 (ptpt) cc_final: 0.7154 (pttt) REVERT: B 221 LYS cc_start: 0.6747 (mtmt) cc_final: 0.6364 (pttm) REVERT: B 365 CYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6407 (t) REVERT: B 407 GLU cc_start: 0.7361 (tt0) cc_final: 0.7059 (mt-10) REVERT: B 517 SER cc_start: 0.9018 (p) cc_final: 0.8672 (p) REVERT: B 528 TYR cc_start: 0.7986 (t80) cc_final: 0.7303 (t80) REVERT: B 594 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6782 (mt-10) outliers start: 37 outliers final: 28 residues processed: 181 average time/residue: 0.2312 time to fit residues: 62.0857 Evaluate side-chains 182 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12652 Z= 0.225 Angle : 0.544 7.840 17126 Z= 0.290 Chirality : 0.040 0.136 1854 Planarity : 0.005 0.046 2120 Dihedral : 8.666 134.893 1694 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.14 % Allowed : 15.64 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.22), residues: 1442 helix: 1.23 (0.17), residues: 898 sheet: 0.33 (0.75), residues: 42 loop : -1.67 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS A 830 PHE 0.015 0.001 PHE A 685 TYR 0.028 0.002 TYR B 528 ARG 0.005 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 1.295 Fit side-chains REVERT: A 122 LYS cc_start: 0.7453 (ptpt) cc_final: 0.7131 (pttt) REVERT: A 142 MET cc_start: 0.6904 (ptt) cc_final: 0.6374 (ptt) REVERT: A 194 ASP cc_start: 0.6869 (m-30) cc_final: 0.6516 (m-30) REVERT: A 215 PHE cc_start: 0.8216 (t80) cc_final: 0.7842 (t80) REVERT: A 221 LYS cc_start: 0.6922 (mtmt) cc_final: 0.6380 (pttm) REVERT: A 268 LEU cc_start: 0.8899 (tt) cc_final: 0.8643 (pp) REVERT: A 346 ILE cc_start: 0.8607 (mm) cc_final: 0.8274 (mt) REVERT: A 365 CYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6211 (t) REVERT: A 661 LYS cc_start: 0.7340 (pttt) cc_final: 0.7027 (ptmm) REVERT: B 96 ARG cc_start: 0.7213 (mtp-110) cc_final: 0.6987 (mtp-110) REVERT: B 122 LYS cc_start: 0.7626 (ptpt) cc_final: 0.7179 (pttt) REVERT: B 221 LYS cc_start: 0.6754 (mtmt) cc_final: 0.6362 (pttm) REVERT: B 365 CYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6433 (t) REVERT: B 407 GLU cc_start: 0.7379 (tt0) cc_final: 0.7051 (mt-10) REVERT: B 517 SER cc_start: 0.9038 (p) cc_final: 0.8700 (p) REVERT: B 528 TYR cc_start: 0.8042 (t80) cc_final: 0.7332 (t80) outliers start: 42 outliers final: 33 residues processed: 183 average time/residue: 0.2183 time to fit residues: 60.0991 Evaluate side-chains 188 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12652 Z= 0.238 Angle : 0.544 7.795 17126 Z= 0.290 Chirality : 0.040 0.138 1854 Planarity : 0.005 0.045 2120 Dihedral : 8.595 133.319 1694 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.89 % Allowed : 15.34 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.22), residues: 1442 helix: 1.28 (0.17), residues: 894 sheet: 0.35 (0.74), residues: 42 loop : -1.69 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS A 830 PHE 0.024 0.002 PHE B 558 TYR 0.026 0.002 TYR B 528 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 159 time to evaluate : 1.432 Fit side-chains REVERT: A 122 LYS cc_start: 0.7472 (ptpt) cc_final: 0.7137 (pttt) REVERT: A 194 ASP cc_start: 0.6844 (m-30) cc_final: 0.6508 (m-30) REVERT: A 215 PHE cc_start: 0.8194 (t80) cc_final: 0.7969 (t80) REVERT: A 221 LYS cc_start: 0.6936 (mtmt) cc_final: 0.6376 (pttm) REVERT: A 268 LEU cc_start: 0.8935 (tt) cc_final: 0.8669 (pp) REVERT: A 346 ILE cc_start: 0.8581 (mm) cc_final: 0.8249 (mt) REVERT: A 365 CYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6438 (t) REVERT: A 517 SER cc_start: 0.9056 (p) cc_final: 0.8708 (p) REVERT: A 661 LYS cc_start: 0.7313 (pttt) cc_final: 0.7044 (ptmm) REVERT: B 98 ARG cc_start: 0.7739 (ttp-110) cc_final: 0.7236 (ttp-110) REVERT: B 122 LYS cc_start: 0.7632 (ptpt) cc_final: 0.7385 (pttt) REVERT: B 221 LYS cc_start: 0.6765 (mtmt) cc_final: 0.6376 (pttm) REVERT: B 268 LEU cc_start: 0.8889 (tt) cc_final: 0.8654 (pp) REVERT: B 365 CYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6416 (t) REVERT: B 366 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: B 407 GLU cc_start: 0.7407 (tt0) cc_final: 0.7098 (mt-10) REVERT: B 517 SER cc_start: 0.9039 (p) cc_final: 0.8706 (p) REVERT: B 851 PHE cc_start: 0.8262 (m-80) cc_final: 0.8014 (m-80) outliers start: 52 outliers final: 38 residues processed: 194 average time/residue: 0.2282 time to fit residues: 65.7620 Evaluate side-chains 196 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 155 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12652 Z= 0.221 Angle : 0.542 7.543 17126 Z= 0.288 Chirality : 0.040 0.199 1854 Planarity : 0.004 0.045 2120 Dihedral : 8.552 132.748 1694 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.52 % Allowed : 16.09 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.22), residues: 1442 helix: 1.32 (0.17), residues: 890 sheet: 0.32 (0.74), residues: 42 loop : -1.57 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 397 HIS 0.002 0.001 HIS A 830 PHE 0.014 0.001 PHE A 556 TYR 0.025 0.001 TYR B 528 ARG 0.004 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 1.436 Fit side-chains REVERT: A 122 LYS cc_start: 0.7547 (ptpt) cc_final: 0.7271 (pttt) REVERT: A 194 ASP cc_start: 0.6822 (m-30) cc_final: 0.6516 (m-30) REVERT: A 215 PHE cc_start: 0.8233 (t80) cc_final: 0.7995 (t80) REVERT: A 221 LYS cc_start: 0.6918 (mtmt) cc_final: 0.6376 (pttm) REVERT: A 268 LEU cc_start: 0.8916 (tt) cc_final: 0.8700 (pp) REVERT: A 346 ILE cc_start: 0.8567 (mm) cc_final: 0.8231 (mt) REVERT: A 365 CYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6425 (t) REVERT: A 517 SER cc_start: 0.9046 (p) cc_final: 0.8701 (p) REVERT: A 661 LYS cc_start: 0.7300 (pttt) cc_final: 0.7040 (ptmm) REVERT: B 96 ARG cc_start: 0.7019 (mmm160) cc_final: 0.6719 (mtp-110) REVERT: B 98 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.7168 (ttp-110) REVERT: B 122 LYS cc_start: 0.7613 (ptpt) cc_final: 0.7364 (pttt) REVERT: B 221 LYS cc_start: 0.6746 (mtmt) cc_final: 0.6366 (pttm) REVERT: B 268 LEU cc_start: 0.8903 (tt) cc_final: 0.8686 (pp) REVERT: B 365 CYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6414 (t) REVERT: B 366 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: B 407 GLU cc_start: 0.7404 (tt0) cc_final: 0.7101 (mt-10) REVERT: B 517 SER cc_start: 0.9017 (p) cc_final: 0.8683 (p) REVERT: B 528 TYR cc_start: 0.8036 (t80) cc_final: 0.7354 (t80) REVERT: B 851 PHE cc_start: 0.8258 (m-80) cc_final: 0.8009 (m-80) outliers start: 47 outliers final: 37 residues processed: 193 average time/residue: 0.2372 time to fit residues: 67.5319 Evaluate side-chains 198 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 158 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 120 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12652 Z= 0.240 Angle : 0.551 7.406 17126 Z= 0.293 Chirality : 0.041 0.174 1854 Planarity : 0.005 0.045 2120 Dihedral : 8.488 132.139 1694 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.67 % Allowed : 16.17 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1442 helix: 1.33 (0.17), residues: 890 sheet: 0.26 (0.72), residues: 42 loop : -1.57 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 397 HIS 0.002 0.001 HIS B 830 PHE 0.026 0.002 PHE B 558 TYR 0.027 0.002 TYR B 528 ARG 0.003 0.000 ARG B 810 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 153 time to evaluate : 1.438 Fit side-chains REVERT: A 122 LYS cc_start: 0.7517 (ptpt) cc_final: 0.7263 (pttt) REVERT: A 194 ASP cc_start: 0.6805 (m-30) cc_final: 0.6517 (m-30) REVERT: A 215 PHE cc_start: 0.8230 (t80) cc_final: 0.8013 (t80) REVERT: A 221 LYS cc_start: 0.6939 (mtmt) cc_final: 0.6399 (pttm) REVERT: A 346 ILE cc_start: 0.8586 (mm) cc_final: 0.8281 (mt) REVERT: A 365 CYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6439 (t) REVERT: A 517 SER cc_start: 0.9052 (p) cc_final: 0.8706 (p) REVERT: A 554 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7648 (ttpp) REVERT: A 661 LYS cc_start: 0.7282 (pttt) cc_final: 0.7027 (ptmm) REVERT: B 98 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7297 (ttp-110) REVERT: B 221 LYS cc_start: 0.6727 (mtmt) cc_final: 0.6383 (pttm) REVERT: B 365 CYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6408 (t) REVERT: B 366 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: B 407 GLU cc_start: 0.7403 (tt0) cc_final: 0.7086 (mt-10) REVERT: B 517 SER cc_start: 0.9023 (p) cc_final: 0.8691 (p) outliers start: 49 outliers final: 37 residues processed: 189 average time/residue: 0.2352 time to fit residues: 65.7481 Evaluate side-chains 191 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 150 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 135 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12652 Z= 0.219 Angle : 0.539 7.818 17126 Z= 0.286 Chirality : 0.040 0.144 1854 Planarity : 0.005 0.045 2120 Dihedral : 8.426 131.563 1694 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.37 % Allowed : 16.54 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.22), residues: 1442 helix: 1.36 (0.17), residues: 890 sheet: 0.25 (0.72), residues: 42 loop : -1.56 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 397 HIS 0.002 0.001 HIS A 830 PHE 0.021 0.001 PHE B 558 TYR 0.043 0.002 TYR B 528 ARG 0.004 0.000 ARG A 810 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 156 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7186 (ttm-80) cc_final: 0.6881 (mtp-110) REVERT: A 194 ASP cc_start: 0.6879 (m-30) cc_final: 0.6604 (m-30) REVERT: A 221 LYS cc_start: 0.6929 (mtmt) cc_final: 0.6391 (pttm) REVERT: A 346 ILE cc_start: 0.8544 (mm) cc_final: 0.8240 (mt) REVERT: A 365 CYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6421 (t) REVERT: A 517 SER cc_start: 0.9052 (p) cc_final: 0.8706 (p) REVERT: A 554 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7610 (ttpp) REVERT: A 661 LYS cc_start: 0.7286 (pttt) cc_final: 0.7021 (ptmm) REVERT: B 98 ARG cc_start: 0.7708 (ttp-110) cc_final: 0.7300 (ttp-110) REVERT: B 221 LYS cc_start: 0.6745 (mtmt) cc_final: 0.6390 (pttm) REVERT: B 365 CYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6407 (t) REVERT: B 407 GLU cc_start: 0.7407 (tt0) cc_final: 0.7091 (mt-10) REVERT: B 517 SER cc_start: 0.9022 (p) cc_final: 0.8691 (p) REVERT: B 528 TYR cc_start: 0.8003 (t80) cc_final: 0.7437 (t80) REVERT: B 851 PHE cc_start: 0.8251 (m-80) cc_final: 0.7978 (m-80) outliers start: 45 outliers final: 38 residues processed: 189 average time/residue: 0.2304 time to fit residues: 64.9516 Evaluate side-chains 196 residues out of total 1336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 155 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 120 optimal weight: 0.0470 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 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 = 0.4027 r_free = 0.4027 target = 0.183512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142669 restraints weight = 13967.023| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.35 r_work: 0.3206 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 12652 Z= 0.169 Angle : 0.527 8.759 17126 Z= 0.280 Chirality : 0.039 0.140 1854 Planarity : 0.004 0.046 2120 Dihedral : 8.290 131.149 1694 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.14 % Allowed : 16.99 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1442 helix: 1.46 (0.17), residues: 890 sheet: 0.21 (0.72), residues: 42 loop : -1.49 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 397 HIS 0.002 0.001 HIS B 108 PHE 0.022 0.001 PHE B 558 TYR 0.038 0.001 TYR B 528 ARG 0.007 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2414.29 seconds wall clock time: 44 minutes 56.22 seconds (2696.22 seconds total)