Starting phenix.real_space_refine on Thu Feb 5 01:35:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ddb_46763/02_2026/9ddb_46763.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ddb_46763/02_2026/9ddb_46763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ddb_46763/02_2026/9ddb_46763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ddb_46763/02_2026/9ddb_46763.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ddb_46763/02_2026/9ddb_46763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ddb_46763/02_2026/9ddb_46763.map" } resolution = 3.71 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= 0.001 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 8682 2.51 5 N 2388 2.21 5 O 2688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 13821 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4512 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 27, 'TRANS': 532} Chain breaks: 3 Chain: "D" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4512 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 27, 'TRANS': 532} Chain breaks: 3 Chain: "E" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4512 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 27, 'TRANS': 532} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.99, per 1000 atoms: 0.22 Number of scatterers: 13821 At special positions: 0 Unit cell: (113.71, 120.35, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2688 8.00 N 2388 7.00 C 8682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.07 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.03 Simple disulfide: pdb=" SG CYS D 116 " - pdb=" SG CYS D 573 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 529 " distance=2.03 Simple disulfide: pdb=" SG CYS D 207 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 364 " - pdb=" SG CYS D 412 " distance=2.07 Simple disulfide: pdb=" SG CYS D 596 " - pdb=" SG CYS D 633 " distance=2.03 Simple disulfide: pdb=" SG CYS E 116 " - pdb=" SG CYS E 573 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 529 " distance=2.03 Simple disulfide: pdb=" SG CYS E 207 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 364 " - pdb=" SG CYS E 412 " distance=2.07 Simple disulfide: pdb=" SG CYS E 596 " - pdb=" SG CYS E 633 " distance=2.03 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 1 " - " ASN C 141 " " NAG B 1 " - " ASN C 398 " " NAG C 901 " - " ASN C 430 " " NAG C 902 " - " ASN C 674 " " NAG D 901 " - " ASN D 430 " " NAG D 902 " - " ASN D 674 " " NAG E 901 " - " ASN E 430 " " NAG E 902 " - " ASN E 674 " " NAG F 1 " - " ASN D 141 " " NAG G 1 " - " ASN D 398 " " NAG H 1 " - " ASN E 141 " " NAG I 1 " - " ASN E 398 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 622.4 milliseconds 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 36 sheets defined 24.5% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'C' and resid 193 through 200 removed outlier: 3.547A pdb=" N VAL C 197 " --> pdb=" O PRO C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 403 through 408 removed outlier: 5.206A pdb=" N ASP C 408 " --> pdb=" O SER C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 428 removed outlier: 3.687A pdb=" N ASP C 416 " --> pdb=" O CYS C 412 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG C 428 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 473 removed outlier: 3.564A pdb=" N GLU C 462 " --> pdb=" O ASN C 458 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 546 Proline residue: C 516 - end of helix removed outlier: 3.583A pdb=" N VAL C 524 " --> pdb=" O MET C 520 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 541 " --> pdb=" O THR C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 555 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 660 through 664 removed outlier: 3.602A pdb=" N ILE C 664 " --> pdb=" O ARG C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 692 removed outlier: 4.186A pdb=" N TYR C 689 " --> pdb=" O PRO C 685 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 690 " --> pdb=" O LEU C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 721 removed outlier: 4.397A pdb=" N GLN C 710 " --> pdb=" O GLN C 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 200 removed outlier: 3.547A pdb=" N VAL D 197 " --> pdb=" O PRO D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 317 No H-bonds generated for 'chain 'D' and resid 315 through 317' Processing helix chain 'D' and resid 403 through 408 removed outlier: 5.206A pdb=" N ASP D 408 " --> pdb=" O SER D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 428 removed outlier: 3.688A pdb=" N ASP D 416 " --> pdb=" O CYS D 412 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D 428 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 473 removed outlier: 3.562A pdb=" N GLU D 462 " --> pdb=" O ASN D 458 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU D 463 " --> pdb=" O THR D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 546 Proline residue: D 516 - end of helix removed outlier: 3.583A pdb=" N VAL D 524 " --> pdb=" O MET D 520 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 541 " --> pdb=" O THR D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 Processing helix chain 'D' and resid 577 through 579 No H-bonds generated for 'chain 'D' and resid 577 through 579' Processing helix chain 'D' and resid 660 through 664 removed outlier: 3.602A pdb=" N ILE D 664 " --> pdb=" O ARG D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 692 removed outlier: 4.186A pdb=" N TYR D 689 " --> pdb=" O PRO D 685 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 690 " --> pdb=" O LEU D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 721 removed outlier: 4.398A pdb=" N GLN D 710 " --> pdb=" O GLN D 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 200 removed outlier: 3.546A pdb=" N VAL E 197 " --> pdb=" O PRO E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 317 No H-bonds generated for 'chain 'E' and resid 315 through 317' Processing helix chain 'E' and resid 403 through 408 removed outlier: 5.206A pdb=" N ASP E 408 " --> pdb=" O SER E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 428 removed outlier: 3.689A pdb=" N ASP E 416 " --> pdb=" O CYS E 412 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG E 428 " --> pdb=" O ILE E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 473 removed outlier: 3.563A pdb=" N GLU E 462 " --> pdb=" O ASN E 458 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU E 463 " --> pdb=" O THR E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 546 Proline residue: E 516 - end of helix removed outlier: 3.583A pdb=" N VAL E 524 " --> pdb=" O MET E 520 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU E 541 " --> pdb=" O THR E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 555 Processing helix chain 'E' and resid 577 through 579 No H-bonds generated for 'chain 'E' and resid 577 through 579' Processing helix chain 'E' and resid 660 through 664 removed outlier: 3.602A pdb=" N ILE E 664 " --> pdb=" O ARG E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 692 removed outlier: 4.187A pdb=" N TYR E 689 " --> pdb=" O PRO E 685 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR E 690 " --> pdb=" O LEU E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 721 removed outlier: 4.397A pdb=" N GLN E 710 " --> pdb=" O GLN E 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AA2, first strand: chain 'C' and resid 559 through 560 removed outlier: 4.417A pdb=" N THR C 123 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR D 665 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 366 through 372 removed outlier: 6.997A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 13.797A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 456 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 395 through 396 removed outlier: 3.522A pdb=" N THR C 143 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU C 379 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASN C 141 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 13.797A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 191 removed outlier: 3.567A pdb=" N ASP C 188 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 188 through 191 removed outlier: 3.567A pdb=" N ASP C 188 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 206 through 207 removed outlier: 3.563A pdb=" N MET C 232 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 211 through 215 Processing sheet with id=AB1, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AB2, first strand: chain 'C' and resid 596 through 597 Processing sheet with id=AB3, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.703A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 665 through 667 removed outlier: 6.153A pdb=" N THR C 665 " --> pdb=" O GLN E 126 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR E 123 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 113 through 115 Processing sheet with id=AB6, first strand: chain 'D' and resid 559 through 560 removed outlier: 4.418A pdb=" N THR D 123 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR E 665 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 366 through 372 removed outlier: 6.995A pdb=" N VAL D 149 " --> pdb=" O TRP D 369 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU D 371 " --> pdb=" O ALA D 147 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA D 147 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 13.797A pdb=" N TYR D 142 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 9.463A pdb=" N SER D 457 " --> pdb=" O TYR D 142 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU D 144 " --> pdb=" O LEU D 455 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 456 " --> pdb=" O ILE D 434 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 395 through 396 removed outlier: 3.521A pdb=" N THR D 143 " --> pdb=" O ARG D 377 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU D 379 " --> pdb=" O ASN D 141 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASN D 141 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 13.797A pdb=" N TYR D 142 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 9.463A pdb=" N SER D 457 " --> pdb=" O TYR D 142 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU D 144 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 157 through 159 Processing sheet with id=AC1, first strand: chain 'D' and resid 188 through 191 removed outlier: 3.569A pdb=" N ASP D 188 " --> pdb=" O VAL D 168 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 188 through 191 removed outlier: 3.569A pdb=" N ASP D 188 " --> pdb=" O VAL D 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 206 through 207 removed outlier: 3.563A pdb=" N MET D 232 " --> pdb=" O CYS D 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 211 through 215 Processing sheet with id=AC5, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AC6, first strand: chain 'D' and resid 596 through 597 Processing sheet with id=AC7, first strand: chain 'D' and resid 638 through 643 removed outlier: 3.702A pdb=" N HIS D 657 " --> pdb=" O TYR D 649 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU D 651 " --> pdb=" O TYR D 655 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TYR D 655 " --> pdb=" O GLU D 651 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 113 through 115 Processing sheet with id=AC9, first strand: chain 'E' and resid 366 through 372 removed outlier: 6.996A pdb=" N VAL E 149 " --> pdb=" O TRP E 369 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLU E 371 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA E 147 " --> pdb=" O GLU E 371 " (cutoff:3.500A) removed outlier: 13.798A pdb=" N TYR E 142 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N SER E 457 " --> pdb=" O TYR E 142 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU E 144 " --> pdb=" O LEU E 455 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU E 456 " --> pdb=" O ILE E 434 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 395 through 396 removed outlier: 3.520A pdb=" N THR E 143 " --> pdb=" O ARG E 377 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU E 379 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASN E 141 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 13.798A pdb=" N TYR E 142 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N SER E 457 " --> pdb=" O TYR E 142 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU E 144 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 157 through 159 Processing sheet with id=AD3, first strand: chain 'E' and resid 188 through 191 removed outlier: 3.569A pdb=" N ASP E 188 " --> pdb=" O VAL E 168 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 188 through 191 removed outlier: 3.569A pdb=" N ASP E 188 " --> pdb=" O VAL E 168 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 206 through 207 removed outlier: 3.563A pdb=" N MET E 232 " --> pdb=" O CYS E 207 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 211 through 215 Processing sheet with id=AD7, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AD8, first strand: chain 'E' and resid 596 through 597 Processing sheet with id=AD9, first strand: chain 'E' and resid 638 through 643 removed outlier: 3.703A pdb=" N HIS E 657 " --> pdb=" O TYR E 649 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU E 651 " --> pdb=" O TYR E 655 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TYR E 655 " --> pdb=" O GLU E 651 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1467 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: 2.49 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4540 1.34 - 1.46: 3184 1.46 - 1.58: 6319 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 14139 Sorted by residual: bond pdb=" N VAL E 363 " pdb=" CA VAL E 363 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.09e+00 bond pdb=" N VAL D 363 " pdb=" CA VAL D 363 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.45e+00 bond pdb=" N VAL C 363 " pdb=" CA VAL C 363 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.40e+00 bond pdb=" N GLU E 128 " pdb=" CA GLU E 128 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.25e-02 6.40e+03 7.89e+00 bond pdb=" N GLU C 128 " pdb=" CA GLU C 128 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.25e-02 6.40e+03 7.85e+00 ... (remaining 14134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 18733 1.99 - 3.98: 400 3.98 - 5.97: 67 5.97 - 7.96: 6 7.96 - 9.95: 9 Bond angle restraints: 19215 Sorted by residual: angle pdb=" C PHE D 127 " pdb=" CA PHE D 127 " pdb=" CB PHE D 127 " ideal model delta sigma weight residual 109.71 119.31 -9.60 1.83e+00 2.99e-01 2.75e+01 angle pdb=" C PHE E 127 " pdb=" CA PHE E 127 " pdb=" CB PHE E 127 " ideal model delta sigma weight residual 109.71 119.30 -9.59 1.83e+00 2.99e-01 2.75e+01 angle pdb=" C PHE C 127 " pdb=" CA PHE C 127 " pdb=" CB PHE C 127 " ideal model delta sigma weight residual 109.71 119.25 -9.54 1.83e+00 2.99e-01 2.72e+01 angle pdb=" N THR C 365 " pdb=" CA THR C 365 " pdb=" C THR C 365 " ideal model delta sigma weight residual 113.38 107.15 6.23 1.23e+00 6.61e-01 2.56e+01 angle pdb=" N THR E 365 " pdb=" CA THR E 365 " pdb=" C THR E 365 " ideal model delta sigma weight residual 113.38 107.18 6.20 1.23e+00 6.61e-01 2.54e+01 ... (remaining 19210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 7869 17.25 - 34.51: 668 34.51 - 51.76: 157 51.76 - 69.01: 51 69.01 - 86.27: 6 Dihedral angle restraints: 8751 sinusoidal: 3801 harmonic: 4950 Sorted by residual: dihedral pdb=" CB CYS C 364 " pdb=" SG CYS C 364 " pdb=" SG CYS C 412 " pdb=" CB CYS C 412 " ideal model delta sinusoidal sigma weight residual -86.00 -143.81 57.81 1 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" CB CYS D 364 " pdb=" SG CYS D 364 " pdb=" SG CYS D 412 " pdb=" CB CYS D 412 " ideal model delta sinusoidal sigma weight residual -86.00 -143.78 57.78 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS E 364 " pdb=" SG CYS E 364 " pdb=" SG CYS E 412 " pdb=" CB CYS E 412 " ideal model delta sinusoidal sigma weight residual -86.00 -143.73 57.73 1 1.00e+01 1.00e-02 4.47e+01 ... (remaining 8748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1696 0.048 - 0.097: 366 0.097 - 0.145: 92 0.145 - 0.193: 9 0.193 - 0.242: 3 Chirality restraints: 2166 Sorted by residual: chirality pdb=" CA VAL E 363 " pdb=" N VAL E 363 " pdb=" C VAL E 363 " pdb=" CB VAL E 363 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA VAL C 363 " pdb=" N VAL C 363 " pdb=" C VAL C 363 " pdb=" CB VAL C 363 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA VAL D 363 " pdb=" N VAL D 363 " pdb=" C VAL D 363 " pdb=" CB VAL D 363 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2163 not shown) Planarity restraints: 2499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 364 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C CYS E 364 " 0.034 2.00e-02 2.50e+03 pdb=" O CYS E 364 " -0.013 2.00e-02 2.50e+03 pdb=" N THR E 365 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 364 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C CYS D 364 " 0.034 2.00e-02 2.50e+03 pdb=" O CYS D 364 " -0.012 2.00e-02 2.50e+03 pdb=" N THR D 365 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 364 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C CYS C 364 " -0.034 2.00e-02 2.50e+03 pdb=" O CYS C 364 " 0.012 2.00e-02 2.50e+03 pdb=" N THR C 365 " 0.012 2.00e-02 2.50e+03 ... (remaining 2496 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3901 2.81 - 3.33: 13064 3.33 - 3.86: 22284 3.86 - 4.38: 26134 4.38 - 4.90: 45332 Nonbonded interactions: 110715 Sorted by model distance: nonbonded pdb=" OE2 GLU D 401 " pdb=" NE2 GLN D 440 " model vdw 2.290 3.120 nonbonded pdb=" OE2 GLU C 401 " pdb=" NE2 GLN C 440 " model vdw 2.290 3.120 nonbonded pdb=" OE2 GLU E 401 " pdb=" NE2 GLN E 440 " model vdw 2.291 3.120 nonbonded pdb=" OD1 ASP D 701 " pdb=" N TYR D 702 " model vdw 2.303 3.120 nonbonded pdb=" OD1 ASP C 701 " pdb=" N TYR C 702 " model vdw 2.303 3.120 ... (remaining 110710 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } 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 group one per residue 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: 4.820 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.440 Find NCS groups from input model: 0.110 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 : 0.004 0.044 14175 Z= 0.208 Angle : 0.738 9.947 19308 Z= 0.419 Chirality : 0.045 0.242 2166 Planarity : 0.004 0.057 2487 Dihedral : 13.425 86.268 5514 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.18 (0.20), residues: 1656 helix: 0.10 (0.29), residues: 330 sheet: -0.98 (0.24), residues: 429 loop : -0.95 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 131 TYR 0.013 0.001 TYR E 142 PHE 0.010 0.001 PHE D 150 TRP 0.011 0.001 TRP C 247 HIS 0.004 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00371 (14139) covalent geometry : angle 0.72443 (19215) SS BOND : bond 0.01966 ( 15) SS BOND : angle 2.84827 ( 30) hydrogen bonds : bond 0.27837 ( 537) hydrogen bonds : angle 9.81625 ( 1467) link_BETA1-4 : bond 0.00467 ( 9) link_BETA1-4 : angle 1.92762 ( 27) link_NAG-ASN : bond 0.00414 ( 12) link_NAG-ASN : angle 1.60625 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 232 MET cc_start: 0.6145 (ptt) cc_final: 0.5935 (ptt) REVERT: C 297 MET cc_start: 0.7716 (ttm) cc_final: 0.7109 (ttm) REVERT: D 297 MET cc_start: 0.7761 (ttm) cc_final: 0.7512 (ttm) REVERT: E 232 MET cc_start: 0.6262 (ptt) cc_final: 0.6049 (ptt) REVERT: E 297 MET cc_start: 0.7694 (ttm) cc_final: 0.7269 (ttm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2002 time to fit residues: 21.3645 Evaluate side-chains 56 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 GLN C 248 HIS D 681 HIS E 681 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.074692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.054768 restraints weight = 65688.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.056869 restraints weight = 35687.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.058189 restraints weight = 25087.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.059038 restraints weight = 20369.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.059210 restraints weight = 18010.819| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14175 Z= 0.204 Angle : 0.623 6.925 19308 Z= 0.328 Chirality : 0.042 0.175 2166 Planarity : 0.005 0.037 2487 Dihedral : 5.074 54.331 2328 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.57 % Allowed : 9.77 % Favored : 88.66 % 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: -0.41 (0.20), residues: 1656 helix: 1.29 (0.28), residues: 318 sheet: -0.52 (0.24), residues: 435 loop : -0.67 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 131 TYR 0.022 0.002 TYR C 164 PHE 0.027 0.002 PHE D 716 TRP 0.011 0.002 TRP E 354 HIS 0.003 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00444 (14139) covalent geometry : angle 0.61500 (19215) SS BOND : bond 0.00409 ( 15) SS BOND : angle 1.10237 ( 30) hydrogen bonds : bond 0.05103 ( 537) hydrogen bonds : angle 6.50285 ( 1467) link_BETA1-4 : bond 0.00620 ( 9) link_BETA1-4 : angle 1.74316 ( 27) link_NAG-ASN : bond 0.00265 ( 12) link_NAG-ASN : angle 1.75527 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 297 MET cc_start: 0.8034 (ttm) cc_final: 0.7600 (ttm) REVERT: E 297 MET cc_start: 0.8031 (ttm) cc_final: 0.7751 (ttm) outliers start: 23 outliers final: 15 residues processed: 87 average time/residue: 0.1611 time to fit residues: 19.1757 Evaluate side-chains 70 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 505 ARG Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain E residue 505 ARG Chi-restraints excluded: chain E residue 690 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 681 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.074265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.054601 restraints weight = 66127.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.056593 restraints weight = 35834.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.057886 restraints weight = 25321.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.058710 restraints weight = 20701.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.059169 restraints weight = 18336.060| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.003 0.023 14175 Z= 0.125 Angle : 0.546 7.151 19308 Z= 0.283 Chirality : 0.041 0.176 2166 Planarity : 0.004 0.031 2487 Dihedral : 4.935 53.116 2328 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.30 % Allowed : 13.18 % Favored : 85.52 % 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: -0.10 (0.21), residues: 1656 helix: 1.40 (0.28), residues: 324 sheet: 0.02 (0.25), residues: 429 loop : -0.62 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 715 TYR 0.017 0.001 TYR C 164 PHE 0.023 0.001 PHE C 716 TRP 0.008 0.001 TRP E 247 HIS 0.004 0.001 HIS D 224 Details of bonding type rmsd covalent geometry : bond 0.00266 (14139) covalent geometry : angle 0.53936 (19215) SS BOND : bond 0.00250 ( 15) SS BOND : angle 1.03586 ( 30) hydrogen bonds : bond 0.04140 ( 537) hydrogen bonds : angle 5.93528 ( 1467) link_BETA1-4 : bond 0.00450 ( 9) link_BETA1-4 : angle 1.39172 ( 27) link_NAG-ASN : bond 0.00209 ( 12) link_NAG-ASN : angle 1.56417 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 297 MET cc_start: 0.8102 (ttm) cc_final: 0.7733 (ttm) REVERT: D 168 VAL cc_start: 0.9398 (m) cc_final: 0.9092 (p) REVERT: E 168 VAL cc_start: 0.9414 (m) cc_final: 0.9133 (p) outliers start: 19 outliers final: 11 residues processed: 80 average time/residue: 0.1176 time to fit residues: 13.7704 Evaluate side-chains 71 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 690 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 116 optimal weight: 0.9980 chunk 121 optimal weight: 0.3980 chunk 67 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 ASN D 202 ASN E 202 ASN ** E 248 HIS ** 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 = 0.3850 r_free = 0.3850 target = 0.073758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.053588 restraints weight = 67592.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.055672 restraints weight = 37359.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.056979 restraints weight = 26663.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.057776 restraints weight = 21878.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.058226 restraints weight = 19503.121| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14175 Z= 0.165 Angle : 0.557 8.706 19308 Z= 0.287 Chirality : 0.041 0.186 2166 Planarity : 0.004 0.032 2487 Dihedral : 5.230 53.582 2328 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.91 % Allowed : 13.73 % Favored : 84.36 % 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: 0.09 (0.21), residues: 1656 helix: 1.39 (0.28), residues: 324 sheet: 0.41 (0.26), residues: 423 loop : -0.57 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 592 TYR 0.016 0.001 TYR C 164 PHE 0.019 0.002 PHE D 716 TRP 0.005 0.001 TRP E 354 HIS 0.004 0.001 HIS E 224 Details of bonding type rmsd covalent geometry : bond 0.00359 (14139) covalent geometry : angle 0.54899 (19215) SS BOND : bond 0.00260 ( 15) SS BOND : angle 1.02848 ( 30) hydrogen bonds : bond 0.03546 ( 537) hydrogen bonds : angle 5.58369 ( 1467) link_BETA1-4 : bond 0.00424 ( 9) link_BETA1-4 : angle 1.46498 ( 27) link_NAG-ASN : bond 0.00196 ( 12) link_NAG-ASN : angle 1.70534 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 VAL cc_start: 0.9400 (m) cc_final: 0.9084 (p) REVERT: C 297 MET cc_start: 0.8206 (ttm) cc_final: 0.7800 (ttm) REVERT: D 168 VAL cc_start: 0.9379 (m) cc_final: 0.9062 (p) REVERT: D 297 MET cc_start: 0.7897 (ttm) cc_final: 0.7597 (ttm) REVERT: E 168 VAL cc_start: 0.9381 (m) cc_final: 0.9079 (p) outliers start: 28 outliers final: 18 residues processed: 87 average time/residue: 0.1380 time to fit residues: 16.9435 Evaluate side-chains 81 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 563 MET Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 690 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 133 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.088050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.069201 restraints weight = 62592.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.071346 restraints weight = 30613.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.072701 restraints weight = 19765.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.073600 restraints weight = 15103.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.074034 restraints weight = 12788.064| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14175 Z= 0.121 Angle : 0.536 10.001 19308 Z= 0.275 Chirality : 0.040 0.177 2166 Planarity : 0.003 0.031 2487 Dihedral : 5.085 53.185 2328 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.91 % Allowed : 14.48 % Favored : 83.61 % 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: 0.19 (0.21), residues: 1656 helix: 1.45 (0.28), residues: 324 sheet: 0.42 (0.26), residues: 429 loop : -0.48 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 592 TYR 0.017 0.001 TYR D 164 PHE 0.021 0.001 PHE D 716 TRP 0.005 0.001 TRP C 247 HIS 0.003 0.001 HIS C 248 Details of bonding type rmsd covalent geometry : bond 0.00262 (14139) covalent geometry : angle 0.52966 (19215) SS BOND : bond 0.00189 ( 15) SS BOND : angle 0.94468 ( 30) hydrogen bonds : bond 0.03331 ( 537) hydrogen bonds : angle 5.39369 ( 1467) link_BETA1-4 : bond 0.00437 ( 9) link_BETA1-4 : angle 1.26892 ( 27) link_NAG-ASN : bond 0.00219 ( 12) link_NAG-ASN : angle 1.52877 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 VAL cc_start: 0.9328 (m) cc_final: 0.9009 (p) REVERT: C 297 MET cc_start: 0.8139 (ttm) cc_final: 0.7858 (ttm) REVERT: D 168 VAL cc_start: 0.9352 (m) cc_final: 0.9034 (p) REVERT: E 168 VAL cc_start: 0.9351 (m) cc_final: 0.9051 (p) outliers start: 28 outliers final: 23 residues processed: 91 average time/residue: 0.1174 time to fit residues: 15.6902 Evaluate side-chains 86 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 563 MET Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 563 MET Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 690 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 119 optimal weight: 20.0000 chunk 27 optimal weight: 0.2980 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 HIS ** 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 = 0.3848 r_free = 0.3848 target = 0.073441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.053378 restraints weight = 65389.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.055453 restraints weight = 35615.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.056761 restraints weight = 25112.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.057568 restraints weight = 20482.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.058045 restraints weight = 18131.914| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14175 Z= 0.172 Angle : 0.569 11.539 19308 Z= 0.291 Chirality : 0.041 0.184 2166 Planarity : 0.004 0.032 2487 Dihedral : 5.265 53.458 2328 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.53 % Allowed : 14.41 % Favored : 83.06 % 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: 0.27 (0.21), residues: 1656 helix: 1.57 (0.28), residues: 324 sheet: 0.65 (0.27), residues: 408 loop : -0.53 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 592 TYR 0.015 0.001 TYR D 164 PHE 0.020 0.002 PHE D 716 TRP 0.006 0.001 TRP C 539 HIS 0.004 0.001 HIS D 657 Details of bonding type rmsd covalent geometry : bond 0.00378 (14139) covalent geometry : angle 0.56211 (19215) SS BOND : bond 0.00261 ( 15) SS BOND : angle 0.95272 ( 30) hydrogen bonds : bond 0.03301 ( 537) hydrogen bonds : angle 5.35655 ( 1467) link_BETA1-4 : bond 0.00407 ( 9) link_BETA1-4 : angle 1.38731 ( 27) link_NAG-ASN : bond 0.00208 ( 12) link_NAG-ASN : angle 1.61692 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 VAL cc_start: 0.9374 (m) cc_final: 0.9046 (p) REVERT: C 297 MET cc_start: 0.8251 (ttm) cc_final: 0.7955 (ttm) REVERT: C 605 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8009 (mtm-85) REVERT: D 168 VAL cc_start: 0.9374 (m) cc_final: 0.9048 (p) REVERT: D 421 MET cc_start: 0.8512 (mmt) cc_final: 0.8246 (mmt) REVERT: D 605 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8225 (mtm110) REVERT: E 168 VAL cc_start: 0.9386 (m) cc_final: 0.9081 (p) REVERT: E 605 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8196 (mtm-85) outliers start: 37 outliers final: 29 residues processed: 96 average time/residue: 0.1276 time to fit residues: 17.7620 Evaluate side-chains 93 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 563 MET Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 563 MET Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 605 ARG Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 563 MET Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 605 ARG Chi-restraints excluded: chain E residue 690 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 4 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.073821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.053807 restraints weight = 65086.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.055882 restraints weight = 35362.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.057213 restraints weight = 24924.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.058040 restraints weight = 20284.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.058506 restraints weight = 17960.351| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14175 Z= 0.138 Angle : 0.555 12.187 19308 Z= 0.282 Chirality : 0.040 0.174 2166 Planarity : 0.003 0.031 2487 Dihedral : 5.142 52.996 2328 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.46 % Allowed : 15.23 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.21), residues: 1656 helix: 1.62 (0.27), residues: 324 sheet: 0.62 (0.27), residues: 423 loop : -0.49 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 715 TYR 0.016 0.001 TYR D 164 PHE 0.022 0.001 PHE D 716 TRP 0.005 0.001 TRP C 539 HIS 0.003 0.001 HIS D 534 Details of bonding type rmsd covalent geometry : bond 0.00303 (14139) covalent geometry : angle 0.54951 (19215) SS BOND : bond 0.00182 ( 15) SS BOND : angle 0.90701 ( 30) hydrogen bonds : bond 0.03152 ( 537) hydrogen bonds : angle 5.22840 ( 1467) link_BETA1-4 : bond 0.00423 ( 9) link_BETA1-4 : angle 1.24379 ( 27) link_NAG-ASN : bond 0.00209 ( 12) link_NAG-ASN : angle 1.46799 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 66 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 VAL cc_start: 0.9364 (m) cc_final: 0.9036 (p) REVERT: C 297 MET cc_start: 0.8241 (ttm) cc_final: 0.7993 (ttm) REVERT: C 605 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8216 (mtm110) REVERT: D 168 VAL cc_start: 0.9365 (m) cc_final: 0.9066 (p) REVERT: D 605 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8228 (mtm110) REVERT: E 168 VAL cc_start: 0.9384 (m) cc_final: 0.9087 (p) REVERT: E 605 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8144 (mtm-85) outliers start: 36 outliers final: 28 residues processed: 98 average time/residue: 0.1094 time to fit residues: 16.1030 Evaluate side-chains 94 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 563 MET Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 563 MET Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 605 ARG Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 605 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 248 HIS ** 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 = 0.3814 r_free = 0.3814 target = 0.072489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.053239 restraints weight = 61803.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.055196 restraints weight = 32040.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.056413 restraints weight = 22005.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.057178 restraints weight = 17683.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.057626 restraints weight = 15571.887| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14175 Z= 0.171 Angle : 0.587 13.589 19308 Z= 0.297 Chirality : 0.041 0.172 2166 Planarity : 0.004 0.035 2487 Dihedral : 5.302 53.265 2328 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.53 % Allowed : 15.44 % Favored : 82.04 % 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: 0.29 (0.21), residues: 1656 helix: 1.67 (0.27), residues: 324 sheet: 0.69 (0.27), residues: 408 loop : -0.57 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 661 TYR 0.014 0.001 TYR D 164 PHE 0.022 0.002 PHE D 716 TRP 0.006 0.001 TRP C 539 HIS 0.003 0.001 HIS D 657 Details of bonding type rmsd covalent geometry : bond 0.00378 (14139) covalent geometry : angle 0.58152 (19215) SS BOND : bond 0.00233 ( 15) SS BOND : angle 0.91333 ( 30) hydrogen bonds : bond 0.03188 ( 537) hydrogen bonds : angle 5.24595 ( 1467) link_BETA1-4 : bond 0.00407 ( 9) link_BETA1-4 : angle 1.34849 ( 27) link_NAG-ASN : bond 0.00209 ( 12) link_NAG-ASN : angle 1.50936 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 VAL cc_start: 0.9354 (m) cc_final: 0.9049 (p) REVERT: C 605 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8131 (mtm110) REVERT: D 168 VAL cc_start: 0.9369 (m) cc_final: 0.9045 (p) REVERT: D 605 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8312 (mtm110) REVERT: E 168 VAL cc_start: 0.9368 (m) cc_final: 0.9093 (p) REVERT: E 587 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7653 (ptp) REVERT: E 605 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8274 (mtm-85) outliers start: 37 outliers final: 30 residues processed: 100 average time/residue: 0.1034 time to fit residues: 15.2971 Evaluate side-chains 100 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 66 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 563 MET Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 563 MET Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 605 ARG Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 563 MET Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 587 MET Chi-restraints excluded: chain E residue 605 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 128 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 HIS ** 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 = 0.3806 r_free = 0.3806 target = 0.072289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.052948 restraints weight = 62983.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.054928 restraints weight = 32677.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.056167 restraints weight = 22421.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.056931 restraints weight = 17976.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.057374 restraints weight = 15824.144| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14175 Z= 0.166 Angle : 0.586 14.140 19308 Z= 0.296 Chirality : 0.041 0.173 2166 Planarity : 0.004 0.037 2487 Dihedral : 5.325 52.837 2328 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.05 % Allowed : 16.26 % Favored : 81.69 % 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: 0.29 (0.21), residues: 1656 helix: 1.67 (0.27), residues: 324 sheet: 0.66 (0.28), residues: 408 loop : -0.56 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 661 TYR 0.015 0.001 TYR D 164 PHE 0.028 0.001 PHE D 716 TRP 0.006 0.001 TRP C 539 HIS 0.003 0.001 HIS D 534 Details of bonding type rmsd covalent geometry : bond 0.00368 (14139) covalent geometry : angle 0.58124 (19215) SS BOND : bond 0.00224 ( 15) SS BOND : angle 0.88677 ( 30) hydrogen bonds : bond 0.03146 ( 537) hydrogen bonds : angle 5.21983 ( 1467) link_BETA1-4 : bond 0.00380 ( 9) link_BETA1-4 : angle 1.25919 ( 27) link_NAG-ASN : bond 0.00232 ( 12) link_NAG-ASN : angle 1.43471 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 VAL cc_start: 0.9344 (m) cc_final: 0.9013 (p) REVERT: C 605 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8283 (mtm110) REVERT: D 605 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8214 (ptp90) REVERT: E 168 VAL cc_start: 0.9388 (m) cc_final: 0.9089 (p) REVERT: E 232 MET cc_start: 0.7839 (ppp) cc_final: 0.7614 (ppp) REVERT: E 587 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7606 (ptp) REVERT: E 605 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8181 (ptp90) outliers start: 30 outliers final: 25 residues processed: 94 average time/residue: 0.1113 time to fit residues: 15.4302 Evaluate side-chains 95 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 563 MET Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 563 MET Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 605 ARG Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 563 MET Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 587 MET Chi-restraints excluded: chain E residue 605 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 164 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 HIS ** 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 = 0.3974 r_free = 0.3974 target = 0.076109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.056528 restraints weight = 60988.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.058606 restraints weight = 31506.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.059938 restraints weight = 21608.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.060771 restraints weight = 17281.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.061117 restraints weight = 15160.376| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14175 Z= 0.143 Angle : 0.584 14.362 19308 Z= 0.292 Chirality : 0.041 0.172 2166 Planarity : 0.004 0.039 2487 Dihedral : 5.266 52.920 2328 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.12 % Allowed : 16.26 % Favored : 81.63 % 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: 0.31 (0.21), residues: 1656 helix: 1.74 (0.27), residues: 324 sheet: 0.59 (0.27), residues: 423 loop : -0.53 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 592 TYR 0.015 0.001 TYR C 164 PHE 0.033 0.001 PHE E 716 TRP 0.006 0.001 TRP C 539 HIS 0.003 0.001 HIS D 534 Details of bonding type rmsd covalent geometry : bond 0.00318 (14139) covalent geometry : angle 0.57943 (19215) SS BOND : bond 0.00198 ( 15) SS BOND : angle 0.89072 ( 30) hydrogen bonds : bond 0.03051 ( 537) hydrogen bonds : angle 5.14267 ( 1467) link_BETA1-4 : bond 0.00436 ( 9) link_BETA1-4 : angle 1.25716 ( 27) link_NAG-ASN : bond 0.00221 ( 12) link_NAG-ASN : angle 1.36371 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 605 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8255 (mtm110) REVERT: D 297 MET cc_start: 0.7878 (tpt) cc_final: 0.7520 (tpt) REVERT: D 605 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8238 (ptp90) REVERT: E 168 VAL cc_start: 0.9345 (m) cc_final: 0.9041 (p) REVERT: E 587 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7667 (ptp) REVERT: E 605 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8069 (mtm110) outliers start: 31 outliers final: 26 residues processed: 93 average time/residue: 0.1151 time to fit residues: 15.6874 Evaluate side-chains 96 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 563 MET Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 605 ARG Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 563 MET Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 605 ARG Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 563 MET Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 587 MET Chi-restraints excluded: chain E residue 605 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 49 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 HIS ** 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 = 0.3940 r_free = 0.3940 target = 0.074592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.054828 restraints weight = 61590.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.056856 restraints weight = 32867.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.058110 restraints weight = 22948.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.058900 restraints weight = 18538.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.059302 restraints weight = 16386.282| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 14175 Z= 0.261 Angle : 0.662 14.689 19308 Z= 0.336 Chirality : 0.043 0.189 2166 Planarity : 0.004 0.039 2487 Dihedral : 5.775 53.124 2328 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.91 % Allowed : 16.53 % Favored : 81.56 % 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: 0.13 (0.21), residues: 1656 helix: 1.60 (0.27), residues: 324 sheet: 0.56 (0.27), residues: 408 loop : -0.68 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 592 TYR 0.016 0.002 TYR E 301 PHE 0.032 0.002 PHE E 716 TRP 0.007 0.001 TRP C 539 HIS 0.004 0.001 HIS D 657 Details of bonding type rmsd covalent geometry : bond 0.00583 (14139) covalent geometry : angle 0.65698 (19215) SS BOND : bond 0.00329 ( 15) SS BOND : angle 0.93758 ( 30) hydrogen bonds : bond 0.03337 ( 537) hydrogen bonds : angle 5.32108 ( 1467) link_BETA1-4 : bond 0.00373 ( 9) link_BETA1-4 : angle 1.46665 ( 27) link_NAG-ASN : bond 0.00345 ( 12) link_NAG-ASN : angle 1.49603 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.97 seconds wall clock time: 37 minutes 23.21 seconds (2243.21 seconds total)