Starting phenix.real_space_refine on Fri Aug 7 00:15:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dd7_46759/08_2026/9dd7_46759.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dd7_46759/08_2026/9dd7_46759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dd7_46759/08_2026/9dd7_46759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dd7_46759/08_2026/9dd7_46759.map" model { file = "/net/cci-nas-00/data/ceres_data/9dd7_46759/08_2026/9dd7_46759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dd7_46759/08_2026/9dd7_46759.cif" } resolution = 4.1 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= 0.004 sd= 0.014 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 96 5.16 5 C 11010 2.51 5 N 3012 2.21 5 O 3384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17502 Number of models: 1 Model: "" Number of chains: 18 Chain: "E" Number of atoms: 3973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3973 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 26, 'TRANS': 471} Chain breaks: 4 Chain: "F" Number of atoms: 3973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3973 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 26, 'TRANS': 471} Chain breaks: 4 Chain: "G" Number of atoms: 3973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3973 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 26, 'TRANS': 471} Chain breaks: 4 Chain: "I" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 935 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "J" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 935 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "K" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 935 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "M" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "N" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "O" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" 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: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.82, per 1000 atoms: 0.28 Number of scatterers: 17502 At special positions: 0 Unit cell: (143.59, 142.76, 126.99, 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 96 16.00 O 3384 8.00 N 3012 7.00 C 11010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 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 240 " - pdb=" SG CYS E 607 " distance=2.04 Simple disulfide: pdb=" SG CYS E 364 " - pdb=" SG CYS E 412 " distance=2.03 Simple disulfide: pdb=" SG CYS E 596 " - pdb=" SG CYS E 633 " distance=2.04 Simple disulfide: pdb=" SG CYS F 116 " - pdb=" SG CYS F 573 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 529 " distance=2.03 Simple disulfide: pdb=" SG CYS F 207 " - pdb=" SG CYS F 271 " distance=2.03 Simple disulfide: pdb=" SG CYS F 240 " - pdb=" SG CYS F 607 " distance=2.04 Simple disulfide: pdb=" SG CYS F 364 " - pdb=" SG CYS F 412 " distance=2.03 Simple disulfide: pdb=" SG CYS F 596 " - pdb=" SG CYS F 633 " distance=2.04 Simple disulfide: pdb=" SG CYS G 116 " - pdb=" SG CYS G 573 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 529 " distance=2.03 Simple disulfide: pdb=" SG CYS G 207 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 240 " - pdb=" SG CYS G 607 " distance=2.03 Simple disulfide: pdb=" SG CYS G 364 " - pdb=" SG CYS G 412 " distance=2.03 Simple disulfide: pdb=" SG CYS G 596 " - pdb=" SG CYS G 633 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 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 ALPHA1-6 " BMA A 3 " - " MAN A 4 " " MAN A 4 " - " MAN A 5 " " BMA C 3 " - " MAN C 4 " " MAN C 4 " - " MAN C 5 " " BMA H 3 " - " MAN H 4 " " MAN H 4 " - " MAN H 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 1 " - " ASN E 141 " " NAG B 1 " - " ASN E 398 " " NAG C 1 " - " ASN F 141 " " NAG D 1 " - " ASN F 398 " " NAG E 901 " - " ASN E 430 " " NAG F 901 " - " ASN F 430 " " NAG G 901 " - " ASN G 430 " " NAG H 1 " - " ASN G 141 " " NAG L 1 " - " ASN G 398 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 874.8 milliseconds 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4050 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 55 sheets defined 14.3% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'E' and resid 193 through 200 Processing helix chain 'E' and resid 223 through 227 removed outlier: 3.987A pdb=" N ASP E 226 " --> pdb=" O PHE E 223 " (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 410 through 429 Processing helix chain 'E' and resid 445 through 447 No H-bonds generated for 'chain 'E' and resid 445 through 447' Processing helix chain 'E' and resid 513 through 546 removed outlier: 4.211A pdb=" N VAL E 517 " --> pdb=" O ILE E 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E 519 " --> pdb=" O ARG E 515 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR E 537 " --> pdb=" O ASN E 533 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 538 " --> pdb=" O HIS E 534 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU E 541 " --> pdb=" O THR E 537 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS E 544 " --> pdb=" O ASN E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 556 removed outlier: 3.611A pdb=" N ILE E 550 " --> pdb=" O ASN E 546 " (cutoff:3.500A) 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: 3.577A pdb=" N ILE E 664 " --> pdb=" O ARG E 661 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 200 Processing helix chain 'F' and resid 223 through 227 removed outlier: 3.989A pdb=" N ASP F 226 " --> pdb=" O PHE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 317 No H-bonds generated for 'chain 'F' and resid 315 through 317' Processing helix chain 'F' and resid 402 through 407 removed outlier: 4.733A pdb=" N ARG F 406 " --> pdb=" O TYR F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 429 Processing helix chain 'F' and resid 445 through 447 No H-bonds generated for 'chain 'F' and resid 445 through 447' Processing helix chain 'F' and resid 513 through 546 removed outlier: 4.258A pdb=" N VAL F 517 " --> pdb=" O ILE F 513 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR F 537 " --> pdb=" O ASN F 533 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU F 538 " --> pdb=" O HIS F 534 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU F 541 " --> pdb=" O THR F 537 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS F 544 " --> pdb=" O ASN F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 removed outlier: 3.775A pdb=" N ILE F 550 " --> pdb=" O ASN F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 579 No H-bonds generated for 'chain 'F' and resid 577 through 579' Processing helix chain 'F' and resid 660 through 664 Processing helix chain 'G' and resid 193 through 200 Processing helix chain 'G' and resid 223 through 227 removed outlier: 3.992A pdb=" N ASP G 226 " --> pdb=" O PHE G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 317 No H-bonds generated for 'chain 'G' and resid 315 through 317' Processing helix chain 'G' and resid 410 through 429 Processing helix chain 'G' and resid 445 through 447 No H-bonds generated for 'chain 'G' and resid 445 through 447' Processing helix chain 'G' and resid 513 through 546 removed outlier: 4.048A pdb=" N VAL G 517 " --> pdb=" O ILE G 513 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR G 537 " --> pdb=" O ASN G 533 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU G 538 " --> pdb=" O HIS G 534 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS G 544 " --> pdb=" O ASN G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 556 removed outlier: 3.607A pdb=" N ILE G 550 " --> pdb=" O ASN G 546 " (cutoff:3.500A) Processing helix chain 'G' and resid 577 through 579 No H-bonds generated for 'chain 'G' and resid 577 through 579' Processing helix chain 'G' and resid 660 through 664 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.752A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.882A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.511A pdb=" N VAL E 576 " --> pdb=" O PHE E 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 559 through 563 removed outlier: 3.688A pdb=" N ARG E 562 " --> pdb=" O ALA E 569 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR E 123 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR G 665 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 395 through 396 removed outlier: 4.092A pdb=" N TYR E 380 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL E 149 " --> pdb=" O TRP E 369 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU E 371 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA E 147 " --> pdb=" O GLU E 371 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP E 373 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY E 145 " --> pdb=" O ASP E 373 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU E 144 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 395 through 396 removed outlier: 4.092A pdb=" N TYR E 380 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL E 149 " --> pdb=" O TRP E 369 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU E 371 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA E 147 " --> pdb=" O GLU E 371 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP E 373 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY E 145 " --> pdb=" O ASP E 373 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU E 144 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 157 through 158 removed outlier: 3.546A pdb=" N PHE E 287 " --> pdb=" O VAL E 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 188 through 190 removed outlier: 3.841A pdb=" N ASP E 188 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL E 168 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 188 through 190 removed outlier: 3.841A pdb=" N ASP E 188 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL E 168 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR E 340 " --> pdb=" O GLY E 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 206 through 207 Processing sheet with id=AA9, first strand: chain 'E' and resid 211 through 214 removed outlier: 3.828A pdb=" N ALA E 211 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AB2, first strand: chain 'E' and resid 596 through 597 Processing sheet with id=AB3, first strand: chain 'E' and resid 638 through 643 removed outlier: 4.353A pdb=" N HIS E 657 " --> pdb=" O TYR E 649 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU E 651 " --> pdb=" O TYR E 655 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TYR E 655 " --> pdb=" O GLU E 651 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 665 through 666 removed outlier: 6.930A pdb=" N THR E 665 " --> pdb=" O GLN F 126 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR F 123 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG F 562 " --> pdb=" O ALA F 569 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 113 through 115 Processing sheet with id=AB6, first strand: chain 'F' and resid 366 through 372 removed outlier: 6.938A pdb=" N VAL F 149 " --> pdb=" O TRP F 369 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU F 371 " --> pdb=" O ALA F 147 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA F 147 " --> pdb=" O GLU F 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 366 through 372 removed outlier: 6.938A pdb=" N VAL F 149 " --> pdb=" O TRP F 369 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU F 371 " --> pdb=" O ALA F 147 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA F 147 " --> pdb=" O GLU F 371 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 157 through 158 removed outlier: 3.536A pdb=" N PHE F 287 " --> pdb=" O VAL F 295 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 188 through 190 removed outlier: 3.700A pdb=" N ASP F 188 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 168 " --> pdb=" O ASP F 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 188 through 190 removed outlier: 3.700A pdb=" N ASP F 188 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 168 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR F 340 " --> pdb=" O GLY F 324 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 206 through 208 Processing sheet with id=AC3, first strand: chain 'F' and resid 212 through 214 Processing sheet with id=AC4, first strand: chain 'F' and resid 376 through 380 removed outlier: 3.970A pdb=" N TYR F 380 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 581 through 583 Processing sheet with id=AC6, first strand: chain 'F' and resid 596 through 597 Processing sheet with id=AC7, first strand: chain 'F' and resid 638 through 643 removed outlier: 4.336A pdb=" N HIS F 657 " --> pdb=" O TYR F 649 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU F 651 " --> pdb=" O TYR F 655 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR F 655 " --> pdb=" O GLU F 651 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 665 through 666 removed outlier: 7.076A pdb=" N THR F 665 " --> pdb=" O GLN G 126 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR G 123 " --> pdb=" O VAL G 570 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG G 562 " --> pdb=" O ALA G 569 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 113 through 115 removed outlier: 3.501A pdb=" N VAL G 576 " --> pdb=" O PHE G 113 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 366 through 372 removed outlier: 6.920A pdb=" N VAL G 149 " --> pdb=" O TRP G 369 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU G 371 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ALA G 147 " --> pdb=" O GLU G 371 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU G 144 " --> pdb=" O LEU G 455 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 366 through 372 removed outlier: 6.920A pdb=" N VAL G 149 " --> pdb=" O TRP G 369 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU G 371 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ALA G 147 " --> pdb=" O GLU G 371 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU G 144 " --> pdb=" O LEU G 455 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 157 through 158 removed outlier: 3.627A pdb=" N PHE G 287 " --> pdb=" O VAL G 295 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 188 through 190 removed outlier: 3.632A pdb=" N ASP G 188 " --> pdb=" O VAL G 168 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 188 through 190 removed outlier: 3.632A pdb=" N ASP G 188 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG G 342 " --> pdb=" O ASP G 323 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP G 323 " --> pdb=" O ARG G 342 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU G 344 " --> pdb=" O GLN G 321 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLN G 321 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR G 346 " --> pdb=" O PHE G 319 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE G 319 " --> pdb=" O THR G 346 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 206 through 207 Processing sheet with id=AD7, first strand: chain 'G' and resid 211 through 214 removed outlier: 3.825A pdb=" N ALA G 211 " --> pdb=" O ALA G 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 376 through 380 removed outlier: 4.134A pdb=" N TYR G 380 " --> pdb=" O SER G 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 581 through 583 Processing sheet with id=AE1, first strand: chain 'G' and resid 596 through 597 Processing sheet with id=AE2, first strand: chain 'G' and resid 638 through 643 removed outlier: 4.374A pdb=" N HIS G 657 " --> pdb=" O TYR G 649 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU G 651 " --> pdb=" O TYR G 655 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TYR G 655 " --> pdb=" O GLU G 651 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.551A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU I 18 " --> pdb=" O MET I 82 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.802A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN I 58 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.597A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU J 18 " --> pdb=" O MET J 82 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.674A pdb=" N GLN J 58 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA J 93 " --> pdb=" O HIS J 35 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.674A pdb=" N GLN J 58 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA J 93 " --> pdb=" O HIS J 35 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.538A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL K 77 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP K 72 " --> pdb=" O VAL K 77 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.791A pdb=" N GLY K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA K 93 " --> pdb=" O HIS K 35 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN K 58 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.791A pdb=" N GLY K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 4 through 7 removed outlier: 4.039A pdb=" N SER M 7 " --> pdb=" O THR M 22 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR M 22 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL M 19 " --> pdb=" O ILE M 75 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 11 through 13 removed outlier: 3.542A pdb=" N THR M 85 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 11 through 13 removed outlier: 3.989A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.935A pdb=" N SER N 7 " --> pdb=" O THR N 22 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.765A pdb=" N ILE N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TYR N 49 " --> pdb=" O ILE N 33 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 11 through 13 removed outlier: 4.024A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.879A pdb=" N SER O 7 " --> pdb=" O THR O 22 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR O 22 " --> pdb=" O SER O 7 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 10 through 13 removed outlier: 3.587A pdb=" N THR O 85 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR O 49 " --> pdb=" O ILE O 33 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 10 through 13 removed outlier: 4.060A pdb=" N THR O 97 " --> pdb=" O GLN O 90 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1743 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 2.21 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: 5660 1.34 - 1.46: 4546 1.46 - 1.59: 7560 1.59 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 17910 Sorted by residual: bond pdb=" C ARG F 136 " pdb=" N PRO F 137 " ideal model delta sigma weight residual 1.340 1.391 -0.051 2.76e-02 1.31e+03 3.45e+00 bond pdb=" C ARG G 136 " pdb=" N PRO G 137 " ideal model delta sigma weight residual 1.340 1.391 -0.051 2.76e-02 1.31e+03 3.36e+00 bond pdb=" C ARG E 136 " pdb=" N PRO E 137 " ideal model delta sigma weight residual 1.340 1.390 -0.049 2.76e-02 1.31e+03 3.21e+00 bond pdb=" C ALA K 40 " pdb=" N PRO K 41 " ideal model delta sigma weight residual 1.332 1.352 -0.020 1.12e-02 7.97e+03 3.18e+00 bond pdb=" N ASP F 110 " pdb=" CA ASP F 110 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 ... (remaining 17905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 23622 2.37 - 4.75: 650 4.75 - 7.12: 54 7.12 - 9.50: 8 9.50 - 11.87: 2 Bond angle restraints: 24336 Sorted by residual: angle pdb=" N TYR E 429 " pdb=" CA TYR E 429 " pdb=" C TYR E 429 " ideal model delta sigma weight residual 110.44 117.93 -7.49 1.20e+00 6.94e-01 3.90e+01 angle pdb=" N ALA G 327 " pdb=" CA ALA G 327 " pdb=" C ALA G 327 " ideal model delta sigma weight residual 110.80 122.67 -11.87 2.13e+00 2.20e-01 3.11e+01 angle pdb=" N SER M 32 " pdb=" CA SER M 32 " pdb=" C SER M 32 " ideal model delta sigma weight residual 108.56 116.41 -7.85 1.74e+00 3.30e-01 2.04e+01 angle pdb=" N TYR F 429 " pdb=" CA TYR F 429 " pdb=" C TYR F 429 " ideal model delta sigma weight residual 111.30 117.09 -5.79 1.43e+00 4.89e-01 1.64e+01 angle pdb=" N SER K 82B" pdb=" CA SER K 82B" pdb=" C SER K 82B" ideal model delta sigma weight residual 110.91 115.50 -4.59 1.17e+00 7.31e-01 1.54e+01 ... (remaining 24331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 10066 17.16 - 34.33: 708 34.33 - 51.49: 178 51.49 - 68.65: 23 68.65 - 85.82: 11 Dihedral angle restraints: 10986 sinusoidal: 4665 harmonic: 6321 Sorted by residual: 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 -162.56 76.56 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS G 364 " pdb=" SG CYS G 364 " pdb=" SG CYS G 412 " pdb=" CB CYS G 412 " ideal model delta sinusoidal sigma weight residual -86.00 -159.58 73.58 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS F 364 " pdb=" SG CYS F 364 " pdb=" SG CYS F 412 " pdb=" CB CYS F 412 " ideal model delta sinusoidal sigma weight residual -86.00 -141.33 55.33 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 10983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1995 0.047 - 0.094: 517 0.094 - 0.141: 199 0.141 - 0.188: 23 0.188 - 0.234: 2 Chirality restraints: 2736 Sorted by residual: chirality pdb=" CA ALA G 327 " pdb=" N ALA G 327 " pdb=" C ALA G 327 " pdb=" CB ALA G 327 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.01e+00 chirality pdb=" CB ILE N 75 " pdb=" CA ILE N 75 " pdb=" CG1 ILE N 75 " pdb=" CG2 ILE N 75 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.04e-01 ... (remaining 2733 not shown) Planarity restraints: 3126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 326 " -0.015 2.00e-02 2.50e+03 1.79e-02 6.39e+00 pdb=" CG TYR G 326 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR G 326 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR G 326 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR G 326 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 326 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR G 326 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 326 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR F 402 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.81e+00 pdb=" N PRO F 403 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO F 403 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 403 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 402 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO G 403 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO G 403 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 403 " 0.031 5.00e-02 4.00e+02 ... (remaining 3123 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 325 2.66 - 3.22: 16883 3.22 - 3.78: 26878 3.78 - 4.34: 36410 4.34 - 4.90: 59877 Nonbonded interactions: 140373 Sorted by model distance: nonbonded pdb=" OG1 THR E 249 " pdb=" OD1 ASN E 270 " model vdw 2.100 3.040 nonbonded pdb=" OE1 GLN E 440 " pdb=" OH TYR E 442 " model vdw 2.139 3.040 nonbonded pdb=" OG SER I 52 " pdb=" OD1 ASP I 53 " model vdw 2.147 3.040 nonbonded pdb=" OG1 THR G 249 " pdb=" OD1 ASN G 270 " model vdw 2.172 3.040 nonbonded pdb=" OG1 THR E 143 " pdb=" O ARG E 377 " model vdw 2.189 3.040 ... (remaining 140368 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 5.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.790 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 0.051 17958 Z= 0.198 Angle : 0.936 11.869 24456 Z= 0.517 Chirality : 0.049 0.234 2736 Planarity : 0.005 0.060 3117 Dihedral : 12.120 85.816 6864 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.13 (0.17), residues: 2133 helix: -0.27 (0.33), residues: 234 sheet: -2.05 (0.17), residues: 696 loop : -1.17 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 38 TYR 0.044 0.002 TYR G 326 PHE 0.014 0.002 PHE E 127 TRP 0.014 0.001 TRP I 103 HIS 0.015 0.002 HIS G 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (17910) covalent geometry : angle 0.90965 / 0.51 (24336) SS BOND : bond 0.00445 / 0.30 ( 24) SS BOND : angle 2.32100 / 1.47 ( 48) hydrogen bonds : bond 0.23295 / 15.09 ( 612) hydrogen bonds : angle 9.46855 / 6.50 ( 1743) link_ALPHA1-6 : bond 0.01062 / 0.57 ( 6) link_ALPHA1-6 : angle 2.46928 / 1.63 ( 18) link_BETA1-4 : bond 0.00795 / 0.49 ( 9) link_BETA1-4 : angle 4.63114 / 2.73 ( 27) link_NAG-ASN : bond 0.00391 / 0.23 ( 9) link_NAG-ASN : angle 3.46641 / 2.40 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 421 MET cc_start: 0.8253 (mmt) cc_final: 0.8026 (mmt) REVERT: F 566 ASP cc_start: 0.7536 (m-30) cc_final: 0.7281 (m-30) REVERT: G 167 ASP cc_start: 0.9052 (t0) cc_final: 0.8402 (p0) REVERT: I 101 ASP cc_start: 0.8787 (p0) cc_final: 0.7032 (p0) REVERT: J 35 HIS cc_start: 0.7752 (m-70) cc_final: 0.7075 (m-70) REVERT: M 73 LEU cc_start: 0.9581 (tp) cc_final: 0.8197 (tp) REVERT: M 97 THR cc_start: 0.8720 (p) cc_final: 0.8325 (p) REVERT: N 19 VAL cc_start: 0.8580 (t) cc_final: 0.8318 (t) REVERT: N 76 LYS cc_start: 0.8527 (mmpt) cc_final: 0.8259 (mmtm) REVERT: N 93 ASP cc_start: 0.7450 (t0) cc_final: 0.7188 (t0) REVERT: N 97 THR cc_start: 0.8570 (p) cc_final: 0.8282 (p) REVERT: O 19 VAL cc_start: 0.8681 (t) cc_final: 0.8401 (t) REVERT: O 73 LEU cc_start: 0.9420 (tt) cc_final: 0.8390 (tt) REVERT: O 93 ASP cc_start: 0.7485 (t0) cc_final: 0.7232 (t0) REVERT: O 97 THR cc_start: 0.8651 (p) cc_final: 0.8337 (p) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1296 time to fit residues: 43.8303 Evaluate side-chains 162 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 35 HIS I 73 ASN M 89 GLN N 89 GLN O 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.084199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.059935 restraints weight = 90229.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.061321 restraints weight = 47687.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.061804 restraints weight = 30230.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062112 restraints weight = 26814.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062093 restraints weight = 26201.123| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17958 Z= 0.198 Angle : 0.706 9.268 24456 Z= 0.359 Chirality : 0.047 0.263 2736 Planarity : 0.005 0.041 3117 Dihedral : 5.234 35.226 2910 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.11 % Allowed : 4.84 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.50 (0.18), residues: 2133 helix: 0.59 (0.33), residues: 237 sheet: -1.59 (0.17), residues: 708 loop : -0.85 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 38 TYR 0.021 0.002 TYR G 326 PHE 0.015 0.002 PHE K 67 TRP 0.017 0.001 TRP M 35 HIS 0.006 0.001 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (17910) covalent geometry : angle 0.68307 / 0.35 (24336) SS BOND : bond 0.00376 / 0.25 ( 24) SS BOND : angle 1.57420 / 0.98 ( 48) hydrogen bonds : bond 0.04210 / 2.69 ( 612) hydrogen bonds : angle 6.66860 / 4.52 ( 1743) link_ALPHA1-6 : bond 0.00250 / 0.14 ( 6) link_ALPHA1-6 : angle 1.65986 / 1.07 ( 18) link_BETA1-4 : bond 0.00381 / 0.22 ( 9) link_BETA1-4 : angle 3.59112 / 2.25 ( 27) link_NAG-ASN : bond 0.00601 / 0.33 ( 9) link_NAG-ASN : angle 3.45574 / 2.28 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 587 MET cc_start: 0.7355 (pmm) cc_final: 0.7054 (pmm) REVERT: G 163 MET cc_start: 0.8533 (ttt) cc_final: 0.8203 (tmm) REVERT: I 59 TYR cc_start: 0.7405 (m-10) cc_final: 0.7201 (m-10) REVERT: I 67 PHE cc_start: 0.8167 (m-80) cc_final: 0.7888 (m-80) REVERT: I 94 ARG cc_start: 0.9012 (tmt170) cc_final: 0.8557 (tmt170) REVERT: J 59 TYR cc_start: 0.7262 (m-10) cc_final: 0.6391 (m-10) REVERT: J 75 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8335 (tptp) REVERT: J 78 LEU cc_start: 0.8502 (tp) cc_final: 0.8221 (pp) REVERT: J 94 ARG cc_start: 0.8482 (tmt170) cc_final: 0.8209 (ttt90) REVERT: J 102 PHE cc_start: 0.8121 (m-80) cc_final: 0.7556 (m-80) REVERT: K 59 TYR cc_start: 0.7314 (m-10) cc_final: 0.7005 (m-10) REVERT: K 67 PHE cc_start: 0.7991 (m-80) cc_final: 0.7602 (m-80) REVERT: K 69 ILE cc_start: 0.9162 (tt) cc_final: 0.8959 (tt) REVERT: M 73 LEU cc_start: 0.9691 (tp) cc_final: 0.9174 (tp) REVERT: M 97 THR cc_start: 0.9099 (p) cc_final: 0.8802 (p) REVERT: N 32 SER cc_start: 0.8977 (m) cc_final: 0.8090 (p) REVERT: N 36 TYR cc_start: 0.7719 (m-80) cc_final: 0.7331 (m-80) REVERT: N 73 LEU cc_start: 0.9559 (tt) cc_final: 0.8401 (tt) REVERT: N 93 ASP cc_start: 0.7671 (t0) cc_final: 0.7378 (t0) REVERT: N 97 THR cc_start: 0.9045 (p) cc_final: 0.8735 (p) REVERT: O 24 ARG cc_start: 0.7879 (mtm-85) cc_final: 0.7375 (mpp-170) REVERT: O 93 ASP cc_start: 0.7785 (t0) cc_final: 0.7429 (t0) REVERT: O 97 THR cc_start: 0.8963 (p) cc_final: 0.8663 (p) outliers start: 2 outliers final: 0 residues processed: 202 average time/residue: 0.1469 time to fit residues: 43.9366 Evaluate side-chains 162 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 46 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 140 GLN ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 ASN I 35 HIS ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN ** N 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.083143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057587 restraints weight = 90287.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.059456 restraints weight = 44557.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.060595 restraints weight = 29279.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.061284 restraints weight = 23258.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.061594 restraints weight = 20500.231| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17958 Z= 0.231 Angle : 0.709 8.583 24456 Z= 0.361 Chirality : 0.046 0.221 2736 Planarity : 0.005 0.042 3117 Dihedral : 5.446 36.117 2910 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.38 (0.18), residues: 2133 helix: 1.01 (0.36), residues: 216 sheet: -1.34 (0.18), residues: 675 loop : -0.97 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 543 TYR 0.020 0.002 TYR K 91 PHE 0.020 0.002 PHE J 100G TRP 0.030 0.002 TRP M 35 HIS 0.005 0.001 HIS J 52A Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 (17910) covalent geometry : angle 0.68831 / 0.36 (24336) SS BOND : bond 0.00480 / 0.32 ( 24) SS BOND : angle 1.49839 / 0.94 ( 48) hydrogen bonds : bond 0.04087 / 2.63 ( 612) hydrogen bonds : angle 6.26494 / 4.21 ( 1743) link_ALPHA1-6 : bond 0.00367 / 0.19 ( 6) link_ALPHA1-6 : angle 1.76026 / 1.14 ( 18) link_BETA1-4 : bond 0.00525 / 0.28 ( 9) link_BETA1-4 : angle 3.33098 / 2.12 ( 27) link_NAG-ASN : bond 0.00442 / 0.27 ( 9) link_NAG-ASN : angle 3.29034 / 2.20 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 242 ARG cc_start: 0.7406 (tpt170) cc_final: 0.6914 (ttm170) REVERT: I 67 PHE cc_start: 0.8137 (m-80) cc_final: 0.7884 (m-80) REVERT: I 91 TYR cc_start: 0.8416 (m-80) cc_final: 0.7341 (m-80) REVERT: I 101 ASP cc_start: 0.8873 (p0) cc_final: 0.8033 (p0) REVERT: J 59 TYR cc_start: 0.7209 (m-10) cc_final: 0.6359 (m-10) REVERT: J 75 LYS cc_start: 0.8713 (mtmm) cc_final: 0.8410 (tptp) REVERT: J 94 ARG cc_start: 0.8169 (tmt170) cc_final: 0.7812 (ttt90) REVERT: J 102 PHE cc_start: 0.8028 (m-80) cc_final: 0.7284 (m-80) REVERT: K 67 PHE cc_start: 0.7950 (m-80) cc_final: 0.7687 (m-80) REVERT: K 78 LEU cc_start: 0.8333 (tp) cc_final: 0.7913 (pp) REVERT: M 93 ASP cc_start: 0.7927 (t0) cc_final: 0.7685 (t0) REVERT: M 97 THR cc_start: 0.9082 (p) cc_final: 0.8834 (p) REVERT: N 93 ASP cc_start: 0.7800 (t0) cc_final: 0.7482 (t0) REVERT: N 97 THR cc_start: 0.9058 (p) cc_final: 0.8814 (p) REVERT: O 36 TYR cc_start: 0.7602 (m-80) cc_final: 0.7157 (m-80) REVERT: O 93 ASP cc_start: 0.7946 (t0) cc_final: 0.7619 (t0) REVERT: O 97 THR cc_start: 0.9056 (p) cc_final: 0.8820 (p) outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.1279 time to fit residues: 36.5017 Evaluate side-chains 151 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 208 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 195 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 140 GLN I 73 ASN O 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.082890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.058068 restraints weight = 90256.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.059992 restraints weight = 44550.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.061178 restraints weight = 28956.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.061854 restraints weight = 22731.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.062165 restraints weight = 20010.861| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17958 Z= 0.181 Angle : 0.660 8.438 24456 Z= 0.336 Chirality : 0.045 0.277 2736 Planarity : 0.005 0.035 3117 Dihedral : 5.353 35.482 2910 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.22 (0.18), residues: 2133 helix: 1.13 (0.36), residues: 216 sheet: -1.15 (0.18), residues: 690 loop : -0.91 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 543 TYR 0.016 0.002 TYR F 649 PHE 0.015 0.002 PHE J 100G TRP 0.030 0.002 TRP M 35 HIS 0.009 0.001 HIS F 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (17910) covalent geometry : angle 0.63885 / 0.33 (24336) SS BOND : bond 0.00440 / 0.30 ( 24) SS BOND : angle 1.56972 / 1.02 ( 48) hydrogen bonds : bond 0.03569 / 2.30 ( 612) hydrogen bonds : angle 6.03973 / 4.04 ( 1743) link_ALPHA1-6 : bond 0.00318 / 0.18 ( 6) link_ALPHA1-6 : angle 1.63832 / 1.05 ( 18) link_BETA1-4 : bond 0.00590 / 0.34 ( 9) link_BETA1-4 : angle 3.17500 / 2.00 ( 27) link_NAG-ASN : bond 0.00446 / 0.27 ( 9) link_NAG-ASN : angle 3.16124 / 2.15 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 669 THR cc_start: 0.9469 (t) cc_final: 0.9095 (m) REVERT: I 67 PHE cc_start: 0.7995 (m-80) cc_final: 0.7677 (m-80) REVERT: J 59 TYR cc_start: 0.7205 (m-10) cc_final: 0.6326 (m-10) REVERT: J 67 PHE cc_start: 0.8345 (m-80) cc_final: 0.8003 (m-80) REVERT: J 75 LYS cc_start: 0.8707 (mtmm) cc_final: 0.8441 (tptp) REVERT: J 102 PHE cc_start: 0.8088 (m-80) cc_final: 0.7858 (m-80) REVERT: K 34 MET cc_start: 0.8851 (tpp) cc_final: 0.8561 (tpp) REVERT: K 67 PHE cc_start: 0.7855 (m-80) cc_final: 0.7621 (m-80) REVERT: M 93 ASP cc_start: 0.7840 (t0) cc_final: 0.7549 (t0) REVERT: M 97 THR cc_start: 0.8879 (p) cc_final: 0.8552 (p) REVERT: N 39 ARG cc_start: 0.8566 (mpt180) cc_final: 0.8139 (mmt180) REVERT: N 93 ASP cc_start: 0.7744 (t0) cc_final: 0.7438 (t0) REVERT: N 97 THR cc_start: 0.9018 (p) cc_final: 0.8785 (p) REVERT: O 24 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.6951 (mtm-85) REVERT: O 36 TYR cc_start: 0.7446 (m-80) cc_final: 0.7046 (m-80) REVERT: O 79 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6260 (mp10) REVERT: O 93 ASP cc_start: 0.7916 (t0) cc_final: 0.7625 (t0) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1270 time to fit residues: 34.7785 Evaluate side-chains 153 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 185 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 197 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.4635 > 50:) chunk 208 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 121 optimal weight: 0.1980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 35 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 = 0.3870 r_free = 0.3870 target = 0.084515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.061376 restraints weight = 89386.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.062515 restraints weight = 46351.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062261 restraints weight = 30914.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.062602 restraints weight = 30954.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.062725 restraints weight = 26630.689| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17958 Z= 0.108 Angle : 0.629 10.639 24456 Z= 0.315 Chirality : 0.045 0.306 2736 Planarity : 0.004 0.038 3117 Dihedral : 4.929 32.591 2910 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.04 (0.18), residues: 2133 helix: 1.12 (0.35), residues: 234 sheet: -0.86 (0.19), residues: 714 loop : -0.90 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 71 TYR 0.015 0.001 TYR G 326 PHE 0.011 0.001 PHE E 425 TRP 0.030 0.001 TRP M 35 HIS 0.006 0.001 HIS F 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (17910) covalent geometry : angle 0.60988 / 0.31 (24336) SS BOND : bond 0.00412 / 0.27 ( 24) SS BOND : angle 1.29807 / 0.81 ( 48) hydrogen bonds : bond 0.03257 / 2.11 ( 612) hydrogen bonds : angle 5.71800 / 3.83 ( 1743) link_ALPHA1-6 : bond 0.00430 / 0.23 ( 6) link_ALPHA1-6 : angle 1.52884 / 0.98 ( 18) link_BETA1-4 : bond 0.00732 / 0.44 ( 9) link_BETA1-4 : angle 3.03463 / 1.88 ( 27) link_NAG-ASN : bond 0.00394 / 0.22 ( 9) link_NAG-ASN : angle 3.05774 / 2.06 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 163 MET cc_start: 0.8099 (tpt) cc_final: 0.7837 (tpp) REVERT: I 59 TYR cc_start: 0.7327 (m-10) cc_final: 0.6475 (m-10) REVERT: I 91 TYR cc_start: 0.8399 (m-80) cc_final: 0.7307 (m-80) REVERT: I 101 ASP cc_start: 0.8680 (p0) cc_final: 0.8159 (p0) REVERT: J 59 TYR cc_start: 0.7198 (m-10) cc_final: 0.6323 (m-10) REVERT: J 67 PHE cc_start: 0.8401 (m-80) cc_final: 0.8037 (m-80) REVERT: J 75 LYS cc_start: 0.8735 (mtmm) cc_final: 0.8460 (tptp) REVERT: J 102 PHE cc_start: 0.8062 (m-80) cc_final: 0.7842 (m-80) REVERT: J 108 MET cc_start: 0.8779 (mmp) cc_final: 0.8553 (tpt) REVERT: K 67 PHE cc_start: 0.8093 (m-80) cc_final: 0.7794 (m-80) REVERT: M 93 ASP cc_start: 0.7666 (t0) cc_final: 0.7367 (t0) REVERT: M 97 THR cc_start: 0.8820 (p) cc_final: 0.8454 (p) REVERT: N 93 ASP cc_start: 0.7604 (t0) cc_final: 0.7380 (t0) REVERT: O 24 ARG cc_start: 0.7753 (mtm-85) cc_final: 0.6988 (mtm-85) REVERT: O 36 TYR cc_start: 0.7440 (m-80) cc_final: 0.6999 (m-80) REVERT: O 93 ASP cc_start: 0.7830 (t0) cc_final: 0.7520 (t0) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1415 time to fit residues: 39.9211 Evaluate side-chains 152 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 11 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 202 ASN E 512 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.082435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.057184 restraints weight = 90964.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059025 restraints weight = 45802.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.060168 restraints weight = 30407.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.060816 restraints weight = 24136.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.061101 restraints weight = 21361.298| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17958 Z= 0.216 Angle : 0.660 8.139 24456 Z= 0.337 Chirality : 0.044 0.281 2736 Planarity : 0.005 0.040 3117 Dihedral : 5.307 34.265 2910 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.09 (0.18), residues: 2133 helix: 1.25 (0.36), residues: 216 sheet: -0.95 (0.19), residues: 693 loop : -0.90 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 543 TYR 0.019 0.002 TYR F 649 PHE 0.017 0.002 PHE G 127 TRP 0.020 0.002 TRP M 35 HIS 0.005 0.001 HIS F 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.22 (17910) covalent geometry : angle 0.64026 / 0.33 (24336) SS BOND : bond 0.00400 / 0.27 ( 24) SS BOND : angle 1.53234 / 1.00 ( 48) hydrogen bonds : bond 0.03452 / 2.22 ( 612) hydrogen bonds : angle 5.82862 / 3.89 ( 1743) link_ALPHA1-6 : bond 0.00402 / 0.19 ( 6) link_ALPHA1-6 : angle 1.68886 / 1.09 ( 18) link_BETA1-4 : bond 0.00593 / 0.32 ( 9) link_BETA1-4 : angle 3.15227 / 1.97 ( 27) link_NAG-ASN : bond 0.00403 / 0.24 ( 9) link_NAG-ASN : angle 2.97950 / 2.03 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 59 TYR cc_start: 0.7373 (m-10) cc_final: 0.6622 (m-10) REVERT: I 82 MET cc_start: 0.7648 (ppp) cc_final: 0.7432 (ppp) REVERT: I 91 TYR cc_start: 0.8342 (m-80) cc_final: 0.7194 (m-80) REVERT: I 92 CYS cc_start: 0.1011 (p) cc_final: -0.1345 (p) REVERT: I 101 ASP cc_start: 0.8732 (p0) cc_final: 0.8490 (p0) REVERT: J 59 TYR cc_start: 0.7293 (m-10) cc_final: 0.6434 (m-10) REVERT: J 67 PHE cc_start: 0.8360 (m-80) cc_final: 0.8034 (m-80) REVERT: J 75 LYS cc_start: 0.8816 (mtmm) cc_final: 0.8574 (tptp) REVERT: J 102 PHE cc_start: 0.8106 (m-80) cc_final: 0.7754 (m-80) REVERT: K 34 MET cc_start: 0.8768 (tpp) cc_final: 0.8417 (tpp) REVERT: K 59 TYR cc_start: 0.7266 (m-10) cc_final: 0.6542 (m-10) REVERT: K 108 MET cc_start: 0.8700 (mmp) cc_final: 0.8392 (tpp) REVERT: M 93 ASP cc_start: 0.7861 (t0) cc_final: 0.7575 (t0) REVERT: M 97 THR cc_start: 0.8939 (p) cc_final: 0.8624 (p) REVERT: N 93 ASP cc_start: 0.7840 (t0) cc_final: 0.7546 (t0) REVERT: O 24 ARG cc_start: 0.7655 (mtm-85) cc_final: 0.6891 (mtm-85) REVERT: O 36 TYR cc_start: 0.7613 (m-80) cc_final: 0.7136 (m-80) REVERT: O 93 ASP cc_start: 0.8018 (t0) cc_final: 0.7705 (t0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1427 time to fit residues: 37.5728 Evaluate side-chains 149 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 149 optimal weight: 10.0000 chunk 97 optimal weight: 0.4980 chunk 140 optimal weight: 0.3980 chunk 204 optimal weight: 20.0000 chunk 93 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 134 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.084374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.061361 restraints weight = 90115.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.062386 restraints weight = 50167.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.062857 restraints weight = 30398.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063094 restraints weight = 28436.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.063260 restraints weight = 26157.717| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17958 Z= 0.107 Angle : 0.619 8.538 24456 Z= 0.311 Chirality : 0.044 0.254 2736 Planarity : 0.004 0.040 3117 Dihedral : 4.940 31.481 2910 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.93 (0.18), residues: 2133 helix: 1.63 (0.36), residues: 216 sheet: -0.78 (0.19), residues: 699 loop : -0.89 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 328 TYR 0.036 0.001 TYR G 326 PHE 0.016 0.001 PHE K 67 TRP 0.022 0.001 TRP M 35 HIS 0.004 0.001 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (17910) covalent geometry : angle 0.60013 / 0.31 (24336) SS BOND : bond 0.00284 / 0.20 ( 24) SS BOND : angle 1.32854 / 0.88 ( 48) hydrogen bonds : bond 0.03160 / 2.05 ( 612) hydrogen bonds : angle 5.59788 / 3.75 ( 1743) link_ALPHA1-6 : bond 0.00382 / 0.20 ( 6) link_ALPHA1-6 : angle 1.53622 / 0.99 ( 18) link_BETA1-4 : bond 0.00695 / 0.42 ( 9) link_BETA1-4 : angle 2.99349 / 1.84 ( 27) link_NAG-ASN : bond 0.00357 / 0.20 ( 9) link_NAG-ASN : angle 3.00163 / 2.03 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 587 MET cc_start: 0.7823 (pmm) cc_final: 0.7447 (pmm) REVERT: I 34 MET cc_start: 0.8299 (tpt) cc_final: 0.7946 (tmm) REVERT: I 59 TYR cc_start: 0.7364 (m-10) cc_final: 0.7112 (m-10) REVERT: I 67 PHE cc_start: 0.8323 (m-10) cc_final: 0.8054 (m-80) REVERT: I 82 MET cc_start: 0.7644 (ppp) cc_final: 0.7403 (ppp) REVERT: I 91 TYR cc_start: 0.8513 (m-80) cc_final: 0.8068 (m-80) REVERT: J 59 TYR cc_start: 0.7204 (m-10) cc_final: 0.6360 (m-10) REVERT: J 67 PHE cc_start: 0.8462 (m-80) cc_final: 0.8111 (m-80) REVERT: J 75 LYS cc_start: 0.8809 (mtmm) cc_final: 0.8542 (tptp) REVERT: J 102 PHE cc_start: 0.8057 (m-80) cc_final: 0.7748 (m-80) REVERT: K 34 MET cc_start: 0.8814 (tpp) cc_final: 0.8422 (tpp) REVERT: K 59 TYR cc_start: 0.7319 (m-10) cc_final: 0.6569 (m-10) REVERT: K 67 PHE cc_start: 0.8275 (m-80) cc_final: 0.7955 (m-80) REVERT: K 89 MET cc_start: 0.7790 (tpt) cc_final: 0.7435 (tpp) REVERT: K 108 MET cc_start: 0.8787 (mmp) cc_final: 0.8341 (tpp) REVERT: M 93 ASP cc_start: 0.7711 (t0) cc_final: 0.7444 (t0) REVERT: M 97 THR cc_start: 0.8931 (p) cc_final: 0.8630 (p) REVERT: N 93 ASP cc_start: 0.7723 (t0) cc_final: 0.7502 (t0) REVERT: O 24 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.6954 (mtm-85) REVERT: O 36 TYR cc_start: 0.7564 (m-80) cc_final: 0.7167 (m-80) REVERT: O 93 ASP cc_start: 0.7830 (t0) cc_final: 0.7555 (t0) REVERT: O 97 THR cc_start: 0.8871 (p) cc_final: 0.8564 (p) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1500 time to fit residues: 42.0433 Evaluate side-chains 159 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 123 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 30.0000 chunk 165 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 42 optimal weight: 0.0770 chunk 194 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 overall best weight: 1.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 35 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 = 0.3852 r_free = 0.3852 target = 0.083553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.060418 restraints weight = 89472.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.061501 restraints weight = 49540.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.062095 restraints weight = 29945.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.062514 restraints weight = 27361.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.062482 restraints weight = 24991.929| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17958 Z= 0.127 Angle : 0.603 8.359 24456 Z= 0.305 Chirality : 0.043 0.226 2736 Planarity : 0.004 0.039 3117 Dihedral : 4.937 31.129 2910 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.87 (0.18), residues: 2133 helix: 1.57 (0.36), residues: 216 sheet: -0.76 (0.20), residues: 633 loop : -0.83 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 71 TYR 0.014 0.001 TYR F 649 PHE 0.019 0.001 PHE G 127 TRP 0.021 0.001 TRP M 35 HIS 0.005 0.001 HIS E 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (17910) covalent geometry : angle 0.58442 / 0.30 (24336) SS BOND : bond 0.00326 / 0.23 ( 24) SS BOND : angle 1.24620 / 0.79 ( 48) hydrogen bonds : bond 0.03101 / 2.01 ( 612) hydrogen bonds : angle 5.51403 / 3.68 ( 1743) link_ALPHA1-6 : bond 0.00377 / 0.20 ( 6) link_ALPHA1-6 : angle 1.57431 / 1.01 ( 18) link_BETA1-4 : bond 0.00572 / 0.35 ( 9) link_BETA1-4 : angle 2.99562 / 1.85 ( 27) link_NAG-ASN : bond 0.00345 / 0.20 ( 9) link_NAG-ASN : angle 2.87996 / 1.95 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 163 MET cc_start: 0.8052 (tpt) cc_final: 0.7761 (tpp) REVERT: I 59 TYR cc_start: 0.7307 (m-10) cc_final: 0.7063 (m-10) REVERT: I 67 PHE cc_start: 0.8279 (m-10) cc_final: 0.7998 (m-80) REVERT: I 82 MET cc_start: 0.7548 (ppp) cc_final: 0.7341 (ppp) REVERT: I 91 TYR cc_start: 0.8370 (m-80) cc_final: 0.7900 (m-80) REVERT: I 92 CYS cc_start: 0.1042 (p) cc_final: -0.0979 (p) REVERT: I 101 ASP cc_start: 0.8749 (p0) cc_final: 0.8462 (p0) REVERT: J 59 TYR cc_start: 0.7255 (m-10) cc_final: 0.6429 (m-10) REVERT: J 67 PHE cc_start: 0.8420 (m-80) cc_final: 0.8074 (m-80) REVERT: J 75 LYS cc_start: 0.8831 (mtmm) cc_final: 0.8579 (tptp) REVERT: J 102 PHE cc_start: 0.8032 (m-80) cc_final: 0.7742 (m-80) REVERT: K 34 MET cc_start: 0.8754 (tpp) cc_final: 0.8431 (tpp) REVERT: K 59 TYR cc_start: 0.7287 (m-10) cc_final: 0.6584 (m-10) REVERT: K 108 MET cc_start: 0.8848 (mmp) cc_final: 0.8605 (tpp) REVERT: M 93 ASP cc_start: 0.7712 (t0) cc_final: 0.7390 (t0) REVERT: M 97 THR cc_start: 0.8880 (p) cc_final: 0.8566 (p) REVERT: N 93 ASP cc_start: 0.7787 (t0) cc_final: 0.7553 (t0) REVERT: O 5 THR cc_start: 0.7958 (p) cc_final: 0.6186 (p) REVERT: O 93 ASP cc_start: 0.7866 (t0) cc_final: 0.7550 (t0) REVERT: O 97 THR cc_start: 0.8862 (p) cc_final: 0.8531 (p) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1319 time to fit residues: 36.4918 Evaluate side-chains 154 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 161 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 540 ASN G 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.081383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.056031 restraints weight = 91005.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.057800 restraints weight = 46586.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058903 restraints weight = 31230.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.059502 restraints weight = 24936.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.059875 restraints weight = 22141.918| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 17958 Z= 0.287 Angle : 0.722 8.170 24456 Z= 0.374 Chirality : 0.046 0.287 2736 Planarity : 0.005 0.044 3117 Dihedral : 5.651 35.171 2910 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.20 (0.18), residues: 2133 helix: 0.87 (0.36), residues: 216 sheet: -0.93 (0.21), residues: 612 loop : -1.01 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 543 TYR 0.023 0.002 TYR E 649 PHE 0.049 0.003 PHE G 127 TRP 0.025 0.002 TRP M 35 HIS 0.006 0.001 HIS E 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.29 (17910) covalent geometry : angle 0.70440 / 0.37 (24336) SS BOND : bond 0.00353 / 0.24 ( 24) SS BOND : angle 1.51532 / 0.94 ( 48) hydrogen bonds : bond 0.03772 / 2.44 ( 612) hydrogen bonds : angle 5.88069 / 3.93 ( 1743) link_ALPHA1-6 : bond 0.00200 / 0.09 ( 6) link_ALPHA1-6 : angle 1.68752 / 1.08 ( 18) link_BETA1-4 : bond 0.00589 / 0.33 ( 9) link_BETA1-4 : angle 3.19105 / 2.01 ( 27) link_NAG-ASN : bond 0.00438 / 0.27 ( 9) link_NAG-ASN : angle 3.02529 / 2.07 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 163 MET cc_start: 0.7765 (tpt) cc_final: 0.7492 (tpp) REVERT: I 59 TYR cc_start: 0.7346 (m-10) cc_final: 0.6714 (m-10) REVERT: I 91 TYR cc_start: 0.8322 (m-80) cc_final: 0.7955 (m-80) REVERT: I 92 CYS cc_start: 0.1168 (p) cc_final: 0.0172 (p) REVERT: I 101 ASP cc_start: 0.8760 (p0) cc_final: 0.7500 (p0) REVERT: J 59 TYR cc_start: 0.7320 (m-10) cc_final: 0.6417 (m-10) REVERT: J 67 PHE cc_start: 0.8383 (m-80) cc_final: 0.8089 (m-80) REVERT: J 75 LYS cc_start: 0.8887 (mtmm) cc_final: 0.8623 (tptp) REVERT: J 102 PHE cc_start: 0.8157 (m-80) cc_final: 0.7422 (m-80) REVERT: K 34 MET cc_start: 0.8764 (tpp) cc_final: 0.8351 (tpp) REVERT: K 67 PHE cc_start: 0.8092 (m-80) cc_final: 0.7765 (m-80) REVERT: M 36 TYR cc_start: 0.7394 (m-80) cc_final: 0.7128 (m-80) REVERT: M 93 ASP cc_start: 0.7965 (t0) cc_final: 0.7597 (t0) REVERT: N 93 ASP cc_start: 0.7927 (t0) cc_final: 0.7650 (t0) REVERT: O 93 ASP cc_start: 0.7972 (t0) cc_final: 0.7624 (t0) REVERT: O 97 THR cc_start: 0.9108 (p) cc_final: 0.8863 (p) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1348 time to fit residues: 35.3893 Evaluate side-chains 147 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 111 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 133 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.082015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.058006 restraints weight = 90416.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.059558 restraints weight = 49999.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.059456 restraints weight = 30727.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.059619 restraints weight = 34055.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059715 restraints weight = 30680.103| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17958 Z= 0.208 Angle : 0.678 8.187 24456 Z= 0.347 Chirality : 0.045 0.272 2736 Planarity : 0.005 0.048 3117 Dihedral : 5.522 35.110 2910 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.18), residues: 2133 helix: 0.99 (0.36), residues: 216 sheet: -0.93 (0.21), residues: 615 loop : -1.01 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 543 TYR 0.018 0.002 TYR G 649 PHE 0.024 0.002 PHE K 67 TRP 0.028 0.002 TRP M 35 HIS 0.005 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 (17910) covalent geometry : angle 0.65736 / 0.34 (24336) SS BOND : bond 0.00304 / 0.21 ( 24) SS BOND : angle 1.74343 / 1.11 ( 48) hydrogen bonds : bond 0.03479 / 2.25 ( 612) hydrogen bonds : angle 5.80369 / 3.88 ( 1743) link_ALPHA1-6 : bond 0.00315 / 0.15 ( 6) link_ALPHA1-6 : angle 1.64261 / 1.05 ( 18) link_BETA1-4 : bond 0.00540 / 0.31 ( 9) link_BETA1-4 : angle 3.11190 / 1.95 ( 27) link_NAG-ASN : bond 0.00329 / 0.20 ( 9) link_NAG-ASN : angle 3.07751 / 2.10 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 59 TYR cc_start: 0.7449 (m-10) cc_final: 0.6645 (m-10) REVERT: I 91 TYR cc_start: 0.8426 (m-80) cc_final: 0.8061 (m-80) REVERT: I 101 ASP cc_start: 0.8906 (p0) cc_final: 0.7629 (p0) REVERT: J 59 TYR cc_start: 0.7352 (m-10) cc_final: 0.6400 (m-10) REVERT: J 67 PHE cc_start: 0.8439 (m-80) cc_final: 0.8122 (m-80) REVERT: J 75 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8604 (tptp) REVERT: J 91 TYR cc_start: 0.8361 (m-80) cc_final: 0.7692 (m-80) REVERT: J 100 PHE cc_start: 0.8673 (m-80) cc_final: 0.8174 (m-80) REVERT: K 34 MET cc_start: 0.8495 (tpp) cc_final: 0.8200 (tpp) REVERT: K 67 PHE cc_start: 0.8118 (m-80) cc_final: 0.7782 (m-80) REVERT: K 89 MET cc_start: 0.7890 (tpt) cc_final: 0.7072 (tpt) REVERT: K 108 MET cc_start: 0.9005 (mmp) cc_final: 0.8269 (tpt) REVERT: M 36 TYR cc_start: 0.7460 (m-80) cc_final: 0.7077 (m-80) REVERT: M 93 ASP cc_start: 0.7914 (t0) cc_final: 0.7557 (t0) REVERT: N 93 ASP cc_start: 0.7763 (t0) cc_final: 0.7517 (t0) REVERT: O 93 ASP cc_start: 0.7902 (t0) cc_final: 0.7587 (t0) REVERT: O 97 THR cc_start: 0.9084 (p) cc_final: 0.8824 (p) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1538 time to fit residues: 40.7752 Evaluate side-chains 152 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 139 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 8 optimal weight: 0.0030 chunk 103 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 11 optimal weight: 0.0170 overall best weight: 0.7430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 540 ASN I 35 HIS I 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.083916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.060514 restraints weight = 90087.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.061911 restraints weight = 47621.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.062432 restraints weight = 29909.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.062749 restraints weight = 25491.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.062730 restraints weight = 25092.855| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17958 Z= 0.110 Angle : 0.643 9.124 24456 Z= 0.322 Chirality : 0.045 0.269 2736 Planarity : 0.004 0.038 3117 Dihedral : 5.049 31.895 2910 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.93 (0.18), residues: 2133 helix: 1.32 (0.36), residues: 216 sheet: -0.77 (0.20), residues: 651 loop : -0.85 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 406 TYR 0.013 0.001 TYR G 653 PHE 0.020 0.001 PHE E 127 TRP 0.033 0.002 TRP M 35 HIS 0.007 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (17910) covalent geometry : angle 0.62346 / 0.32 (24336) SS BOND : bond 0.00348 / 0.24 ( 24) SS BOND : angle 1.53893 / 0.96 ( 48) hydrogen bonds : bond 0.03210 / 2.08 ( 612) hydrogen bonds : angle 5.56601 / 3.72 ( 1743) link_ALPHA1-6 : bond 0.00456 / 0.22 ( 6) link_ALPHA1-6 : angle 1.55758 / 1.00 ( 18) link_BETA1-4 : bond 0.00705 / 0.44 ( 9) link_BETA1-4 : angle 2.98732 / 1.83 ( 27) link_NAG-ASN : bond 0.00337 / 0.19 ( 9) link_NAG-ASN : angle 2.96841 / 2.01 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3004.39 seconds wall clock time: 52 minutes 48.08 seconds (3168.08 seconds total)