Starting phenix.real_space_refine on Thu Feb 5 14:23:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dd7_46759/02_2026/9dd7_46759.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dd7_46759/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dd7_46759/02_2026/9dd7_46759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dd7_46759/02_2026/9dd7_46759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dd7_46759/02_2026/9dd7_46759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dd7_46759/02_2026/9dd7_46759.map" } 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-2.0-5952/lib/python3.9/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: 4.60, per 1000 atoms: 0.26 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: 1.79 Conformation dependent library (CDL) restraints added in 780.0 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: 1.18 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: 3.79 Time building geometry restraints manager: 2.29 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: 5.780 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.270 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 covalent geometry : bond 0.00414 (17910) covalent geometry : angle 0.90965 (24336) SS BOND : bond 0.00445 ( 24) SS BOND : angle 2.32100 ( 48) hydrogen bonds : bond 0.23295 ( 612) hydrogen bonds : angle 9.46855 ( 1743) link_ALPHA1-6 : bond 0.01062 ( 6) link_ALPHA1-6 : angle 2.46928 ( 18) link_BETA1-4 : bond 0.00795 ( 9) link_BETA1-4 : angle 4.63114 ( 27) link_NAG-ASN : bond 0.00391 ( 9) link_NAG-ASN : angle 3.46641 ( 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 : 0.691 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: 0.1641 time to fit residues: 55.1483 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 : 0.799 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.8017 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 covalent geometry : bond 0.00431 (17910) covalent geometry : angle 0.68307 (24336) SS BOND : bond 0.00376 ( 24) SS BOND : angle 1.57420 ( 48) hydrogen bonds : bond 0.04210 ( 612) hydrogen bonds : angle 6.66860 ( 1743) link_ALPHA1-6 : bond 0.00250 ( 6) link_ALPHA1-6 : angle 1.65986 ( 18) link_BETA1-4 : bond 0.00381 ( 9) link_BETA1-4 : angle 3.59112 ( 27) link_NAG-ASN : bond 0.00601 ( 9) link_NAG-ASN : angle 3.45574 ( 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 : 0.699 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: 0.1653 time to fit residues: 48.7462 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 : 0.732 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.8007 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 covalent geometry : bond 0.00501 (17910) covalent geometry : angle 0.68831 (24336) SS BOND : bond 0.00480 ( 24) SS BOND : angle 1.49839 ( 48) hydrogen bonds : bond 0.04087 ( 612) hydrogen bonds : angle 6.26494 ( 1743) link_ALPHA1-6 : bond 0.00367 ( 6) link_ALPHA1-6 : angle 1.76026 ( 18) link_BETA1-4 : bond 0.00525 ( 9) link_BETA1-4 : angle 3.33098 ( 27) link_NAG-ASN : bond 0.00442 ( 9) link_NAG-ASN : angle 3.29034 ( 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 : 0.731 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: 0.1650 time to fit residues: 47.1946 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 : 0.849 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.7965 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 covalent geometry : bond 0.00395 (17910) covalent geometry : angle 0.63885 (24336) SS BOND : bond 0.00440 ( 24) SS BOND : angle 1.56972 ( 48) hydrogen bonds : bond 0.03569 ( 612) hydrogen bonds : angle 6.03973 ( 1743) link_ALPHA1-6 : bond 0.00318 ( 6) link_ALPHA1-6 : angle 1.63832 ( 18) link_BETA1-4 : bond 0.00590 ( 9) link_BETA1-4 : angle 3.17500 ( 27) link_NAG-ASN : bond 0.00446 ( 9) link_NAG-ASN : angle 3.16124 ( 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 : 0.743 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: 0.1620 time to fit residues: 43.8340 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 : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.4635 > 50: distance: 54 - 149: 19.000 distance: 69 - 135: 16.764 distance: 72 - 132: 20.582 distance: 91 - 100: 13.566 distance: 100 - 101: 5.180 distance: 100 - 106: 35.786 distance: 101 - 102: 7.296 distance: 101 - 104: 20.938 distance: 102 - 103: 13.589 distance: 102 - 107: 23.438 distance: 104 - 105: 18.025 distance: 105 - 106: 33.222 distance: 107 - 108: 10.802 distance: 108 - 109: 22.692 distance: 109 - 110: 24.619 distance: 109 - 111: 29.997 distance: 111 - 112: 17.795 distance: 112 - 113: 16.319 distance: 112 - 115: 29.326 distance: 113 - 114: 12.549 distance: 113 - 120: 29.264 distance: 115 - 116: 17.445 distance: 116 - 117: 28.227 distance: 117 - 118: 14.086 distance: 118 - 119: 30.764 distance: 120 - 121: 28.152 distance: 121 - 122: 16.356 distance: 121 - 124: 18.774 distance: 122 - 123: 42.192 distance: 122 - 125: 18.439 distance: 125 - 126: 13.971 distance: 125 - 131: 20.056 distance: 126 - 127: 36.650 distance: 126 - 129: 23.898 distance: 127 - 128: 23.087 distance: 127 - 132: 16.375 distance: 129 - 130: 51.757 distance: 130 - 131: 29.620 distance: 132 - 133: 10.949 distance: 133 - 134: 23.038 distance: 133 - 136: 12.665 distance: 134 - 135: 20.523 distance: 134 - 141: 18.982 distance: 136 - 137: 19.745 distance: 137 - 138: 11.486 distance: 138 - 139: 12.159 distance: 138 - 140: 14.863 distance: 141 - 142: 27.302 distance: 142 - 143: 24.894 distance: 142 - 145: 30.554 distance: 143 - 144: 47.080 distance: 143 - 149: 46.322 distance: 145 - 146: 15.260 distance: 146 - 147: 20.253 distance: 146 - 148: 27.647 distance: 149 - 150: 32.902 distance: 150 - 151: 29.578 distance: 150 - 153: 47.256 distance: 151 - 152: 28.006 distance: 151 - 157: 25.416 distance: 153 - 154: 25.282 distance: 154 - 155: 13.914 distance: 154 - 156: 20.875 distance: 157 - 158: 18.519 distance: 158 - 159: 30.453 distance: 158 - 161: 36.983 distance: 159 - 160: 11.396 distance: 159 - 164: 28.325 distance: 161 - 162: 28.456 distance: 161 - 163: 23.328 distance: 164 - 165: 14.082 distance: 165 - 166: 8.775 distance: 165 - 168: 16.392 distance: 166 - 167: 31.158 distance: 166 - 176: 20.386 distance: 168 - 169: 9.671 distance: 169 - 170: 10.712 distance: 169 - 171: 14.743 distance: 170 - 172: 16.851 distance: 171 - 173: 23.814 distance: 172 - 174: 9.289 distance: 173 - 174: 10.243 distance: 174 - 175: 10.140