Starting phenix.real_space_refine on Fri Aug 22 22:03:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpk_29367/08_2025/8fpk_29367.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpk_29367/08_2025/8fpk_29367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fpk_29367/08_2025/8fpk_29367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpk_29367/08_2025/8fpk_29367.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpk_29367/08_2025/8fpk_29367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpk_29367/08_2025/8fpk_29367.cif" } resolution = 2.76 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= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 4 4.86 5 C 5186 2.51 5 N 1351 2.21 5 O 1551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8156 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1992 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 1994 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Conformer: "B" Number of residues, atoms: 256, 1994 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 bond proxies already assigned to first conformer: 2012 Chain: "A" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1992 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 1999 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 1994 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Conformer: "B" Number of residues, atoms: 256, 1994 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 bond proxies already assigned to first conformer: 2024 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CYZ': 1, 'Y4Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CYZ': 1, 'Y4Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CYZ': 1, 'Y4Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CYZ': 1, 'Y4Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS C 435 " occ=0.80 ... (18 atoms not shown) pdb=" NE2BHIS C 435 " occ=0.20 Time building chain proxies: 2.76, per 1000 atoms: 0.34 Number of scatterers: 8156 At special positions: 0 Unit cell: (115.55, 97.5205, 72.9355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 64 16.00 O 1551 8.00 N 1351 7.00 C 5186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 460.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1878 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 44.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.897A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 489 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.860A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 488 removed outlier: 3.828A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.760A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.732A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.977A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.540A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.806A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 489 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 removed outlier: 4.034A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing sheet with id=AA1, first strand: chain 'B' and resid 439 through 444 removed outlier: 3.562A pdb=" N ILE B 476 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 439 through 444 removed outlier: 3.562A pdb=" N ILE B 476 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA4, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.749A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.453A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'C' and resid 453 through 454 removed outlier: 3.783A pdb=" N ILE C 459 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.799A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.555A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AB3, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.644A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AB6, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.799A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 646 through 648 removed outlier: 8.442A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.663A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D 476 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.663A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D 476 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.826A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1046 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: 1.08 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2545 1.35 - 1.47: 2028 1.47 - 1.60: 3601 1.60 - 1.72: 40 1.72 - 1.85: 104 Bond restraints: 8318 Sorted by residual: bond pdb=" C3 CYZ D 902 " pdb=" C4 CYZ D 902 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ B 902 " pdb=" C4 CYZ B 902 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ C 902 " pdb=" C4 CYZ C 902 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ A 902 " pdb=" C4 CYZ A 902 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C2 Y4Y D 901 " pdb=" O2 Y4Y D 901 " ideal model delta sigma weight residual 1.208 1.447 -0.239 2.00e-02 2.50e+03 1.43e+02 ... (remaining 8313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 10992 1.97 - 3.94: 145 3.94 - 5.91: 55 5.91 - 7.88: 33 7.88 - 9.85: 11 Bond angle restraints: 11236 Sorted by residual: angle pdb=" C9 CYZ D 902 " pdb=" S1 CYZ D 902 " pdb=" N1 CYZ D 902 " ideal model delta sigma weight residual 101.75 111.60 -9.85 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C9 CYZ A 902 " pdb=" S1 CYZ A 902 " pdb=" N1 CYZ A 902 " ideal model delta sigma weight residual 101.75 111.40 -9.65 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C9 CYZ C 902 " pdb=" S1 CYZ C 902 " pdb=" N1 CYZ C 902 " ideal model delta sigma weight residual 101.75 111.35 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C9 CYZ B 902 " pdb=" S1 CYZ B 902 " pdb=" N1 CYZ B 902 " ideal model delta sigma weight residual 101.75 111.21 -9.46 3.00e+00 1.11e-01 9.94e+00 angle pdb=" N GLY B 743 " pdb=" CA GLY B 743 " pdb=" C GLY B 743 " ideal model delta sigma weight residual 112.50 116.03 -3.53 1.16e+00 7.43e-01 9.24e+00 ... (remaining 11231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.69: 4577 22.69 - 45.38: 427 45.38 - 68.07: 69 68.07 - 90.76: 17 90.76 - 113.44: 12 Dihedral angle restraints: 5102 sinusoidal: 2150 harmonic: 2952 Sorted by residual: dihedral pdb=" N2 CYZ A 902 " pdb=" C8 CYZ A 902 " pdb=" N1 CYZ A 902 " pdb=" S1 CYZ A 902 " ideal model delta sinusoidal sigma weight residual 55.73 -57.71 113.44 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" N2 CYZ C 902 " pdb=" C8 CYZ C 902 " pdb=" N1 CYZ C 902 " pdb=" S1 CYZ C 902 " ideal model delta sinusoidal sigma weight residual 55.73 -57.69 113.42 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" N2 CYZ B 902 " pdb=" C8 CYZ B 902 " pdb=" N1 CYZ B 902 " pdb=" S1 CYZ B 902 " ideal model delta sinusoidal sigma weight residual 55.73 -57.21 112.94 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 5099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1153 0.090 - 0.179: 70 0.179 - 0.269: 0 0.269 - 0.359: 0 0.359 - 0.449: 16 Chirality restraints: 1239 Sorted by residual: chirality pdb=" C8 CYZ A 902 " pdb=" C1 CYZ A 902 " pdb=" N1 CYZ A 902 " pdb=" N2 CYZ A 902 " both_signs ideal model delta sigma weight residual False 2.20 2.65 -0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" C8 CYZ C 902 " pdb=" C1 CYZ C 902 " pdb=" N1 CYZ C 902 " pdb=" N2 CYZ C 902 " both_signs ideal model delta sigma weight residual False 2.20 2.64 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" C8 CYZ D 902 " pdb=" C1 CYZ D 902 " pdb=" N1 CYZ D 902 " pdb=" N2 CYZ D 902 " both_signs ideal model delta sigma weight residual False 2.20 2.64 -0.43 2.00e-01 2.50e+01 4.70e+00 ... (remaining 1236 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 673 " 0.006 2.00e-02 2.50e+03 9.03e-03 1.63e+00 pdb=" CG TYR A 673 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 673 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 673 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 673 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 673 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 673 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 673 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO C 737 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 673 " -0.005 2.00e-02 2.50e+03 8.97e-03 1.61e+00 pdb=" CG TYR C 673 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 673 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR C 673 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR C 673 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 673 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 673 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 673 " 0.001 2.00e-02 2.50e+03 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 274 2.71 - 3.26: 7796 3.26 - 3.81: 13355 3.81 - 4.35: 17468 4.35 - 4.90: 29117 Nonbonded interactions: 68010 Sorted by model distance: nonbonded pdb=" OG SER C 497 " pdb=" O2 CYZ C 902 " model vdw 2.164 3.040 nonbonded pdb=" OG1 THR B 685 " pdb=" OE1 GLU B 688 " model vdw 2.195 3.040 nonbonded pdb=" OG SER A 497 " pdb=" O2 CYZ A 902 " model vdw 2.208 3.040 nonbonded pdb=" OG SER D 729 " pdb=" O1 CYZ A 902 " model vdw 2.227 3.040 nonbonded pdb=" OE1 GLU A 402 " pdb=" OH TYR A 450 " model vdw 2.230 3.040 ... (remaining 68005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 763 or resid 765 through 902)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 763 or resid 765 through 902)) selection = (chain 'C' and (resid 393 through 434 or resid 436 through 666 or (resid 667 and \ (name N or name CA or name C or name O or name CB )) or resid 668 through 763 o \ r resid 765 through 902)) selection = (chain 'D' and (resid 393 through 434 or resid 436 through 666 or (resid 667 and \ (name N or name CA or name C or name O or name CB )) or resid 668 through 763 o \ r resid 765 through 902)) } 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.510 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.018 0.243 8322 Z= 0.885 Angle : 0.763 9.852 11244 Z= 0.322 Chirality : 0.063 0.449 1239 Planarity : 0.003 0.032 1385 Dihedral : 18.102 113.444 3212 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.05 % Allowed : 22.00 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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 aren not related in a simple way. whole: -0.24 (0.26), residues: 1013 helix: 0.76 (0.25), residues: 445 sheet: -1.51 (0.40), residues: 148 loop : -0.50 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 660 TYR 0.022 0.001 TYR A 673 PHE 0.010 0.002 PHE B 495 TRP 0.009 0.001 TRP A 766 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.01774 ( 8318) covalent geometry : angle 0.76331 (11236) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.75979 ( 8) hydrogen bonds : bond 0.18211 ( 356) hydrogen bonds : angle 6.63200 ( 1046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.288 Fit side-chains REVERT: B 414 MET cc_start: 0.5262 (mtm) cc_final: 0.5052 (ttp) outliers start: 9 outliers final: 8 residues processed: 116 average time/residue: 0.6223 time to fit residues: 75.9805 Evaluate side-chains 117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 686 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112446 restraints weight = 27866.842| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.81 r_work: 0.3118 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8322 Z= 0.112 Angle : 0.473 5.694 11244 Z= 0.252 Chirality : 0.042 0.131 1239 Planarity : 0.003 0.035 1385 Dihedral : 11.251 106.283 1281 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.75 % Allowed : 21.19 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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 aren not related in a simple way. whole: 0.00 (0.26), residues: 1013 helix: 0.99 (0.24), residues: 449 sheet: -1.29 (0.41), residues: 140 loop : -0.50 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 420 TYR 0.020 0.001 TYR C 673 PHE 0.009 0.001 PHE B 495 TRP 0.013 0.002 TRP C 766 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8318) covalent geometry : angle 0.47291 (11236) SS BOND : bond 0.00065 ( 4) SS BOND : angle 0.59670 ( 8) hydrogen bonds : bond 0.03806 ( 356) hydrogen bonds : angle 4.67678 ( 1046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.329 Fit side-chains REVERT: B 414 MET cc_start: 0.5519 (mtm) cc_final: 0.5175 (ttp) REVERT: B 688 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6725 (mm-30) REVERT: C 670 MET cc_start: 0.7383 (mtp) cc_final: 0.7176 (mtm) REVERT: D 408 MET cc_start: 0.7302 (mmt) cc_final: 0.7044 (mmt) REVERT: D 414 MET cc_start: 0.5821 (mtm) cc_final: 0.5425 (ttp) REVERT: D 644 GLU cc_start: 0.5867 (OUTLIER) cc_final: 0.5373 (tp30) outliers start: 15 outliers final: 4 residues processed: 126 average time/residue: 0.6318 time to fit residues: 83.8607 Evaluate side-chains 114 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 688 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain D residue 644 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109193 restraints weight = 26479.712| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.76 r_work: 0.3056 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8322 Z= 0.137 Angle : 0.500 7.079 11244 Z= 0.262 Chirality : 0.043 0.154 1239 Planarity : 0.003 0.036 1385 Dihedral : 10.742 105.013 1272 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.75 % Allowed : 21.77 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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 aren not related in a simple way. whole: -0.09 (0.26), residues: 1013 helix: 0.92 (0.24), residues: 449 sheet: -1.30 (0.40), residues: 140 loop : -0.57 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 420 TYR 0.020 0.001 TYR C 673 PHE 0.012 0.002 PHE B 495 TRP 0.013 0.001 TRP C 766 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8318) covalent geometry : angle 0.49964 (11236) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.96337 ( 8) hydrogen bonds : bond 0.04038 ( 356) hydrogen bonds : angle 4.57711 ( 1046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.304 Fit side-chains REVERT: B 414 MET cc_start: 0.5493 (mtm) cc_final: 0.5102 (ttp) REVERT: C 459 ILE cc_start: 0.7554 (mm) cc_final: 0.7269 (mp) REVERT: A 439 LYS cc_start: 0.7707 (ttpp) cc_final: 0.7432 (ptpt) REVERT: A 471 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7652 (mttm) REVERT: D 408 MET cc_start: 0.7246 (mmt) cc_final: 0.6935 (mmt) REVERT: D 644 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.5398 (tp30) outliers start: 15 outliers final: 6 residues processed: 113 average time/residue: 0.6112 time to fit residues: 72.5790 Evaluate side-chains 112 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 471 LYS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 686 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 0.0010 chunk 38 optimal weight: 2.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.142321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108972 restraints weight = 27126.050| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.68 r_work: 0.3082 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8322 Z= 0.166 Angle : 0.537 7.387 11244 Z= 0.280 Chirality : 0.044 0.229 1239 Planarity : 0.004 0.036 1385 Dihedral : 10.424 106.580 1271 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.33 % Allowed : 22.12 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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 aren not related in a simple way. whole: -0.37 (0.26), residues: 1013 helix: 0.72 (0.24), residues: 449 sheet: -1.59 (0.39), residues: 148 loop : -0.66 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 692 TYR 0.020 0.002 TYR D 673 PHE 0.014 0.002 PHE D 495 TRP 0.013 0.002 TRP A 766 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8318) covalent geometry : angle 0.53598 (11236) SS BOND : bond 0.00083 ( 4) SS BOND : angle 1.11112 ( 8) hydrogen bonds : bond 0.04369 ( 356) hydrogen bonds : angle 4.66213 ( 1046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.339 Fit side-chains REVERT: B 414 MET cc_start: 0.5486 (mtm) cc_final: 0.5131 (ttp) REVERT: B 420 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6748 (ttp-170) REVERT: B 463 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8165 (mtp) REVERT: C 459 ILE cc_start: 0.7558 (mm) cc_final: 0.7279 (mp) REVERT: C 696 SER cc_start: 0.7875 (t) cc_final: 0.7671 (m) REVERT: A 471 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7636 (mttm) REVERT: D 644 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.5350 (tp30) outliers start: 20 outliers final: 10 residues processed: 123 average time/residue: 0.6632 time to fit residues: 85.8499 Evaluate side-chains 120 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 471 LYS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 686 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.109684 restraints weight = 24663.075| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.47 r_work: 0.3090 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8322 Z= 0.135 Angle : 0.495 6.047 11244 Z= 0.262 Chirality : 0.043 0.229 1239 Planarity : 0.003 0.035 1385 Dihedral : 9.701 105.505 1271 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.86 % Allowed : 22.47 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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 aren not related in a simple way. whole: -0.20 (0.26), residues: 1013 helix: 0.83 (0.24), residues: 449 sheet: -1.37 (0.40), residues: 140 loop : -0.62 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 715 TYR 0.019 0.001 TYR D 673 PHE 0.011 0.002 PHE D 495 TRP 0.013 0.001 TRP A 766 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8318) covalent geometry : angle 0.49479 (11236) SS BOND : bond 0.00060 ( 4) SS BOND : angle 0.77171 ( 8) hydrogen bonds : bond 0.03836 ( 356) hydrogen bonds : angle 4.50202 ( 1046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.333 Fit side-chains REVERT: B 414 MET cc_start: 0.5513 (mtm) cc_final: 0.5144 (ttp) REVERT: B 420 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6735 (ttp-110) REVERT: C 459 ILE cc_start: 0.7585 (mm) cc_final: 0.7315 (mp) REVERT: C 696 SER cc_start: 0.7885 (t) cc_final: 0.7666 (m) REVERT: A 471 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7650 (mttm) REVERT: D 644 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.5272 (tp30) REVERT: D 760 ASP cc_start: 0.7423 (m-30) cc_final: 0.7125 (m-30) outliers start: 16 outliers final: 9 residues processed: 119 average time/residue: 0.6890 time to fit residues: 86.1352 Evaluate side-chains 119 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 471 LYS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 686 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109530 restraints weight = 28285.208| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.87 r_work: 0.3052 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8322 Z= 0.132 Angle : 0.485 5.744 11244 Z= 0.258 Chirality : 0.043 0.181 1239 Planarity : 0.003 0.035 1385 Dihedral : 9.376 104.967 1271 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.98 % Allowed : 22.58 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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 aren not related in a simple way. whole: -0.15 (0.26), residues: 1013 helix: 0.88 (0.24), residues: 449 sheet: -1.33 (0.41), residues: 140 loop : -0.61 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 715 TYR 0.022 0.002 TYR C 673 PHE 0.011 0.002 PHE D 495 TRP 0.015 0.001 TRP C 766 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8318) covalent geometry : angle 0.48465 (11236) SS BOND : bond 0.00057 ( 4) SS BOND : angle 0.74940 ( 8) hydrogen bonds : bond 0.03768 ( 356) hydrogen bonds : angle 4.46274 ( 1046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.254 Fit side-chains REVERT: B 414 MET cc_start: 0.5526 (mtm) cc_final: 0.5146 (ttp) REVERT: B 420 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6769 (ttp-110) REVERT: C 459 ILE cc_start: 0.7553 (mm) cc_final: 0.7277 (mp) REVERT: A 471 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7669 (mttm) REVERT: A 708 MET cc_start: 0.8555 (tpt) cc_final: 0.8051 (tpp) REVERT: D 644 GLU cc_start: 0.5769 (OUTLIER) cc_final: 0.5421 (tp30) REVERT: D 760 ASP cc_start: 0.7447 (m-30) cc_final: 0.7163 (m-30) outliers start: 17 outliers final: 10 residues processed: 120 average time/residue: 0.6860 time to fit residues: 86.5396 Evaluate side-chains 119 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 471 LYS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 686 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.111229 restraints weight = 26972.200| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.72 r_work: 0.3101 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8322 Z= 0.110 Angle : 0.457 6.092 11244 Z= 0.246 Chirality : 0.041 0.134 1239 Planarity : 0.003 0.035 1385 Dihedral : 8.922 102.990 1271 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.40 % Allowed : 23.63 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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 aren not related in a simple way. whole: 0.00 (0.26), residues: 1013 helix: 1.05 (0.24), residues: 449 sheet: -1.31 (0.41), residues: 140 loop : -0.57 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 660 TYR 0.015 0.001 TYR B 673 PHE 0.009 0.001 PHE D 495 TRP 0.014 0.001 TRP C 766 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8318) covalent geometry : angle 0.45740 (11236) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.50255 ( 8) hydrogen bonds : bond 0.03319 ( 356) hydrogen bonds : angle 4.32415 ( 1046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.227 Fit side-chains REVERT: B 414 MET cc_start: 0.5537 (mtm) cc_final: 0.5166 (ttp) REVERT: B 420 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6688 (ttp-110) REVERT: C 459 ILE cc_start: 0.7550 (mm) cc_final: 0.7276 (mp) REVERT: C 760 ASP cc_start: 0.8423 (m-30) cc_final: 0.8220 (m-30) REVERT: A 708 MET cc_start: 0.8495 (tpt) cc_final: 0.7993 (tpp) REVERT: D 760 ASP cc_start: 0.7385 (m-30) cc_final: 0.7160 (m-30) outliers start: 12 outliers final: 7 residues processed: 118 average time/residue: 0.6525 time to fit residues: 80.9450 Evaluate side-chains 116 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain D residue 686 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109649 restraints weight = 28234.980| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.88 r_work: 0.3075 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8322 Z= 0.136 Angle : 0.491 6.250 11244 Z= 0.262 Chirality : 0.042 0.134 1239 Planarity : 0.003 0.034 1385 Dihedral : 9.260 107.378 1271 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.63 % Allowed : 23.52 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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 aren not related in a simple way. whole: -0.08 (0.26), residues: 1013 helix: 0.96 (0.24), residues: 449 sheet: -1.30 (0.41), residues: 140 loop : -0.60 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 660 TYR 0.021 0.002 TYR C 673 PHE 0.012 0.002 PHE D 495 TRP 0.014 0.001 TRP C 766 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8318) covalent geometry : angle 0.49030 (11236) SS BOND : bond 0.00062 ( 4) SS BOND : angle 0.74647 ( 8) hydrogen bonds : bond 0.03790 ( 356) hydrogen bonds : angle 4.42997 ( 1046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.281 Fit side-chains REVERT: B 414 MET cc_start: 0.5520 (mtm) cc_final: 0.5131 (ttp) REVERT: B 420 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6759 (ttp-110) REVERT: C 459 ILE cc_start: 0.7535 (mm) cc_final: 0.7256 (mp) REVERT: C 760 ASP cc_start: 0.8454 (m-30) cc_final: 0.8250 (m-30) REVERT: A 471 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7677 (mttm) REVERT: A 708 MET cc_start: 0.8540 (tpt) cc_final: 0.8039 (tpp) REVERT: D 760 ASP cc_start: 0.7393 (m-30) cc_final: 0.7135 (m-30) outliers start: 14 outliers final: 9 residues processed: 118 average time/residue: 0.6035 time to fit residues: 75.0184 Evaluate side-chains 117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 471 LYS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain D residue 686 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108636 restraints weight = 21334.009| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.17 r_work: 0.3078 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8322 Z= 0.150 Angle : 0.511 6.396 11244 Z= 0.273 Chirality : 0.043 0.135 1239 Planarity : 0.003 0.034 1385 Dihedral : 9.366 107.711 1271 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.51 % Allowed : 23.75 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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 aren not related in a simple way. whole: -0.20 (0.26), residues: 1013 helix: 0.85 (0.24), residues: 449 sheet: -1.33 (0.41), residues: 140 loop : -0.66 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 715 TYR 0.022 0.002 TYR C 673 PHE 0.013 0.002 PHE D 495 TRP 0.014 0.001 TRP C 766 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8318) covalent geometry : angle 0.51025 (11236) SS BOND : bond 0.00076 ( 4) SS BOND : angle 0.89040 ( 8) hydrogen bonds : bond 0.03991 ( 356) hydrogen bonds : angle 4.49496 ( 1046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.332 Fit side-chains REVERT: B 414 MET cc_start: 0.5503 (mtm) cc_final: 0.5131 (ttp) REVERT: C 459 ILE cc_start: 0.7517 (mm) cc_final: 0.7238 (mp) REVERT: C 760 ASP cc_start: 0.8386 (m-30) cc_final: 0.8181 (m-30) REVERT: A 471 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7640 (mttm) REVERT: A 708 MET cc_start: 0.8519 (tpt) cc_final: 0.8011 (tpp) REVERT: D 644 GLU cc_start: 0.5755 (OUTLIER) cc_final: 0.5417 (tp30) REVERT: D 760 ASP cc_start: 0.7374 (m-30) cc_final: 0.7094 (m-30) outliers start: 13 outliers final: 8 residues processed: 117 average time/residue: 0.6871 time to fit residues: 84.2995 Evaluate side-chains 117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain A residue 471 LYS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 686 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110635 restraints weight = 22540.059| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.34 r_work: 0.3069 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8322 Z= 0.163 Angle : 0.527 6.427 11244 Z= 0.281 Chirality : 0.043 0.136 1239 Planarity : 0.003 0.034 1385 Dihedral : 9.429 108.174 1271 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.16 % Allowed : 24.10 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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 aren not related in a simple way. whole: -0.36 (0.26), residues: 1013 helix: 0.75 (0.24), residues: 449 sheet: -1.55 (0.40), residues: 148 loop : -0.71 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 660 TYR 0.022 0.002 TYR D 673 PHE 0.014 0.002 PHE D 495 TRP 0.013 0.001 TRP C 766 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8318) covalent geometry : angle 0.52708 (11236) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.94765 ( 8) hydrogen bonds : bond 0.04161 ( 356) hydrogen bonds : angle 4.55123 ( 1046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.273 Fit side-chains REVERT: B 414 MET cc_start: 0.5500 (mtm) cc_final: 0.5130 (ttp) REVERT: C 459 ILE cc_start: 0.7541 (mm) cc_final: 0.7263 (mp) REVERT: C 760 ASP cc_start: 0.8416 (m-30) cc_final: 0.8212 (m-30) REVERT: A 471 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7627 (mttm) REVERT: A 708 MET cc_start: 0.8537 (tpt) cc_final: 0.8030 (tpp) REVERT: D 644 GLU cc_start: 0.5769 (OUTLIER) cc_final: 0.5440 (tp30) REVERT: D 760 ASP cc_start: 0.7417 (m-30) cc_final: 0.7116 (m-30) outliers start: 10 outliers final: 8 residues processed: 113 average time/residue: 0.6428 time to fit residues: 76.3870 Evaluate side-chains 116 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain A residue 471 LYS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 686 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 0.5980 chunk 89 optimal weight: 0.0020 chunk 33 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110661 restraints weight = 28267.347| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.94 r_work: 0.3097 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8322 Z= 0.105 Angle : 0.461 6.686 11244 Z= 0.248 Chirality : 0.041 0.134 1239 Planarity : 0.003 0.034 1385 Dihedral : 9.037 106.400 1271 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.81 % Allowed : 24.56 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % 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 aren not related in a simple way. whole: 0.03 (0.26), residues: 1013 helix: 1.08 (0.24), residues: 449 sheet: -1.27 (0.42), residues: 140 loop : -0.56 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 660 TYR 0.015 0.001 TYR D 673 PHE 0.009 0.001 PHE D 495 TRP 0.013 0.001 TRP C 766 HIS 0.002 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8318) covalent geometry : angle 0.46097 (11236) SS BOND : bond 0.00040 ( 4) SS BOND : angle 0.41480 ( 8) hydrogen bonds : bond 0.03217 ( 356) hydrogen bonds : angle 4.32833 ( 1046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2798.07 seconds wall clock time: 48 minutes 25.19 seconds (2905.19 seconds total)