Starting phenix.real_space_refine on Fri Nov 15 03:57:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpk_29367/11_2024/8fpk_29367.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpk_29367/11_2024/8fpk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpk_29367/11_2024/8fpk_29367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpk_29367/11_2024/8fpk_29367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpk_29367/11_2024/8fpk_29367.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpk_29367/11_2024/8fpk_29367.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 7.93, per 1000 atoms: 0.97 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: 2.36 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.12 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: 2.42 Time building geometry restraints manager: 2.58 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 773 or resid 901 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 773 or resid 901 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 773 or resid 901 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 773 or resid 901 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.760 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.760 ------------------------------------------------------------------------------- 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 8318 Z= 1.271 Angle : 0.763 9.852 11236 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (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 TRP 0.009 0.001 TRP A 766 HIS 0.002 0.001 HIS C 412 PHE 0.010 0.002 PHE B 495 TYR 0.022 0.001 TYR A 673 ARG 0.007 0.001 ARG A 660 *********************** 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 : 1.099 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: 1.4335 time to fit residues: 175.2502 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 : 0.933 ------------------------------------------------------------------------------- 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 84 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8318 Z= 0.297 Angle : 0.565 6.424 11236 Z= 0.298 Chirality : 0.045 0.142 1239 Planarity : 0.004 0.033 1385 Dihedral : 11.511 107.919 1281 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.56 % Allowed : 20.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.26), residues: 1013 helix: 0.53 (0.24), residues: 449 sheet: -1.57 (0.39), residues: 148 loop : -0.72 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 766 HIS 0.003 0.001 HIS C 412 PHE 0.014 0.002 PHE B 495 TYR 0.022 0.002 TYR D 673 ARG 0.004 0.001 ARG C 675 *********************** 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 135 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.023 Fit side-chains REVERT: B 414 MET cc_start: 0.5232 (mtm) cc_final: 0.4977 (ttp) REVERT: A 471 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7504 (mttm) REVERT: A 760 ASP cc_start: 0.8294 (m-30) cc_final: 0.8083 (m-30) REVERT: D 644 GLU cc_start: 0.5817 (OUTLIER) cc_final: 0.5377 (tp30) REVERT: D 692 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7555 (ttt90) outliers start: 22 outliers final: 12 residues processed: 126 average time/residue: 1.5411 time to fit residues: 204.1479 Evaluate side-chains 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 459 ILE 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 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 A residue 686 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 686 THR Chi-restraints excluded: chain D residue 692 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8318 Z= 0.209 Angle : 0.502 7.367 11236 Z= 0.264 Chirality : 0.043 0.181 1239 Planarity : 0.003 0.034 1385 Dihedral : 10.766 105.569 1273 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.21 % Allowed : 22.00 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.26), residues: 1013 helix: 0.69 (0.24), residues: 449 sheet: -1.37 (0.40), residues: 140 loop : -0.66 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 766 HIS 0.003 0.001 HIS C 412 PHE 0.011 0.002 PHE B 495 TYR 0.020 0.001 TYR C 673 ARG 0.003 0.000 ARG C 420 *********************** 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 129 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.970 Fit side-chains REVERT: B 414 MET cc_start: 0.5222 (mtm) cc_final: 0.4954 (ttp) REVERT: C 459 ILE cc_start: 0.7623 (mm) cc_final: 0.7357 (mp) REVERT: A 471 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7473 (mttm) REVERT: A 760 ASP cc_start: 0.8205 (m-30) cc_final: 0.7996 (m-30) REVERT: D 644 GLU cc_start: 0.5723 (OUTLIER) cc_final: 0.5219 (tp30) outliers start: 19 outliers final: 9 residues processed: 121 average time/residue: 1.4624 time to fit residues: 186.5106 Evaluate side-chains 118 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 497 SER 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 68 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8318 Z= 0.319 Angle : 0.583 7.296 11236 Z= 0.304 Chirality : 0.046 0.250 1239 Planarity : 0.004 0.034 1385 Dihedral : 10.652 107.745 1273 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.68 % Allowed : 22.00 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1013 helix: 0.42 (0.24), residues: 449 sheet: -1.60 (0.39), residues: 148 loop : -0.81 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 766 HIS 0.004 0.001 HIS C 412 PHE 0.016 0.003 PHE D 495 TYR 0.024 0.002 TYR D 673 ARG 0.005 0.001 ARG A 660 *********************** 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 137 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.937 Fit side-chains REVERT: B 414 MET cc_start: 0.5247 (mtm) cc_final: 0.4992 (ttp) REVERT: B 760 ASP cc_start: 0.7419 (m-30) cc_final: 0.7212 (m-30) REVERT: A 471 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7463 (mttm) REVERT: A 760 ASP cc_start: 0.8170 (m-30) cc_final: 0.7952 (m-30) REVERT: D 644 GLU cc_start: 0.5649 (OUTLIER) cc_final: 0.5221 (tp30) REVERT: D 760 ASP cc_start: 0.7224 (m-30) cc_final: 0.6939 (m-30) outliers start: 23 outliers final: 12 residues processed: 129 average time/residue: 1.4297 time to fit residues: 194.4169 Evaluate side-chains 123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 459 ILE 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 640 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain D residue 459 ILE 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 1 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8318 Z= 0.252 Angle : 0.535 6.241 11236 Z= 0.281 Chirality : 0.044 0.234 1239 Planarity : 0.003 0.033 1385 Dihedral : 10.043 106.317 1273 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.10 % Allowed : 22.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1013 helix: 0.54 (0.24), residues: 449 sheet: -1.38 (0.40), residues: 140 loop : -0.82 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 766 HIS 0.003 0.001 HIS C 412 PHE 0.013 0.002 PHE D 495 TYR 0.021 0.002 TYR D 673 ARG 0.004 0.001 ARG C 660 *********************** 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 130 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.953 Fit side-chains REVERT: B 414 MET cc_start: 0.5258 (mtm) cc_final: 0.4965 (ttp) REVERT: B 756 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6540 (mp10) REVERT: B 760 ASP cc_start: 0.7439 (m-30) cc_final: 0.7158 (m-30) REVERT: A 471 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7457 (mttm) REVERT: A 708 MET cc_start: 0.8583 (tpt) cc_final: 0.8054 (tpp) REVERT: A 760 ASP cc_start: 0.8163 (m-30) cc_final: 0.7945 (m-30) REVERT: D 644 GLU cc_start: 0.5639 (OUTLIER) cc_final: 0.5152 (tp30) REVERT: D 760 ASP cc_start: 0.7213 (m-30) cc_final: 0.6893 (m-30) outliers start: 18 outliers final: 9 residues processed: 122 average time/residue: 1.4360 time to fit residues: 184.6435 Evaluate side-chains 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 756 GLN 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 640 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 686 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 19 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8318 Z= 0.204 Angle : 0.500 5.739 11236 Z= 0.265 Chirality : 0.043 0.209 1239 Planarity : 0.003 0.033 1385 Dihedral : 9.540 104.833 1273 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.33 % Allowed : 22.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1013 helix: 0.72 (0.24), residues: 449 sheet: -1.32 (0.41), residues: 140 loop : -0.77 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 766 HIS 0.002 0.001 HIS C 412 PHE 0.011 0.002 PHE D 495 TYR 0.021 0.001 TYR C 673 ARG 0.004 0.000 ARG C 660 *********************** 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 133 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.998 Fit side-chains REVERT: B 414 MET cc_start: 0.5304 (mtm) cc_final: 0.4978 (ttp) REVERT: B 463 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8261 (mtp) REVERT: B 760 ASP cc_start: 0.7369 (m-30) cc_final: 0.7060 (m-30) REVERT: C 760 ASP cc_start: 0.8271 (m-30) cc_final: 0.8050 (m-30) REVERT: A 471 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7459 (mttm) REVERT: A 708 MET cc_start: 0.8569 (tpt) cc_final: 0.8051 (tpp) REVERT: A 760 ASP cc_start: 0.8168 (m-30) cc_final: 0.7946 (m-30) REVERT: D 644 GLU cc_start: 0.5555 (OUTLIER) cc_final: 0.5108 (tp30) REVERT: D 760 ASP cc_start: 0.7169 (m-30) cc_final: 0.6890 (m-30) outliers start: 20 outliers final: 11 residues processed: 125 average time/residue: 1.4638 time to fit residues: 192.8168 Evaluate side-chains 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 463 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 414 MET 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 A residue 686 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 55 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 57 optimal weight: 0.0270 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8318 Z= 0.192 Angle : 0.487 5.735 11236 Z= 0.260 Chirality : 0.042 0.163 1239 Planarity : 0.003 0.033 1385 Dihedral : 9.119 103.397 1272 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.33 % Allowed : 22.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1013 helix: 0.85 (0.24), residues: 449 sheet: -1.29 (0.41), residues: 140 loop : -0.70 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 766 HIS 0.002 0.001 HIS C 412 PHE 0.010 0.002 PHE D 495 TYR 0.017 0.001 TYR D 673 ARG 0.004 0.000 ARG C 660 *********************** 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 131 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.977 Fit side-chains REVERT: B 414 MET cc_start: 0.5307 (mtm) cc_final: 0.5002 (ttp) REVERT: B 463 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8257 (mtp) REVERT: B 760 ASP cc_start: 0.7242 (m-30) cc_final: 0.6920 (m-30) REVERT: C 760 ASP cc_start: 0.8266 (m-30) cc_final: 0.8043 (m-30) REVERT: A 471 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7460 (mttm) REVERT: A 708 MET cc_start: 0.8566 (tpt) cc_final: 0.8053 (tpp) REVERT: A 760 ASP cc_start: 0.8106 (m-30) cc_final: 0.7875 (m-30) REVERT: D 760 ASP cc_start: 0.7140 (m-30) cc_final: 0.6911 (m-30) outliers start: 20 outliers final: 10 residues processed: 124 average time/residue: 1.4215 time to fit residues: 187.1170 Evaluate side-chains 123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 463 MET Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A 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 686 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 0.0370 chunk 8 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.0970 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8318 Z= 0.200 Angle : 0.494 6.247 11236 Z= 0.264 Chirality : 0.043 0.139 1239 Planarity : 0.003 0.032 1385 Dihedral : 9.285 108.016 1272 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.63 % Allowed : 24.10 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1013 helix: 0.87 (0.24), residues: 449 sheet: -1.28 (0.41), residues: 140 loop : -0.68 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 766 HIS 0.002 0.001 HIS C 412 PHE 0.011 0.002 PHE D 495 TYR 0.021 0.001 TYR C 673 ARG 0.004 0.000 ARG C 660 *********************** 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 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.967 Fit side-chains REVERT: B 414 MET cc_start: 0.5313 (mtm) cc_final: 0.5012 (ttp) REVERT: B 463 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8216 (mtp) REVERT: B 756 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6603 (mp10) REVERT: C 760 ASP cc_start: 0.8280 (m-30) cc_final: 0.8060 (m-30) REVERT: A 471 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7459 (mttm) REVERT: A 708 MET cc_start: 0.8572 (tpt) cc_final: 0.8060 (tpp) REVERT: A 760 ASP cc_start: 0.8092 (m-30) cc_final: 0.7862 (m-30) REVERT: D 760 ASP cc_start: 0.7197 (m-30) cc_final: 0.6961 (m-30) outliers start: 14 outliers final: 9 residues processed: 118 average time/residue: 1.4770 time to fit residues: 183.6227 Evaluate side-chains 120 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 756 GLN Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A 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 A residue 686 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 92 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.0970 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8318 Z= 0.149 Angle : 0.456 6.502 11236 Z= 0.246 Chirality : 0.041 0.134 1239 Planarity : 0.003 0.033 1385 Dihedral : 8.776 104.332 1272 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.28 % Allowed : 24.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1013 helix: 1.09 (0.24), residues: 449 sheet: -1.27 (0.41), residues: 140 loop : -0.57 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 766 HIS 0.002 0.001 HIS B 412 PHE 0.008 0.001 PHE D 495 TYR 0.013 0.001 TYR B 673 ARG 0.003 0.000 ARG C 660 *********************** 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: 11 poor density : 109 time to evaluate : 1.077 Fit side-chains REVERT: B 414 MET cc_start: 0.5333 (mtm) cc_final: 0.5044 (ttp) REVERT: B 756 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6668 (mp10) REVERT: C 760 ASP cc_start: 0.8252 (m-30) cc_final: 0.8051 (m-30) REVERT: A 708 MET cc_start: 0.8538 (tpt) cc_final: 0.8089 (tpp) REVERT: D 644 GLU cc_start: 0.5638 (OUTLIER) cc_final: 0.5412 (tp30) REVERT: D 760 ASP cc_start: 0.7125 (m-30) cc_final: 0.6893 (m-30) outliers start: 11 outliers final: 4 residues processed: 116 average time/residue: 1.4900 time to fit residues: 182.1513 Evaluate side-chains 112 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain D residue 644 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 8318 Z= 0.449 Angle : 0.671 6.406 11236 Z= 0.352 Chirality : 0.049 0.155 1239 Planarity : 0.005 0.046 1385 Dihedral : 9.880 109.041 1271 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.28 % Allowed : 24.21 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.25), residues: 1013 helix: 0.25 (0.24), residues: 449 sheet: -1.61 (0.37), residues: 168 loop : -0.92 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 460 HIS 0.005 0.002 HIS C 412 PHE 0.018 0.003 PHE D 495 TYR 0.031 0.003 TYR D 673 ARG 0.005 0.001 ARG B 684 ********************** 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 118 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.985 Fit side-chains REVERT: B 414 MET cc_start: 0.5254 (mtm) cc_final: 0.4899 (ttp) REVERT: B 756 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6518 (mp10) REVERT: B 760 ASP cc_start: 0.7363 (m-30) cc_final: 0.6986 (m-30) REVERT: C 471 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7481 (mttm) REVERT: C 760 ASP cc_start: 0.8222 (m-30) cc_final: 0.8002 (m-30) REVERT: A 661 ARG cc_start: 0.6556 (ttp-110) cc_final: 0.6181 (tmm-80) REVERT: A 708 MET cc_start: 0.8654 (tpt) cc_final: 0.8115 (tpp) REVERT: D 644 GLU cc_start: 0.5589 (OUTLIER) cc_final: 0.5216 (tp30) REVERT: D 651 ASP cc_start: 0.7525 (m-30) cc_final: 0.7135 (m-30) REVERT: D 760 ASP cc_start: 0.7378 (m-30) cc_final: 0.7052 (m-30) outliers start: 11 outliers final: 4 residues processed: 113 average time/residue: 1.6144 time to fit residues: 191.4004 Evaluate side-chains 112 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain C residue 471 LYS Chi-restraints excluded: chain A residue 457 THR 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 73 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 chunk 14 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.145394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.112927 restraints weight = 24610.259| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.52 r_work: 0.3116 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8318 Z= 0.144 Angle : 0.473 6.846 11236 Z= 0.255 Chirality : 0.041 0.135 1239 Planarity : 0.003 0.032 1385 Dihedral : 9.141 107.772 1271 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.70 % Allowed : 25.15 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 42.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1013 helix: 0.85 (0.24), residues: 449 sheet: -1.29 (0.42), residues: 140 loop : -0.67 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 766 HIS 0.002 0.001 HIS D 412 PHE 0.008 0.001 PHE D 495 TYR 0.018 0.001 TYR D 673 ARG 0.008 0.001 ARG C 660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3434.28 seconds wall clock time: 62 minutes 16.47 seconds (3736.47 seconds total)