Starting phenix.real_space_refine on Fri Aug 22 22:58:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fq8_29380/08_2025/8fq8_29380.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fq8_29380/08_2025/8fq8_29380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fq8_29380/08_2025/8fq8_29380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fq8_29380/08_2025/8fq8_29380.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fq8_29380/08_2025/8fq8_29380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fq8_29380/08_2025/8fq8_29380.map" } resolution = 3.11 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= 0.002 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 5332 2.51 5 N 1384 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s 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: 8392 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.12, per 1000 atoms: 0.25 Number of scatterers: 8392 At special positions: 0 Unit cell: (117.189, 89.3255, 84.4085, 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 1608 8.00 N 1384 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 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 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: 0.70 Conformation dependent library (CDL) restraints added in 393.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 22 sheets defined 42.7% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.578A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 421 " --> pdb=" O ASN A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 421' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 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 Processing helix chain 'A' and resid 685 through 695 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 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.510A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.649A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.639A pdb=" N VAL B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.588A 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 487 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 695 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 'D' and resid 423 through 436 removed outlier: 3.543A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 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 removed outlier: 3.599A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 767 Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.468A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA3, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.478A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.478A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 395 through 399 removed outlier: 3.528A pdb=" N LYS B 441 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA8, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.035A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 removed outlier: 8.358A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 509 through 510 removed outlier: 3.504A pdb=" N ARG B 628 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.451A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.054A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.403A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 395 through 399 Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AC1, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.534A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.534A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.564A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 509 through 510 removed outlier: 3.710A pdb=" N ARG D 628 " --> pdb=" O SER D 510 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 999 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: 1.12 Time building geometry restraints manager: 0.97 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: 2630 1.35 - 1.47: 2035 1.47 - 1.60: 3729 1.60 - 1.72: 40 1.72 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " 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 A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.576 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C5 CYZ A1302 " pdb=" C6 CYZ A1302 " ideal model delta sigma weight residual 1.553 1.328 0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11279 1.92 - 3.84: 161 3.84 - 5.76: 33 5.76 - 7.68: 30 7.68 - 9.60: 17 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " 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 B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.32 -9.57 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 110.59 -8.84 3.00e+00 1.11e-01 8.69e+00 angle pdb=" O3 CYZ A1302 " pdb=" S2 CYZ A1302 " pdb=" O4 CYZ A1302 " ideal model delta sigma weight residual 118.35 109.51 8.84 3.00e+00 1.11e-01 8.67e+00 angle pdb=" O3 CYZ D1302 " pdb=" S2 CYZ D1302 " pdb=" O4 CYZ D1302 " ideal model delta sigma weight residual 118.35 109.57 8.78 3.00e+00 1.11e-01 8.57e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.05: 4719 23.05 - 46.10: 441 46.10 - 69.14: 62 69.14 - 92.19: 14 92.19 - 115.24: 12 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 59.79 33.21 1 1.00e+01 1.00e-02 1.57e+01 dihedral pdb=" N2 CYZ B1302 " pdb=" C8 CYZ B1302 " pdb=" N1 CYZ B1302 " pdb=" S1 CYZ B1302 " ideal model delta sinusoidal sigma weight residual 55.73 -59.51 115.24 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" N2 CYZ D1302 " pdb=" C8 CYZ D1302 " pdb=" N1 CYZ D1302 " pdb=" S1 CYZ D1302 " ideal model delta sinusoidal sigma weight residual 55.73 -59.13 114.86 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1182 0.087 - 0.173: 86 0.173 - 0.259: 0 0.259 - 0.346: 0 0.346 - 0.432: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C2 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" C3 CYZ C1302 " pdb=" C7 CYZ C1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" C2 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" C3 CYZ A1302 " pdb=" C7 CYZ A1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" C2 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" C3 CYZ D1302 " pdb=" C7 CYZ D1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 678 " 0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO C 679 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 679 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 679 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 643 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C THR C 643 " 0.020 2.00e-02 2.50e+03 pdb=" O THR C 643 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU C 644 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 631 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.20e+00 pdb=" N PRO C 632 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 632 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 632 " 0.015 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 281 2.71 - 3.26: 8107 3.26 - 3.80: 13551 3.80 - 4.35: 17308 4.35 - 4.90: 29401 Nonbonded interactions: 68648 Sorted by model distance: nonbonded pdb=" OE2 GLU D 705 " pdb=" O HOH D1401 " model vdw 2.160 3.040 nonbonded pdb=" OH TYR C 424 " pdb=" O HOH C1401 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.228 3.040 nonbonded pdb=" O SER B 652 " pdb=" OG SER B 652 " model vdw 2.258 3.040 nonbonded pdb=" O ARG D 692 " pdb=" OG SER D 696 " model vdw 2.262 3.040 ... (remaining 68643 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 773 or resid 1301 through 1302)) 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 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 through 1302)) selection = (chain 'D' 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 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.200 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.230 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 : 0.015 0.243 8542 Z= 0.729 Angle : 0.743 9.599 11528 Z= 0.322 Chirality : 0.063 0.432 1284 Planarity : 0.004 0.039 1422 Dihedral : 18.289 115.238 3288 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 0.34 % Allowed : 24.94 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.44 (0.25), residues: 1044 helix: 0.82 (0.25), residues: 440 sheet: -0.53 (0.41), residues: 148 loop : -1.28 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 684 TYR 0.013 0.001 TYR A 424 PHE 0.017 0.001 PHE D 491 TRP 0.007 0.001 TRP B 767 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.01465 ( 8538) covalent geometry : angle 0.74300 (11520) SS BOND : bond 0.00141 ( 4) SS BOND : angle 0.68665 ( 8) hydrogen bonds : bond 0.18886 ( 341) hydrogen bonds : angle 6.93716 ( 999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 661 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7428 (mtt90) outliers start: 3 outliers final: 3 residues processed: 132 average time/residue: 0.1303 time to fit residues: 22.0648 Evaluate side-chains 128 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 760 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.158842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.137833 restraints weight = 12548.117| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.45 r_work: 0.3659 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 8542 Z= 0.259 Angle : 0.647 7.108 11528 Z= 0.328 Chirality : 0.049 0.199 1284 Planarity : 0.004 0.033 1422 Dihedral : 12.118 108.761 1271 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 3.02 % Allowed : 23.60 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.66 (0.25), residues: 1044 helix: 0.46 (0.25), residues: 438 sheet: -0.85 (0.38), residues: 170 loop : -1.11 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 485 TYR 0.017 0.002 TYR B 673 PHE 0.017 0.002 PHE D 659 TRP 0.007 0.002 TRP C 460 HIS 0.004 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 8538) covalent geometry : angle 0.64681 (11520) SS BOND : bond 0.00162 ( 4) SS BOND : angle 0.94941 ( 8) hydrogen bonds : bond 0.04841 ( 341) hydrogen bonds : angle 5.17773 ( 999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.233 Fit side-chains REVERT: A 661 ARG cc_start: 0.7585 (mtt90) cc_final: 0.7124 (mtt90) REVERT: B 439 LYS cc_start: 0.7003 (ptmt) cc_final: 0.6783 (pttm) REVERT: C 660 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7745 (ttm-80) REVERT: D 422 GLU cc_start: 0.7305 (tp30) cc_final: 0.7101 (pm20) outliers start: 27 outliers final: 18 residues processed: 165 average time/residue: 0.1276 time to fit residues: 26.6721 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.161889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.141521 restraints weight = 12492.067| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.41 r_work: 0.3703 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8542 Z= 0.117 Angle : 0.521 6.526 11528 Z= 0.263 Chirality : 0.044 0.167 1284 Planarity : 0.003 0.027 1422 Dihedral : 10.932 99.492 1269 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.49 % Favored : 97.41 % Rotamer: Outliers : 3.80 % Allowed : 23.15 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.29 (0.26), residues: 1044 helix: 0.86 (0.25), residues: 440 sheet: -0.65 (0.40), residues: 166 loop : -1.02 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 715 TYR 0.011 0.001 TYR A 647 PHE 0.009 0.001 PHE D 491 TRP 0.006 0.001 TRP D 460 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8538) covalent geometry : angle 0.52139 (11520) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.49237 ( 8) hydrogen bonds : bond 0.03329 ( 341) hydrogen bonds : angle 4.66052 ( 999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 661 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7421 (mtt90) REVERT: C 660 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7779 (ttm-80) REVERT: D 422 GLU cc_start: 0.7389 (tp30) cc_final: 0.7093 (pm20) outliers start: 34 outliers final: 22 residues processed: 171 average time/residue: 0.1298 time to fit residues: 28.0000 Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 750 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.160401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139755 restraints weight = 12867.185| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.45 r_work: 0.3683 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8542 Z= 0.140 Angle : 0.534 7.931 11528 Z= 0.269 Chirality : 0.044 0.164 1284 Planarity : 0.004 0.028 1422 Dihedral : 11.162 100.870 1268 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 4.59 % Allowed : 22.04 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.25 (0.26), residues: 1044 helix: 0.96 (0.26), residues: 438 sheet: -0.61 (0.39), residues: 170 loop : -1.09 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 675 TYR 0.012 0.001 TYR B 673 PHE 0.012 0.002 PHE D 491 TRP 0.006 0.001 TRP C 460 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8538) covalent geometry : angle 0.53444 (11520) SS BOND : bond 0.00082 ( 4) SS BOND : angle 0.59139 ( 8) hydrogen bonds : bond 0.03424 ( 341) hydrogen bonds : angle 4.59888 ( 999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 453 ARG cc_start: 0.6848 (ptm160) cc_final: 0.6531 (ptm160) REVERT: A 661 ARG cc_start: 0.7612 (mtt90) cc_final: 0.7288 (mtt90) REVERT: B 439 LYS cc_start: 0.6975 (ptmt) cc_final: 0.6719 (pttm) REVERT: C 660 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7780 (ttm-80) outliers start: 41 outliers final: 33 residues processed: 187 average time/residue: 0.1389 time to fit residues: 32.5031 Evaluate side-chains 182 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 750 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 ASN B 756 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.160816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140160 restraints weight = 12814.028| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.44 r_work: 0.3691 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8542 Z= 0.124 Angle : 0.532 10.888 11528 Z= 0.265 Chirality : 0.043 0.160 1284 Planarity : 0.004 0.027 1422 Dihedral : 10.916 98.588 1268 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.59 % Favored : 97.32 % Rotamer: Outliers : 4.70 % Allowed : 22.48 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.13 (0.26), residues: 1044 helix: 1.08 (0.26), residues: 438 sheet: -0.49 (0.40), residues: 166 loop : -1.08 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 684 TYR 0.011 0.001 TYR B 673 PHE 0.011 0.001 PHE D 491 TRP 0.007 0.001 TRP D 460 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8538) covalent geometry : angle 0.53238 (11520) SS BOND : bond 0.00129 ( 4) SS BOND : angle 0.58182 ( 8) hydrogen bonds : bond 0.03164 ( 341) hydrogen bonds : angle 4.50656 ( 999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: B 439 LYS cc_start: 0.6915 (ptmt) cc_final: 0.6684 (pttm) outliers start: 42 outliers final: 34 residues processed: 192 average time/residue: 0.1424 time to fit residues: 34.4367 Evaluate side-chains 177 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 751 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.0270 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138953 restraints weight = 12687.064| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.48 r_work: 0.3675 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8542 Z= 0.151 Angle : 0.557 9.290 11528 Z= 0.280 Chirality : 0.044 0.165 1284 Planarity : 0.004 0.028 1422 Dihedral : 11.288 102.524 1268 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Rotamer: Outliers : 5.70 % Allowed : 22.48 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.19 (0.26), residues: 1044 helix: 1.01 (0.26), residues: 438 sheet: -0.48 (0.40), residues: 166 loop : -1.10 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 684 TYR 0.012 0.001 TYR C 768 PHE 0.013 0.002 PHE D 491 TRP 0.007 0.001 TRP C 460 HIS 0.004 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8538) covalent geometry : angle 0.55653 (11520) SS BOND : bond 0.00057 ( 4) SS BOND : angle 0.67136 ( 8) hydrogen bonds : bond 0.03431 ( 341) hydrogen bonds : angle 4.55829 ( 999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: B 439 LYS cc_start: 0.6927 (ptmt) cc_final: 0.6695 (pttm) outliers start: 51 outliers final: 44 residues processed: 188 average time/residue: 0.1040 time to fit residues: 24.8648 Evaluate side-chains 183 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 751 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 0.0870 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.163195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142851 restraints weight = 12747.839| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.44 r_work: 0.3724 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8542 Z= 0.100 Angle : 0.528 8.263 11528 Z= 0.264 Chirality : 0.042 0.148 1284 Planarity : 0.004 0.030 1422 Dihedral : 10.326 93.316 1268 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 3.69 % Allowed : 24.83 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 0.01 (0.26), residues: 1044 helix: 1.17 (0.26), residues: 442 sheet: -0.47 (0.40), residues: 166 loop : -0.97 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 684 TYR 0.009 0.001 TYR B 673 PHE 0.008 0.001 PHE D 438 TRP 0.007 0.001 TRP D 460 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8538) covalent geometry : angle 0.52847 (11520) SS BOND : bond 0.00172 ( 4) SS BOND : angle 0.53260 ( 8) hydrogen bonds : bond 0.02724 ( 341) hydrogen bonds : angle 4.35941 ( 999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 721 MET cc_start: 0.7177 (ptp) cc_final: 0.6737 (ttt) REVERT: C 695 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7816 (mtpp) outliers start: 33 outliers final: 28 residues processed: 175 average time/residue: 0.1421 time to fit residues: 31.1803 Evaluate side-chains 179 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 751 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 28 optimal weight: 0.0030 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.162580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.141748 restraints weight = 12583.113| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.46 r_work: 0.3711 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8542 Z= 0.115 Angle : 0.545 9.763 11528 Z= 0.270 Chirality : 0.043 0.167 1284 Planarity : 0.004 0.033 1422 Dihedral : 10.346 95.628 1268 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.13 % Rotamer: Outliers : 4.14 % Allowed : 24.27 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 1044 helix: 1.16 (0.26), residues: 442 sheet: -0.47 (0.40), residues: 166 loop : -0.97 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 684 TYR 0.014 0.001 TYR C 768 PHE 0.011 0.001 PHE D 491 TRP 0.006 0.001 TRP D 460 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8538) covalent geometry : angle 0.54457 (11520) SS BOND : bond 0.00092 ( 4) SS BOND : angle 0.54980 ( 8) hydrogen bonds : bond 0.02902 ( 341) hydrogen bonds : angle 4.36239 ( 999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 661 ARG cc_start: 0.7794 (mpt180) cc_final: 0.7227 (mtm180) REVERT: C 772 GLU cc_start: 0.6477 (tp30) cc_final: 0.6099 (mm-30) outliers start: 37 outliers final: 30 residues processed: 175 average time/residue: 0.1459 time to fit residues: 32.0094 Evaluate side-chains 178 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 751 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.161870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140996 restraints weight = 12690.659| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.47 r_work: 0.3700 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8542 Z= 0.125 Angle : 0.559 9.853 11528 Z= 0.277 Chirality : 0.043 0.170 1284 Planarity : 0.004 0.036 1422 Dihedral : 10.360 97.736 1266 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.13 % Rotamer: Outliers : 4.25 % Allowed : 24.27 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.05 (0.26), residues: 1044 helix: 1.12 (0.26), residues: 442 sheet: -0.49 (0.40), residues: 166 loop : -1.00 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 684 TYR 0.009 0.001 TYR B 673 PHE 0.012 0.001 PHE D 491 TRP 0.006 0.001 TRP C 460 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8538) covalent geometry : angle 0.55886 (11520) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.58838 ( 8) hydrogen bonds : bond 0.03025 ( 341) hydrogen bonds : angle 4.37293 ( 999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 ARG cc_start: 0.6740 (ptm160) cc_final: 0.6525 (ptm160) REVERT: A 721 MET cc_start: 0.7235 (ptp) cc_final: 0.6726 (ttt) REVERT: C 772 GLU cc_start: 0.6566 (tp30) cc_final: 0.6222 (mm-30) outliers start: 38 outliers final: 33 residues processed: 179 average time/residue: 0.1352 time to fit residues: 30.6316 Evaluate side-chains 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 751 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.158710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.137744 restraints weight = 12761.799| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.47 r_work: 0.3658 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8542 Z= 0.192 Angle : 0.609 7.145 11528 Z= 0.308 Chirality : 0.046 0.195 1284 Planarity : 0.004 0.039 1422 Dihedral : 11.405 105.768 1266 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.93 % Favored : 95.98 % Rotamer: Outliers : 4.36 % Allowed : 24.16 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.25 (0.26), residues: 1044 helix: 0.86 (0.25), residues: 440 sheet: -0.50 (0.41), residues: 162 loop : -1.02 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 684 TYR 0.015 0.002 TYR C 768 PHE 0.013 0.002 PHE D 491 TRP 0.007 0.001 TRP C 460 HIS 0.004 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 8538) covalent geometry : angle 0.60887 (11520) SS BOND : bond 0.00076 ( 4) SS BOND : angle 0.81399 ( 8) hydrogen bonds : bond 0.03751 ( 341) hydrogen bonds : angle 4.61389 ( 999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 ARG cc_start: 0.6821 (ptm160) cc_final: 0.6601 (ptm160) REVERT: B 408 MET cc_start: 0.5139 (tpp) cc_final: 0.4759 (mmt) REVERT: B 439 LYS cc_start: 0.6884 (ptmt) cc_final: 0.6681 (pttm) REVERT: C 692 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7495 (ttp-170) outliers start: 39 outliers final: 38 residues processed: 178 average time/residue: 0.1352 time to fit residues: 30.5000 Evaluate side-chains 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 751 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 8 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.161342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141157 restraints weight = 12684.187| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.42 r_work: 0.3700 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8542 Z= 0.117 Angle : 0.559 6.900 11528 Z= 0.281 Chirality : 0.043 0.143 1284 Planarity : 0.004 0.038 1422 Dihedral : 10.451 95.810 1266 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.11 % Favored : 97.80 % Rotamer: Outliers : 4.03 % Allowed : 24.94 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.12 (0.26), residues: 1044 helix: 1.02 (0.26), residues: 442 sheet: -0.56 (0.40), residues: 166 loop : -0.97 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 684 TYR 0.010 0.001 TYR D 711 PHE 0.010 0.001 PHE D 491 TRP 0.006 0.001 TRP D 460 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8538) covalent geometry : angle 0.55889 (11520) SS BOND : bond 0.00073 ( 4) SS BOND : angle 0.58285 ( 8) hydrogen bonds : bond 0.02942 ( 341) hydrogen bonds : angle 4.37948 ( 999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2005.61 seconds wall clock time: 35 minutes 13.58 seconds (2113.58 seconds total)