Starting phenix.real_space_refine on Sat Jun 7 04:02:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fq8_29380/06_2025/8fq8_29380.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fq8_29380/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fq8_29380/06_2025/8fq8_29380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fq8_29380/06_2025/8fq8_29380.map" model { file = "/net/cci-nas-00/data/ceres_data/8fq8_29380/06_2025/8fq8_29380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fq8_29380/06_2025/8fq8_29380.cif" } resolution = 3.11 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= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.56, per 1000 atoms: 0.78 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: 1.99 Conformation dependent library (CDL) restraints added in 936.5 milliseconds 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: 1.15 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: 2.53 Time building geometry restraints manager: 2.40 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 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 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 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 773 or resid 1301 or resid 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: 3.140 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.390 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.670 ------------------------------------------------------------------------------- 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 (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: -0.44 (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 TRP 0.007 0.001 TRP B 767 HIS 0.002 0.001 HIS C 412 PHE 0.017 0.001 PHE D 491 TYR 0.013 0.001 TYR A 424 ARG 0.008 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.18886 ( 341) hydrogen bonds : angle 6.93716 ( 999) SS BOND : bond 0.00141 ( 4) SS BOND : angle 0.68665 ( 8) covalent geometry : bond 0.01465 ( 8538) covalent geometry : angle 0.74300 (11520) *********************** 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 : 0.973 Fit side-chains revert: symmetry clash REVERT: A 661 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7429 (mtt90) outliers start: 3 outliers final: 3 residues processed: 132 average time/residue: 0.2716 time to fit residues: 46.2857 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 : 0.863 ------------------------------------------------------------------------------- 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 89 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.161928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141308 restraints weight = 12499.816| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.42 r_work: 0.3699 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8542 Z= 0.158 Angle : 0.548 6.601 11528 Z= 0.278 Chirality : 0.045 0.174 1284 Planarity : 0.004 0.028 1422 Dihedral : 11.319 102.683 1271 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.13 % Rotamer: Outliers : 1.90 % Allowed : 23.60 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 1044 helix: 0.88 (0.25), residues: 440 sheet: -0.62 (0.40), residues: 166 loop : -0.97 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 767 HIS 0.003 0.001 HIS A 412 PHE 0.015 0.002 PHE D 491 TYR 0.013 0.002 TYR B 673 ARG 0.004 0.001 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 341) hydrogen bonds : angle 4.90328 ( 999) SS BOND : bond 0.00137 ( 4) SS BOND : angle 0.69886 ( 8) covalent geometry : bond 0.00376 ( 8538) covalent geometry : angle 0.54783 (11520) *********************** 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 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.930 Fit side-chains REVERT: A 661 ARG cc_start: 0.7612 (mtt90) cc_final: 0.7149 (mtt90) REVERT: C 660 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7724 (ttm-80) outliers start: 17 outliers final: 10 residues processed: 156 average time/residue: 0.2951 time to fit residues: 58.2279 Evaluate side-chains 138 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain D residue 491 PHE 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 7 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 0.0670 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.163786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.143343 restraints weight = 12609.144| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.45 r_work: 0.3724 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8542 Z= 0.108 Angle : 0.509 9.711 11528 Z= 0.255 Chirality : 0.042 0.160 1284 Planarity : 0.003 0.027 1422 Dihedral : 10.678 97.438 1268 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.51 % Rotamer: Outliers : 3.58 % Allowed : 23.04 % 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 (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: 1044 helix: 1.15 (0.26), residues: 440 sheet: -0.54 (0.40), residues: 170 loop : -0.98 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 766 HIS 0.003 0.001 HIS C 412 PHE 0.009 0.001 PHE D 491 TYR 0.011 0.001 TYR C 768 ARG 0.005 0.001 ARG D 715 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 341) hydrogen bonds : angle 4.56963 ( 999) SS BOND : bond 0.00147 ( 4) SS BOND : angle 0.53327 ( 8) covalent geometry : bond 0.00254 ( 8538) covalent geometry : angle 0.50880 (11520) *********************** 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 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.934 Fit side-chains REVERT: A 661 ARG cc_start: 0.7540 (mtt90) cc_final: 0.7234 (mtt90) REVERT: C 660 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7742 (ttm-80) outliers start: 32 outliers final: 16 residues processed: 160 average time/residue: 0.2993 time to fit residues: 61.7147 Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 669 LYS 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 748 LEU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 736 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.158583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137560 restraints weight = 12560.912| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.45 r_work: 0.3656 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8542 Z= 0.222 Angle : 0.607 7.893 11528 Z= 0.307 Chirality : 0.047 0.177 1284 Planarity : 0.004 0.028 1422 Dihedral : 11.860 107.196 1268 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.46 % Rotamer: Outliers : 4.59 % Allowed : 22.26 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.29 (0.25), residues: 1044 helix: 0.83 (0.25), residues: 436 sheet: -0.46 (0.40), residues: 162 loop : -1.07 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 460 HIS 0.004 0.001 HIS C 412 PHE 0.014 0.002 PHE D 491 TYR 0.016 0.002 TYR C 424 ARG 0.005 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 341) hydrogen bonds : angle 4.79026 ( 999) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.69850 ( 8) covalent geometry : bond 0.00531 ( 8538) covalent geometry : angle 0.60741 (11520) *********************** 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 196 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 1.125 Fit side-chains REVERT: A 661 ARG cc_start: 0.7669 (mtt90) cc_final: 0.7396 (mtt90) REVERT: B 439 LYS cc_start: 0.6995 (ptmt) cc_final: 0.6738 (pttm) REVERT: C 660 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7749 (ttm-80) REVERT: C 772 GLU cc_start: 0.6294 (tp30) cc_final: 0.6020 (mm-30) REVERT: D 422 GLU cc_start: 0.7219 (tp30) cc_final: 0.7018 (pm20) REVERT: D 466 GLU cc_start: 0.7135 (pt0) cc_final: 0.6811 (pp20) outliers start: 41 outliers final: 32 residues processed: 189 average time/residue: 0.2861 time to fit residues: 68.6881 Evaluate side-chains 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 723 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 750 VAL 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 748 LEU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 498 LEU 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 744 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 458 LYS 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 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 78 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.163347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.142991 restraints weight = 12592.138| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.41 r_work: 0.3723 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8542 Z= 0.103 Angle : 0.527 10.103 11528 Z= 0.264 Chirality : 0.043 0.176 1284 Planarity : 0.004 0.028 1422 Dihedral : 10.450 95.203 1268 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.92 % Favored : 97.99 % Rotamer: Outliers : 3.36 % Allowed : 23.83 % 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 (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: -0.01 (0.26), residues: 1044 helix: 1.20 (0.26), residues: 438 sheet: -0.51 (0.41), residues: 166 loop : -0.99 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 460 HIS 0.003 0.001 HIS C 412 PHE 0.009 0.001 PHE D 491 TYR 0.011 0.001 TYR A 647 ARG 0.006 0.001 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.02838 ( 341) hydrogen bonds : angle 4.39569 ( 999) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.53950 ( 8) covalent geometry : bond 0.00235 ( 8538) covalent geometry : angle 0.52672 (11520) *********************** 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 192 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 453 ARG cc_start: 0.6801 (ptm160) cc_final: 0.6534 (ptm160) REVERT: A 661 ARG cc_start: 0.7553 (mtt90) cc_final: 0.6767 (mtt90) REVERT: C 660 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7716 (ttm-80) REVERT: C 695 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7868 (mtpp) REVERT: C 772 GLU cc_start: 0.6322 (tp30) cc_final: 0.5806 (mm-30) outliers start: 30 outliers final: 24 residues processed: 186 average time/residue: 0.2773 time to fit residues: 65.6489 Evaluate side-chains 175 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 760 ASP 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 748 LEU Chi-restraints excluded: chain C residue 498 LEU 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 31 optimal weight: 0.0980 chunk 16 optimal weight: 0.0570 chunk 87 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 overall best weight: 0.3098 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.165389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.145170 restraints weight = 12481.491| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.43 r_work: 0.3750 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8542 Z= 0.094 Angle : 0.529 8.575 11528 Z= 0.259 Chirality : 0.042 0.179 1284 Planarity : 0.004 0.028 1422 Dihedral : 9.305 84.961 1268 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.01 % Favored : 97.89 % Rotamer: Outliers : 3.47 % Allowed : 24.05 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1044 helix: 1.41 (0.26), residues: 440 sheet: -0.50 (0.40), residues: 166 loop : -0.91 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 460 HIS 0.003 0.001 HIS C 412 PHE 0.008 0.001 PHE D 491 TYR 0.012 0.001 TYR C 768 ARG 0.006 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02489 ( 341) hydrogen bonds : angle 4.25637 ( 999) SS BOND : bond 0.00222 ( 4) SS BOND : angle 1.06333 ( 8) covalent geometry : bond 0.00215 ( 8538) covalent geometry : angle 0.52843 (11520) *********************** 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 186 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 1.285 Fit side-chains REVERT: A 661 ARG cc_start: 0.7497 (mtt90) cc_final: 0.7130 (mtt90) REVERT: B 439 LYS cc_start: 0.6890 (ptmt) cc_final: 0.6666 (pttm) REVERT: C 695 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7809 (mtpp) REVERT: C 772 GLU cc_start: 0.6064 (tp30) cc_final: 0.5665 (mm-30) outliers start: 31 outliers final: 20 residues processed: 179 average time/residue: 0.3388 time to fit residues: 78.7991 Evaluate side-chains 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 727 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 649 THR 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 744 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 760 ASP 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 751 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.163670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.142698 restraints weight = 12571.844| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.47 r_work: 0.3717 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1786 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= 0.116 Angle : 0.562 10.256 11528 Z= 0.273 Chirality : 0.043 0.241 1284 Planarity : 0.004 0.028 1422 Dihedral : 8.865 89.911 1266 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.51 % Rotamer: Outliers : 3.69 % Allowed : 23.83 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1044 helix: 1.34 (0.26), residues: 442 sheet: -0.53 (0.40), residues: 166 loop : -0.85 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 460 HIS 0.003 0.001 HIS C 412 PHE 0.012 0.001 PHE D 491 TYR 0.009 0.001 TYR B 673 ARG 0.007 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 341) hydrogen bonds : angle 4.29016 ( 999) SS BOND : bond 0.00242 ( 4) SS BOND : angle 1.20513 ( 8) covalent geometry : bond 0.00276 ( 8538) covalent geometry : angle 0.56154 (11520) *********************** 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 177 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.890 Fit side-chains REVERT: C 772 GLU cc_start: 0.6196 (tp30) cc_final: 0.5811 (mm-30) outliers start: 33 outliers final: 28 residues processed: 169 average time/residue: 0.2794 time to fit residues: 60.1620 Evaluate side-chains 171 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 681 VAL 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 748 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 27 optimal weight: 0.0020 chunk 100 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 59 optimal weight: 0.0060 overall best weight: 0.5004 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.165322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.145147 restraints weight = 12673.957| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.43 r_work: 0.3751 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8542 Z= 0.099 Angle : 0.523 8.473 11528 Z= 0.259 Chirality : 0.043 0.227 1284 Planarity : 0.004 0.031 1422 Dihedral : 6.913 82.830 1266 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.11 % Favored : 97.80 % Rotamer: Outliers : 3.36 % Allowed : 24.27 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 0.26 (0.26), residues: 1044 helix: 1.46 (0.26), residues: 442 sheet: -0.54 (0.40), residues: 166 loop : -0.85 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 460 HIS 0.003 0.001 HIS C 412 PHE 0.009 0.001 PHE D 491 TYR 0.013 0.001 TYR C 768 ARG 0.007 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02496 ( 341) hydrogen bonds : angle 4.21135 ( 999) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.99744 ( 8) covalent geometry : bond 0.00231 ( 8538) covalent geometry : angle 0.52274 (11520) *********************** 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 181 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.893 Fit side-chains REVERT: A 661 ARG cc_start: 0.7360 (mtt-85) cc_final: 0.7118 (mtt90) REVERT: B 439 LYS cc_start: 0.6855 (ptmt) cc_final: 0.6652 (pttm) REVERT: C 772 GLU cc_start: 0.6031 (tp30) cc_final: 0.5686 (mm-30) outliers start: 30 outliers final: 24 residues processed: 174 average time/residue: 0.2615 time to fit residues: 58.8331 Evaluate side-chains 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 727 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 669 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 0.0270 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.164576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143710 restraints weight = 12640.504| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.47 r_work: 0.3729 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1968 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= 0.111 Angle : 0.560 11.945 11528 Z= 0.276 Chirality : 0.043 0.205 1284 Planarity : 0.004 0.034 1422 Dihedral : 6.473 79.247 1266 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 3.13 % Allowed : 24.50 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 0.25 (0.26), residues: 1044 helix: 1.42 (0.26), residues: 442 sheet: -0.56 (0.40), residues: 166 loop : -0.80 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 460 HIS 0.003 0.001 HIS C 412 PHE 0.010 0.001 PHE D 491 TYR 0.007 0.001 TYR C 424 ARG 0.008 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.02657 ( 341) hydrogen bonds : angle 4.23449 ( 999) SS BOND : bond 0.00130 ( 4) SS BOND : angle 1.03354 ( 8) covalent geometry : bond 0.00265 ( 8538) covalent geometry : angle 0.55989 (11520) *********************** 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 173 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 661 ARG cc_start: 0.7352 (mtt-85) cc_final: 0.6654 (mtt90) REVERT: B 414 MET cc_start: 0.4797 (pmm) cc_final: 0.4238 (pmm) REVERT: B 439 LYS cc_start: 0.6836 (ptmt) cc_final: 0.6614 (pttm) REVERT: C 660 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7648 (ttp-110) REVERT: C 772 GLU cc_start: 0.6088 (tp30) cc_final: 0.5727 (mm-30) outliers start: 28 outliers final: 26 residues processed: 167 average time/residue: 0.2765 time to fit residues: 59.9002 Evaluate side-chains 173 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 669 LYS 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 750 VAL Chi-restraints excluded: chain C residue 760 ASP 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 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 43 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.160601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.139427 restraints weight = 12597.107| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.47 r_work: 0.3677 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8542 Z= 0.173 Angle : 0.605 11.464 11528 Z= 0.303 Chirality : 0.046 0.215 1284 Planarity : 0.004 0.036 1422 Dihedral : 7.239 94.587 1266 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.17 % Rotamer: Outliers : 2.91 % Allowed : 24.83 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.01 (0.26), residues: 1044 helix: 1.06 (0.25), residues: 442 sheet: -0.43 (0.40), residues: 162 loop : -0.88 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 460 HIS 0.003 0.001 HIS C 412 PHE 0.013 0.002 PHE D 491 TYR 0.016 0.002 TYR C 768 ARG 0.008 0.001 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 341) hydrogen bonds : angle 4.47690 ( 999) SS BOND : bond 0.00182 ( 4) SS BOND : angle 1.45892 ( 8) covalent geometry : bond 0.00417 ( 8538) covalent geometry : angle 0.60384 (11520) ********************** 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 172 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.934 Fit side-chains REVERT: B 439 LYS cc_start: 0.6990 (ptmt) cc_final: 0.6745 (pttm) REVERT: C 660 ARG cc_start: 0.7885 (ttm-80) cc_final: 0.7677 (ttp-110) outliers start: 26 outliers final: 25 residues processed: 168 average time/residue: 0.2796 time to fit residues: 59.9746 Evaluate side-chains 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 645 ILE 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 750 VAL Chi-restraints excluded: chain C residue 760 ASP 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 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 18 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 92 optimal weight: 0.0670 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.162738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.142002 restraints weight = 12768.129| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.47 r_work: 0.3708 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8542 Z= 0.121 Angle : 0.590 13.201 11528 Z= 0.293 Chirality : 0.044 0.244 1284 Planarity : 0.004 0.038 1422 Dihedral : 6.989 93.503 1266 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.20 % Favored : 97.70 % Rotamer: Outliers : 2.91 % Allowed : 25.39 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 1044 helix: 1.15 (0.26), residues: 442 sheet: -0.57 (0.40), residues: 166 loop : -0.85 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 460 HIS 0.003 0.001 HIS C 412 PHE 0.010 0.001 PHE D 491 TYR 0.010 0.001 TYR A 647 ARG 0.008 0.001 ARG B 684 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 341) hydrogen bonds : angle 4.32794 ( 999) SS BOND : bond 0.00149 ( 4) SS BOND : angle 1.11447 ( 8) covalent geometry : bond 0.00290 ( 8538) covalent geometry : angle 0.58898 (11520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4655.05 seconds wall clock time: 82 minutes 40.92 seconds (4960.92 seconds total)