Starting phenix.real_space_refine on Fri Nov 15 06:28:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq6_29379/11_2024/8fq6_29379.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq6_29379/11_2024/8fq6_29379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq6_29379/11_2024/8fq6_29379.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq6_29379/11_2024/8fq6_29379.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq6_29379/11_2024/8fq6_29379.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq6_29379/11_2024/8fq6_29379.cif" } resolution = 3.14 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= 0.003 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 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8398 Number of models: 1 Model: "" Number of chains: 16 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: 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: 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: 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 5.99, per 1000 atoms: 0.71 Number of scatterers: 8398 At special positions: 0 Unit cell: (117.936, 87.633, 83.538, 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 1614 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 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 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 42 helices and 20 sheets defined 41.0% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.717A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.597A 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 661 removed outlier: 3.867A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.682A 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 714 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.891A 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 463 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.666A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 697 removed outlier: 3.917A pdb=" N LYS C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) 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: 3.847A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.549A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.504A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.531A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.750A 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 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 removed outlier: 3.526A pdb=" N LYS D 761 " --> pdb=" O GLY D 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.874A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.708A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.926A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) 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 sheet with id=AA1, first strand: chain 'B' and resid 440 through 444 removed outlier: 7.067A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 476 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 440 through 444 removed outlier: 7.067A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 476 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.493A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 440 through 444 removed outlier: 3.602A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AA7, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.101A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.616A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 440 through 444 removed outlier: 7.113A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.889A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.639A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.603A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB9, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AC1, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.167A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.607A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 942 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: 2.49 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2630 1.35 - 1.48: 2042 1.48 - 1.60: 3722 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " 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 C1302 " pdb=" C4 CYZ C1302 " 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 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 B1302 " pdb=" C4 CYZ B1302 " 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 B1302 " pdb=" C6 CYZ B1302 " ideal model delta sigma weight residual 1.553 1.331 0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 11314 1.93 - 3.85: 133 3.85 - 5.78: 32 5.78 - 7.70: 26 7.70 - 9.63: 15 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 101.75 111.38 -9.63 3.00e+00 1.11e-01 1.03e+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 101.75 111.26 -9.51 3.00e+00 1.11e-01 1.00e+01 angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 111.22 -9.47 3.00e+00 1.11e-01 9.97e+00 angle pdb=" O3 CYZ B1302 " pdb=" S2 CYZ B1302 " pdb=" O4 CYZ B1302 " ideal model delta sigma weight residual 118.35 109.28 9.07 3.00e+00 1.11e-01 9.15e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.94: 4701 22.94 - 45.88: 454 45.88 - 68.82: 64 68.82 - 91.76: 17 91.76 - 114.70: 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 -86.00 -174.74 88.74 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 177.54 -84.54 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 176.87 -83.87 1 1.00e+01 1.00e-02 8.58e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1182 0.086 - 0.172: 86 0.172 - 0.258: 0 0.258 - 0.345: 0 0.345 - 0.431: 16 Chirality restraints: 1284 Sorted by residual: 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 4.64e+00 chirality pdb=" C2 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" C3 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.43 2.00e-01 2.50e+01 4.57e+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 0.42 2.00e-01 2.50e+01 4.51e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO C 737 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 477 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO C 478 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 478 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 478 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 493 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO C 494 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 494 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 494 " 0.020 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2266 2.80 - 3.33: 7467 3.33 - 3.85: 14006 3.85 - 4.38: 16485 4.38 - 4.90: 28460 Nonbonded interactions: 68684 Sorted by model distance: nonbonded pdb=" OG SER D 654 " pdb=" O HOH D1401 " model vdw 2.275 3.040 nonbonded pdb=" O PHE B 495 " pdb=" O HOH B1401 " model vdw 2.309 3.040 nonbonded pdb=" O PHE D 495 " pdb=" O HOH D1402 " model vdw 2.321 3.040 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.326 3.040 nonbonded pdb=" OH TYR C 424 " pdb=" O HOH C1401 " model vdw 2.327 3.040 ... (remaining 68679 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 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: 2.590 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.400 Find NCS groups from input model: 0.460 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 8538 Z= 0.973 Angle : 0.701 9.626 11520 Z= 0.300 Chirality : 0.061 0.431 1284 Planarity : 0.003 0.044 1422 Dihedral : 18.124 114.699 3288 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 22.04 % Favored : 77.96 % 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: -0.55 (0.26), residues: 1044 helix: 1.02 (0.26), residues: 428 sheet: -1.04 (0.38), residues: 168 loop : -1.44 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 766 HIS 0.001 0.000 HIS C 412 PHE 0.008 0.001 PHE C 495 TYR 0.009 0.001 TYR D 405 ARG 0.004 0.000 ARG B 661 *********************** 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 135 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.002 Fit side-chains REVERT: B 697 LYS cc_start: 0.8345 (ptpp) cc_final: 0.8010 (pttm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2954 time to fit residues: 50.7455 Evaluate side-chains 132 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 0.0070 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8538 Z= 0.338 Angle : 0.587 9.629 11520 Z= 0.291 Chirality : 0.047 0.175 1284 Planarity : 0.004 0.039 1422 Dihedral : 11.225 103.032 1266 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.13 % Allowed : 19.80 % Favored : 77.07 % 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: -0.76 (0.25), residues: 1044 helix: 0.76 (0.26), residues: 432 sheet: -0.99 (0.40), residues: 142 loop : -1.54 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 671 HIS 0.003 0.001 HIS C 435 PHE 0.015 0.002 PHE A 495 TYR 0.012 0.002 TYR A 673 ARG 0.004 0.001 ARG B 692 *********************** 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 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.056 Fit side-chains REVERT: B 438 PHE cc_start: 0.5994 (OUTLIER) cc_final: 0.5498 (p90) REVERT: C 454 ASP cc_start: 0.5958 (OUTLIER) cc_final: 0.5461 (t70) REVERT: D 438 PHE cc_start: 0.6038 (OUTLIER) cc_final: 0.5619 (p90) REVERT: A 440 TYR cc_start: 0.8668 (p90) cc_final: 0.8445 (p90) REVERT: A 454 ASP cc_start: 0.5966 (OUTLIER) cc_final: 0.5625 (t70) REVERT: A 486 GLU cc_start: 0.8421 (tp30) cc_final: 0.7984 (tp30) outliers start: 28 outliers final: 12 residues processed: 155 average time/residue: 0.2882 time to fit residues: 57.0197 Evaluate side-chains 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 438 PHE Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 758 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8538 Z= 0.334 Angle : 0.584 8.199 11520 Z= 0.289 Chirality : 0.046 0.171 1284 Planarity : 0.004 0.046 1422 Dihedral : 11.398 103.931 1266 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.70 % Allowed : 19.13 % Favored : 76.17 % 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: -0.77 (0.25), residues: 1044 helix: 0.69 (0.25), residues: 432 sheet: -0.96 (0.41), residues: 130 loop : -1.49 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.003 0.001 HIS B 412 PHE 0.016 0.002 PHE D 438 TYR 0.014 0.002 TYR C 673 ARG 0.004 0.000 ARG B 692 *********************** 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 173 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: B 438 PHE cc_start: 0.5966 (OUTLIER) cc_final: 0.5464 (p90) REVERT: D 438 PHE cc_start: 0.6017 (OUTLIER) cc_final: 0.5601 (p90) REVERT: D 705 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8037 (mm-30) REVERT: A 454 ASP cc_start: 0.5914 (OUTLIER) cc_final: 0.5571 (t70) outliers start: 42 outliers final: 21 residues processed: 167 average time/residue: 0.2697 time to fit residues: 57.9105 Evaluate side-chains 149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 438 PHE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 758 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8538 Z= 0.205 Angle : 0.511 6.815 11520 Z= 0.253 Chirality : 0.043 0.144 1284 Planarity : 0.004 0.046 1422 Dihedral : 10.947 99.978 1266 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.36 % Allowed : 21.14 % Favored : 75.50 % 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: -0.63 (0.25), residues: 1044 helix: 0.93 (0.26), residues: 432 sheet: -0.78 (0.42), residues: 124 loop : -1.59 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 766 HIS 0.002 0.001 HIS B 412 PHE 0.011 0.001 PHE D 438 TYR 0.011 0.001 TYR A 673 ARG 0.003 0.000 ARG B 715 *********************** 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 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.031 Fit side-chains REVERT: C 454 ASP cc_start: 0.5883 (OUTLIER) cc_final: 0.5410 (t70) REVERT: D 438 PHE cc_start: 0.5895 (OUTLIER) cc_final: 0.5363 (p90) REVERT: D 705 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.7975 (mm-30) outliers start: 30 outliers final: 19 residues processed: 164 average time/residue: 0.2857 time to fit residues: 60.0898 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 438 PHE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 758 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 8538 Z= 0.419 Angle : 0.629 11.636 11520 Z= 0.309 Chirality : 0.049 0.233 1284 Planarity : 0.005 0.050 1422 Dihedral : 11.608 104.976 1266 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.48 % Allowed : 20.47 % Favored : 74.05 % 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: -0.85 (0.25), residues: 1044 helix: 0.56 (0.25), residues: 432 sheet: -1.28 (0.39), residues: 148 loop : -1.35 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 671 HIS 0.004 0.001 HIS B 412 PHE 0.019 0.003 PHE D 438 TYR 0.014 0.002 TYR A 673 ARG 0.005 0.001 ARG B 692 *********************** 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 176 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 0.998 Fit side-chains REVERT: B 438 PHE cc_start: 0.5991 (OUTLIER) cc_final: 0.5499 (p90) REVERT: B 705 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8184 (mm-30) REVERT: C 454 ASP cc_start: 0.5986 (OUTLIER) cc_final: 0.5595 (t70) REVERT: C 668 ASP cc_start: 0.6571 (OUTLIER) cc_final: 0.6167 (m-30) REVERT: D 438 PHE cc_start: 0.5983 (OUTLIER) cc_final: 0.5493 (p90) REVERT: D 457 THR cc_start: 0.7240 (OUTLIER) cc_final: 0.6976 (p) REVERT: D 466 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7995 (pp20) REVERT: D 705 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: A 454 ASP cc_start: 0.5909 (OUTLIER) cc_final: 0.5425 (t70) REVERT: A 668 ASP cc_start: 0.6546 (OUTLIER) cc_final: 0.6125 (m-30) outliers start: 49 outliers final: 27 residues processed: 168 average time/residue: 0.2566 time to fit residues: 56.0240 Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 438 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 668 ASP Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 438 PHE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 758 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 0.0470 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8538 Z= 0.150 Angle : 0.479 6.238 11520 Z= 0.237 Chirality : 0.042 0.139 1284 Planarity : 0.004 0.045 1422 Dihedral : 10.579 95.903 1266 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.79 % Allowed : 24.05 % Favored : 74.16 % 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: -0.55 (0.26), residues: 1044 helix: 0.99 (0.26), residues: 434 sheet: -0.76 (0.42), residues: 124 loop : -1.53 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 766 HIS 0.001 0.000 HIS B 412 PHE 0.008 0.001 PHE B 495 TYR 0.009 0.001 TYR A 673 ARG 0.004 0.000 ARG C 715 *********************** 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 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.980 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 155 average time/residue: 0.2993 time to fit residues: 59.2857 Evaluate side-chains 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 723 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 0.0470 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8538 Z= 0.217 Angle : 0.512 6.417 11520 Z= 0.251 Chirality : 0.043 0.145 1284 Planarity : 0.004 0.044 1422 Dihedral : 10.487 97.876 1266 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.36 % Allowed : 22.37 % Favored : 74.27 % 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: -0.52 (0.26), residues: 1044 helix: 1.02 (0.26), residues: 432 sheet: -1.04 (0.39), residues: 144 loop : -1.42 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.002 0.001 HIS B 412 PHE 0.011 0.001 PHE A 495 TYR 0.010 0.001 TYR A 673 ARG 0.004 0.000 ARG C 715 *********************** 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 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.021 Fit side-chains REVERT: C 454 ASP cc_start: 0.5950 (OUTLIER) cc_final: 0.5416 (t70) REVERT: D 436 CYS cc_start: 0.6239 (OUTLIER) cc_final: 0.5272 (t) REVERT: D 457 THR cc_start: 0.7109 (OUTLIER) cc_final: 0.6868 (p) REVERT: D 466 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8030 (pp20) outliers start: 30 outliers final: 19 residues processed: 156 average time/residue: 0.2868 time to fit residues: 57.4328 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8538 Z= 0.195 Angle : 0.504 6.896 11520 Z= 0.247 Chirality : 0.043 0.176 1284 Planarity : 0.004 0.045 1422 Dihedral : 9.970 96.669 1266 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.80 % Allowed : 22.82 % Favored : 74.38 % 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: -0.50 (0.26), residues: 1044 helix: 1.04 (0.26), residues: 434 sheet: -1.04 (0.39), residues: 144 loop : -1.41 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.002 0.001 HIS B 412 PHE 0.010 0.001 PHE A 495 TYR 0.009 0.001 TYR A 673 ARG 0.004 0.000 ARG C 715 *********************** 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 160 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.032 Fit side-chains REVERT: C 454 ASP cc_start: 0.5917 (OUTLIER) cc_final: 0.5378 (t70) REVERT: D 436 CYS cc_start: 0.6193 (OUTLIER) cc_final: 0.5247 (t) REVERT: D 457 THR cc_start: 0.7109 (OUTLIER) cc_final: 0.6883 (p) REVERT: A 708 MET cc_start: 0.8328 (mtt) cc_final: 0.8078 (mtt) outliers start: 25 outliers final: 20 residues processed: 155 average time/residue: 0.2775 time to fit residues: 55.3917 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 0.0270 chunk 86 optimal weight: 0.0970 chunk 90 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8538 Z= 0.139 Angle : 0.463 6.207 11520 Z= 0.229 Chirality : 0.042 0.204 1284 Planarity : 0.004 0.046 1422 Dihedral : 8.360 89.161 1266 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.35 % Allowed : 23.49 % Favored : 74.16 % 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: -0.32 (0.26), residues: 1044 helix: 1.19 (0.26), residues: 434 sheet: -0.89 (0.38), residues: 152 loop : -1.35 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.003 0.000 HIS B 412 PHE 0.006 0.001 PHE A 495 TYR 0.008 0.001 TYR B 405 ARG 0.003 0.000 ARG C 715 *********************** 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 156 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.868 Fit side-chains REVERT: C 454 ASP cc_start: 0.5861 (OUTLIER) cc_final: 0.5488 (t0) REVERT: C 708 MET cc_start: 0.8268 (mtt) cc_final: 0.7873 (mtt) REVERT: D 454 ASP cc_start: 0.7197 (p0) cc_final: 0.6677 (m-30) REVERT: D 466 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8372 (pp20) outliers start: 21 outliers final: 15 residues processed: 153 average time/residue: 0.2838 time to fit residues: 55.9171 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.0670 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8538 Z= 0.170 Angle : 0.483 6.304 11520 Z= 0.242 Chirality : 0.042 0.149 1284 Planarity : 0.004 0.045 1422 Dihedral : 8.125 88.108 1266 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.90 % Allowed : 24.27 % Favored : 73.83 % 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: -0.33 (0.26), residues: 1044 helix: 1.20 (0.26), residues: 434 sheet: -0.74 (0.42), residues: 124 loop : -1.41 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 766 HIS 0.001 0.000 HIS B 412 PHE 0.008 0.001 PHE A 495 TYR 0.009 0.001 TYR B 405 ARG 0.003 0.000 ARG C 715 ********************** 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 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.947 Fit side-chains REVERT: C 454 ASP cc_start: 0.5720 (OUTLIER) cc_final: 0.5335 (t0) REVERT: C 708 MET cc_start: 0.8306 (mtt) cc_final: 0.7894 (mtt) REVERT: D 454 ASP cc_start: 0.7222 (p0) cc_final: 0.6735 (m-30) outliers start: 17 outliers final: 16 residues processed: 150 average time/residue: 0.3057 time to fit residues: 59.1472 Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 723 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.0670 chunk 84 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 86 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4856 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.149376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124467 restraints weight = 10180.838| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.99 r_work: 0.3230 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8538 Z= 0.145 Angle : 0.468 6.472 11520 Z= 0.233 Chirality : 0.042 0.141 1284 Planarity : 0.004 0.045 1422 Dihedral : 7.544 82.090 1266 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.24 % Allowed : 23.94 % Favored : 73.83 % 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: 1.24 (0.26), residues: 434 sheet: -0.89 (0.38), residues: 152 loop : -1.27 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.001 0.000 HIS B 412 PHE 0.006 0.001 PHE D 495 TYR 0.009 0.001 TYR C 440 ARG 0.003 0.000 ARG C 715 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2164.20 seconds wall clock time: 40 minutes 13.78 seconds (2413.78 seconds total)