Starting phenix.real_space_refine on Fri Nov 15 06:28:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqe_29385/11_2024/8fqe_29385.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqe_29385/11_2024/8fqe_29385.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/8fqe_29385/11_2024/8fqe_29385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqe_29385/11_2024/8fqe_29385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqe_29385/11_2024/8fqe_29385.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqe_29385/11_2024/8fqe_29385.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= 0.002 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 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 8386 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.01, per 1000 atoms: 0.72 Number of scatterers: 8386 At special positions: 0 Unit cell: (118.755, 90.909, 84.357, 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 1602 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 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: 45 helices and 19 sheets defined 42.7% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.635A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 421 " --> pdb=" O ASN A 418 " (cutoff:3.500A) 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 654 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'B' and resid 416 through 419 removed outlier: 4.061A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.572A 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 488 removed outlier: 4.056A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.682A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.898A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.984A 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 411 through 415 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 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 removed outlier: 3.899A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 705 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: 3.504A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.808A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.628A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.578A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.705A 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 758 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 removed outlier: 6.217A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 480 removed outlier: 9.619A pdb=" N ALA A 475 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 480 removed outlier: 9.619A pdb=" N ALA A 475 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.575A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.690A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.690A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.584A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 509 through 510 removed outlier: 3.716A pdb=" N ARG B 628 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.186A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'C' and resid 475 through 480 removed outlier: 7.687A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 503 through 505 Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.560A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 395 through 399 Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'D' and resid 475 through 480 removed outlier: 5.373A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 475 through 480 removed outlier: 5.373A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.695A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 948 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: 2.59 Time building geometry restraints manager: 2.43 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: 2627 1.35 - 1.47: 2029 1.47 - 1.59: 3738 1.59 - 1.72: 40 1.72 - 1.84: 104 Bond restraints: 8538 Sorted by residual: 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 1.48e+02 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 1.47e+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 1.46e+02 bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.575 -0.241 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 1.327 0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 11161 1.87 - 3.75: 253 3.75 - 5.62: 58 5.62 - 7.49: 29 7.49 - 9.36: 19 Bond angle restraints: 11520 Sorted by residual: angle pdb=" C8 CYZ A1302 " pdb=" N1 CYZ A1302 " pdb=" S1 CYZ A1302 " ideal model delta sigma weight residual 117.40 108.04 9.36 3.00e+00 1.11e-01 9.74e+00 angle pdb=" C8 CYZ C1302 " pdb=" N1 CYZ C1302 " pdb=" S1 CYZ C1302 " ideal model delta sigma weight residual 117.40 108.44 8.96 3.00e+00 1.11e-01 8.92e+00 angle pdb=" O3 CYZ D1302 " pdb=" S2 CYZ D1302 " pdb=" O4 CYZ D1302 " ideal model delta sigma weight residual 118.35 109.53 8.82 3.00e+00 1.11e-01 8.65e+00 angle pdb=" O3 CYZ B1302 " pdb=" S2 CYZ B1302 " pdb=" O4 CYZ B1302 " ideal model delta sigma weight residual 118.35 109.69 8.66 3.00e+00 1.11e-01 8.34e+00 angle pdb=" C1 CYZ D1302 " pdb=" C6 CYZ D1302 " pdb=" C5 CYZ D1302 " ideal model delta sigma weight residual 102.82 111.01 -8.19 3.00e+00 1.11e-01 7.46e+00 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.65: 4710 23.65 - 47.31: 447 47.31 - 70.96: 59 70.96 - 94.61: 20 94.61 - 118.27: 12 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: 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 93.00 178.40 -85.40 1 1.00e+01 1.00e-02 8.83e+01 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 -155.20 69.20 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" N2 CYZ C1302 " pdb=" C8 CYZ C1302 " pdb=" N1 CYZ C1302 " pdb=" S1 CYZ C1302 " ideal model delta sinusoidal sigma weight residual 55.73 -62.54 118.27 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1175 0.087 - 0.175: 93 0.175 - 0.262: 0 0.262 - 0.349: 2 0.349 - 0.437: 14 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 2.87 0.44 2.00e-01 2.50e+01 4.77e+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 2.87 0.44 2.00e-01 2.50e+01 4.73e+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 4.71e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 493 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO D 494 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 494 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 494 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 506 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO D 507 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 507 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 507 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 737 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.021 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 174 2.67 - 3.23: 7921 3.23 - 3.78: 13124 3.78 - 4.34: 17849 4.34 - 4.90: 29650 Nonbonded interactions: 68718 Sorted by model distance: nonbonded pdb=" OE2 GLU D 705 " pdb=" O HOH D1401 " model vdw 2.110 3.040 nonbonded pdb=" OH TYR C 424 " pdb=" O HOH C1401 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.208 3.040 nonbonded pdb=" OG SER C 497 " pdb=" O2 CYZ C1302 " model vdw 2.221 3.040 nonbonded pdb=" NE2 GLN B 642 " pdb=" O ILE B 645 " model vdw 2.231 3.120 ... (remaining 68713 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: 2.950 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.600 Find NCS groups from input model: 0.440 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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= 0.992 Angle : 0.830 9.365 11520 Z= 0.376 Chirality : 0.064 0.437 1284 Planarity : 0.004 0.050 1422 Dihedral : 18.706 118.268 3288 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 0.22 % Allowed : 25.28 % 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: -1.27 (0.25), residues: 1044 helix: 0.31 (0.26), residues: 404 sheet: -1.73 (0.39), residues: 164 loop : -1.47 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 767 HIS 0.003 0.001 HIS A 435 PHE 0.016 0.002 PHE C 495 TYR 0.017 0.002 TYR B 647 ARG 0.004 0.001 ARG C 715 *********************** 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 145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.986 Fit side-chains REVERT: B 415 LEU cc_start: 0.7066 (mt) cc_final: 0.6838 (mt) REVERT: C 453 ARG cc_start: 0.5405 (mtt90) cc_final: 0.5110 (mtt90) outliers start: 2 outliers final: 1 residues processed: 144 average time/residue: 0.2149 time to fit residues: 42.1651 Evaluate side-chains 136 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8538 Z= 0.254 Angle : 0.572 6.444 11520 Z= 0.288 Chirality : 0.045 0.151 1284 Planarity : 0.004 0.040 1422 Dihedral : 10.939 104.755 1267 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.59 % Favored : 97.32 % Rotamer: Outliers : 3.24 % Allowed : 21.48 % Favored : 75.28 % 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: -1.24 (0.25), residues: 1044 helix: 0.33 (0.25), residues: 426 sheet: -1.57 (0.40), residues: 142 loop : -1.63 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 460 HIS 0.002 0.001 HIS A 412 PHE 0.010 0.001 PHE C 495 TYR 0.015 0.002 TYR D 647 ARG 0.003 0.000 ARG C 715 *********************** 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 170 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.009 Fit side-chains REVERT: B 642 GLN cc_start: 0.8233 (pp30) cc_final: 0.7952 (pp30) REVERT: D 642 GLN cc_start: 0.8265 (pp30) cc_final: 0.7868 (pp30) outliers start: 29 outliers final: 16 residues processed: 157 average time/residue: 0.2039 time to fit residues: 44.1035 Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 8538 Z= 0.385 Angle : 0.653 6.640 11520 Z= 0.328 Chirality : 0.048 0.143 1284 Planarity : 0.005 0.045 1422 Dihedral : 11.729 109.566 1266 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.14 % Allowed : 22.82 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.45 (0.24), residues: 1044 helix: 0.07 (0.25), residues: 412 sheet: -1.90 (0.38), residues: 148 loop : -1.50 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 460 HIS 0.003 0.001 HIS A 435 PHE 0.013 0.002 PHE A 495 TYR 0.021 0.002 TYR A 647 ARG 0.004 0.000 ARG C 715 *********************** 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 184 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.965 Fit side-chains REVERT: A 498 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8796 (pt) REVERT: A 705 GLU cc_start: 0.7868 (mm-30) cc_final: 0.6583 (mm-30) REVERT: B 414 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.5922 (mmt) REVERT: B 642 GLN cc_start: 0.8407 (pp30) cc_final: 0.8196 (pp30) REVERT: C 657 GLU cc_start: 0.7171 (mp0) cc_final: 0.6919 (mp0) outliers start: 37 outliers final: 27 residues processed: 170 average time/residue: 0.2087 time to fit residues: 49.0227 Evaluate side-chains 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 655 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 705 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8538 Z= 0.169 Angle : 0.518 6.374 11520 Z= 0.258 Chirality : 0.042 0.135 1284 Planarity : 0.003 0.039 1422 Dihedral : 10.266 100.601 1266 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.59 % Favored : 97.32 % Rotamer: Outliers : 2.68 % Allowed : 25.17 % Favored : 72.15 % 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: -1.18 (0.24), residues: 1044 helix: 0.45 (0.25), residues: 424 sheet: -1.62 (0.39), residues: 142 loop : -1.63 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 460 HIS 0.002 0.001 HIS B 412 PHE 0.008 0.001 PHE C 495 TYR 0.010 0.001 TYR D 647 ARG 0.002 0.000 ARG A 453 *********************** 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 179 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.927 Fit side-chains REVERT: A 458 LYS cc_start: 0.6192 (tppt) cc_final: 0.5982 (tppp) REVERT: A 498 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8758 (pt) REVERT: A 705 GLU cc_start: 0.7865 (mm-30) cc_final: 0.6833 (mm-30) REVERT: B 414 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.5866 (mmt) REVERT: B 503 MET cc_start: 0.7425 (ttt) cc_final: 0.7138 (ttp) REVERT: B 642 GLN cc_start: 0.8364 (pp30) cc_final: 0.8156 (pp30) REVERT: D 642 GLN cc_start: 0.8213 (pp30) cc_final: 0.7953 (pp30) outliers start: 24 outliers final: 16 residues processed: 166 average time/residue: 0.2280 time to fit residues: 50.5594 Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8538 Z= 0.201 Angle : 0.532 6.553 11520 Z= 0.262 Chirality : 0.043 0.140 1284 Planarity : 0.004 0.037 1422 Dihedral : 10.462 102.067 1266 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.58 % Allowed : 24.27 % Favored : 72.15 % 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: -1.08 (0.25), residues: 1044 helix: 0.53 (0.25), residues: 424 sheet: -1.76 (0.36), residues: 162 loop : -1.47 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 460 HIS 0.002 0.001 HIS B 412 PHE 0.008 0.001 PHE B 495 TYR 0.020 0.001 TYR A 647 ARG 0.002 0.000 ARG C 715 *********************** 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 182 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 1.008 Fit side-chains REVERT: A 498 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8773 (pt) REVERT: A 503 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7575 (ptp) REVERT: A 705 GLU cc_start: 0.7804 (mm-30) cc_final: 0.6707 (mm-30) REVERT: B 414 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.5917 (mmt) REVERT: B 435 HIS cc_start: 0.6161 (t-90) cc_final: 0.5916 (t-90) REVERT: B 503 MET cc_start: 0.7462 (ttt) cc_final: 0.7190 (ttp) REVERT: C 408 MET cc_start: 0.3496 (OUTLIER) cc_final: 0.3236 (mtm) REVERT: C 421 TYR cc_start: 0.7303 (m-80) cc_final: 0.6936 (m-80) REVERT: D 642 GLN cc_start: 0.8213 (pp30) cc_final: 0.7976 (pp30) outliers start: 32 outliers final: 21 residues processed: 167 average time/residue: 0.2082 time to fit residues: 47.7233 Evaluate side-chains 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 33 optimal weight: 0.0070 chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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: 0.7333 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8538 Z= 0.149 Angle : 0.511 6.252 11520 Z= 0.251 Chirality : 0.042 0.158 1284 Planarity : 0.003 0.036 1422 Dihedral : 9.632 97.988 1266 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.47 % Allowed : 23.71 % 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: -0.88 (0.25), residues: 1044 helix: 0.73 (0.25), residues: 426 sheet: -1.57 (0.38), residues: 142 loop : -1.46 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 460 HIS 0.002 0.000 HIS B 412 PHE 0.007 0.001 PHE B 495 TYR 0.009 0.001 TYR C 421 ARG 0.001 0.000 ARG D 453 *********************** 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 : 1.059 Fit side-chains REVERT: A 498 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8787 (pt) REVERT: A 503 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7561 (ptp) REVERT: A 705 GLU cc_start: 0.7744 (mm-30) cc_final: 0.6763 (mm-30) REVERT: B 414 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.5917 (mmp) REVERT: B 435 HIS cc_start: 0.6050 (t-90) cc_final: 0.5830 (t-90) REVERT: B 629 MET cc_start: 0.5167 (tmm) cc_final: 0.4896 (ppp) REVERT: B 765 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6950 (ttpt) REVERT: C 408 MET cc_start: 0.3264 (OUTLIER) cc_final: 0.2946 (mtm) REVERT: D 642 GLN cc_start: 0.8167 (pp30) cc_final: 0.7795 (pp30) REVERT: D 1301 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6854 (tp30) outliers start: 31 outliers final: 24 residues processed: 171 average time/residue: 0.2116 time to fit residues: 49.2688 Evaluate side-chains 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS 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: 2.9990 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.7369 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8538 Z= 0.198 Angle : 0.540 7.647 11520 Z= 0.265 Chirality : 0.043 0.162 1284 Planarity : 0.003 0.036 1422 Dihedral : 10.096 101.041 1266 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.14 % Allowed : 24.27 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.89 (0.25), residues: 1044 helix: 0.71 (0.25), residues: 426 sheet: -1.73 (0.36), residues: 162 loop : -1.36 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 460 HIS 0.002 0.001 HIS B 412 PHE 0.010 0.001 PHE B 495 TYR 0.020 0.001 TYR A 647 ARG 0.002 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 187 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 1.027 Fit side-chains REVERT: A 498 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8808 (pt) REVERT: A 503 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7544 (ptp) REVERT: A 705 GLU cc_start: 0.7827 (mm-30) cc_final: 0.6760 (mm-30) REVERT: B 414 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.6000 (mmt) REVERT: B 435 HIS cc_start: 0.6145 (t-90) cc_final: 0.5912 (t-90) REVERT: B 765 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6934 (ttpt) REVERT: C 408 MET cc_start: 0.3302 (OUTLIER) cc_final: 0.2968 (mtm) outliers start: 37 outliers final: 27 residues processed: 170 average time/residue: 0.2040 time to fit residues: 48.1467 Evaluate side-chains 172 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 89 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1896 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= 0.171 Angle : 0.539 6.700 11520 Z= 0.263 Chirality : 0.042 0.172 1284 Planarity : 0.003 0.036 1422 Dihedral : 9.726 98.773 1266 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.36 % Allowed : 25.06 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.83 (0.25), residues: 1044 helix: 0.78 (0.25), residues: 428 sheet: -1.60 (0.43), residues: 114 loop : -1.47 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 460 HIS 0.002 0.001 HIS B 412 PHE 0.009 0.001 PHE B 495 TYR 0.019 0.001 TYR A 647 ARG 0.001 0.000 ARG B 628 *********************** 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 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.913 Fit side-chains REVERT: A 498 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8819 (pt) REVERT: A 503 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7603 (ptp) REVERT: A 705 GLU cc_start: 0.7786 (mm-30) cc_final: 0.6770 (mm-30) REVERT: B 414 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6040 (mmt) REVERT: B 435 HIS cc_start: 0.6202 (t-90) cc_final: 0.5986 (t-90) REVERT: B 765 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6872 (ttpt) REVERT: D 642 GLN cc_start: 0.7983 (pp30) cc_final: 0.7744 (pp30) outliers start: 30 outliers final: 24 residues processed: 167 average time/residue: 0.2184 time to fit residues: 49.7498 Evaluate side-chains 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.0010 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 90 optimal weight: 0.0270 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.4844 ------------------------------------------------------------------------------- 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: 0.7318 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8538 Z= 0.156 Angle : 0.535 6.954 11520 Z= 0.260 Chirality : 0.042 0.194 1284 Planarity : 0.003 0.035 1422 Dihedral : 9.197 96.569 1266 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.80 % Allowed : 26.40 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.72 (0.25), residues: 1044 helix: 0.85 (0.25), residues: 432 sheet: -1.47 (0.41), residues: 136 loop : -1.39 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 460 HIS 0.002 0.000 HIS B 412 PHE 0.008 0.001 PHE B 495 TYR 0.020 0.001 TYR A 647 ARG 0.001 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 173 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 498 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8812 (pt) REVERT: A 705 GLU cc_start: 0.7785 (mm-30) cc_final: 0.6813 (mm-30) REVERT: B 402 GLU cc_start: 0.7208 (mt-10) cc_final: 0.7004 (mt-10) REVERT: B 414 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6041 (mmp) REVERT: B 435 HIS cc_start: 0.6109 (t-90) cc_final: 0.5896 (t-90) REVERT: B 705 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: B 765 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6931 (ttpt) outliers start: 25 outliers final: 20 residues processed: 162 average time/residue: 0.2064 time to fit residues: 45.7972 Evaluate side-chains 162 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 0.0670 chunk 64 optimal weight: 0.0170 chunk 51 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- 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: 0.7367 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8538 Z= 0.213 Angle : 0.566 7.102 11520 Z= 0.276 Chirality : 0.043 0.183 1284 Planarity : 0.003 0.036 1422 Dihedral : 9.901 101.378 1266 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.02 % Allowed : 26.29 % Favored : 70.69 % 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: -0.79 (0.25), residues: 1044 helix: 0.79 (0.25), residues: 428 sheet: -1.47 (0.39), residues: 152 loop : -1.42 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 460 HIS 0.002 0.001 HIS B 412 PHE 0.009 0.001 PHE C 495 TYR 0.022 0.001 TYR A 647 ARG 0.002 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 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.913 Fit side-chains REVERT: A 498 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8811 (pt) REVERT: A 705 GLU cc_start: 0.7800 (mm-30) cc_final: 0.6747 (mm-30) REVERT: B 402 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6990 (mt-10) REVERT: B 414 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6036 (mmt) REVERT: B 435 HIS cc_start: 0.6219 (t-90) cc_final: 0.5969 (t-90) REVERT: B 503 MET cc_start: 0.7457 (ttm) cc_final: 0.7212 (ttp) REVERT: B 705 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: B 765 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6893 (ttpt) outliers start: 27 outliers final: 22 residues processed: 157 average time/residue: 0.2082 time to fit residues: 44.8835 Evaluate side-chains 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 769 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 696 SER Chi-restraints excluded: chain D residue 697 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.196736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.172593 restraints weight = 10982.579| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.43 r_work: 0.4003 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8538 Z= 0.204 Angle : 0.566 6.790 11520 Z= 0.276 Chirality : 0.043 0.168 1284 Planarity : 0.003 0.035 1422 Dihedral : 9.970 100.482 1266 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.13 % Allowed : 26.62 % Favored : 70.25 % 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: -0.81 (0.25), residues: 1044 helix: 0.78 (0.25), residues: 428 sheet: -1.30 (0.42), residues: 132 loop : -1.53 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 460 HIS 0.002 0.001 HIS B 412 PHE 0.008 0.001 PHE B 495 TYR 0.020 0.001 TYR A 647 ARG 0.002 0.000 ARG C 715 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2113.24 seconds wall clock time: 39 minutes 27.31 seconds (2367.31 seconds total)