Starting phenix.real_space_refine on Sun May 11 21:03:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fq2_29375/05_2025/8fq2_29375.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fq2_29375/05_2025/8fq2_29375.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/cci-nas-00/data/ceres_data/8fq2_29375/05_2025/8fq2_29375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fq2_29375/05_2025/8fq2_29375.map" model { file = "/net/cci-nas-00/data/ceres_data/8fq2_29375/05_2025/8fq2_29375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fq2_29375/05_2025/8fq2_29375.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 5338 2.51 5 N 1386 2.21 5 O 1598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8390 Number of models: 1 Model: "" Number of chains: 6 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: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2115 Classifications: {'peptide': 270} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 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: 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} Restraints were copied for chains: D, C Time building chain proxies: 5.86, per 1000 atoms: 0.70 Number of scatterers: 8390 At special positions: 0 Unit cell: (118.755, 90.909, 85.176, 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 1598 8.00 N 1386 7.00 C 5338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 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: 44 helices and 20 sheets defined 41.9% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 417 through 421 removed outlier: 4.052A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR A 421 " --> pdb=" O ASN A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 421' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.502A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.658A pdb=" N LYS A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 662 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.795A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.595A 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 636 through 642 removed outlier: 3.826A pdb=" N SER D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.514A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.795A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.595A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 636 through 642 removed outlier: 3.827A pdb=" N SER B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.514A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 417 through 421 removed outlier: 4.052A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR C 421 " --> pdb=" O ASN C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 421' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.503A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.658A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 662 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 697 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 sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 removed outlier: 6.446A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.743A 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 452 through 453 removed outlier: 3.690A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN A 461 " --> pdb=" O ALA A 452 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 480 removed outlier: 9.826A pdb=" N ALA A 475 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 480 removed outlier: 9.826A pdb=" N ALA A 475 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA A 477 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA A 735 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.385A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 395 through 399 removed outlier: 6.999A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.731A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 475 through 480 removed outlier: 9.731A pdb=" N ALA D 475 " --> pdb=" O PRO D 737 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ALA D 477 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA D 735 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS D 730 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.386A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 395 through 399 removed outlier: 6.999A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.731A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.731A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS B 730 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.386A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.446A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.690A pdb=" N ALA C 452 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN C 461 " --> pdb=" O ALA C 452 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 475 through 480 removed outlier: 9.827A pdb=" N ALA C 475 " --> pdb=" O PRO C 737 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 475 through 480 removed outlier: 9.827A pdb=" N ALA C 475 " --> pdb=" O PRO C 737 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA C 477 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA C 735 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.385A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 912 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: 2.11 Time building geometry restraints manager: 2.12 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: 2046 1.48 - 1.60: 3726 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8546 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 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 C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CYZ D1302 " pdb=" C6 CYZ D1302 " ideal model delta sigma weight residual 1.553 1.330 0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 8541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11257 1.95 - 3.90: 185 3.90 - 5.85: 42 5.85 - 7.80: 32 7.80 - 9.75: 12 Bond angle restraints: 11528 Sorted by residual: angle pdb=" CA MET C 407 " pdb=" CB MET C 407 " pdb=" CG MET C 407 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA MET A 407 " pdb=" CB MET A 407 " pdb=" CG MET A 407 " ideal model delta sigma weight residual 114.10 121.56 -7.46 2.00e+00 2.50e-01 1.39e+01 angle pdb=" C9 CYZ A1302 " pdb=" S1 CYZ A1302 " pdb=" N1 CYZ A1302 " ideal model delta sigma weight residual 101.75 111.50 -9.75 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.44 -9.69 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CB GLU D 416 " pdb=" CG GLU D 416 " pdb=" CD GLU D 416 " ideal model delta sigma weight residual 112.60 118.04 -5.44 1.70e+00 3.46e-01 1.02e+01 ... (remaining 11523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.96: 4879 22.96 - 45.91: 313 45.91 - 68.87: 31 68.87 - 91.83: 20 91.83 - 114.79: 10 Dihedral angle restraints: 5253 sinusoidal: 2201 harmonic: 3052 Sorted by residual: 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 -59.06 114.79 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" N2 CYZ A1302 " pdb=" C8 CYZ A1302 " pdb=" N1 CYZ A1302 " pdb=" S1 CYZ A1302 " ideal model delta sinusoidal sigma weight residual 55.73 -58.98 114.71 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" N2 CYZ D1302 " pdb=" C8 CYZ D1302 " pdb=" N1 CYZ D1302 " pdb=" S1 CYZ D1302 " ideal model delta sinusoidal sigma weight residual 55.73 -56.68 112.41 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 5250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1167 0.084 - 0.169: 101 0.169 - 0.253: 0 0.253 - 0.338: 0 0.338 - 0.422: 16 Chirality restraints: 1284 Sorted by residual: 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 2.89 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C8 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" N1 CYZ C1302 " pdb=" N2 CYZ C1302 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.42 2.00e-01 2.50e+01 4.46e+00 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 2.89 0.42 2.00e-01 2.50e+01 4.45e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 695 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LYS D 695 " 0.024 2.00e-02 2.50e+03 pdb=" O LYS D 695 " -0.009 2.00e-02 2.50e+03 pdb=" N SER D 696 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 695 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C LYS B 695 " 0.024 2.00e-02 2.50e+03 pdb=" O LYS B 695 " -0.009 2.00e-02 2.50e+03 pdb=" N SER B 696 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 660 " -0.083 9.50e-02 1.11e+02 3.75e-02 1.12e+00 pdb=" NE ARG D 660 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG D 660 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 660 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 660 " -0.000 2.00e-02 2.50e+03 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 69 2.61 - 3.18: 7019 3.18 - 3.75: 12763 3.75 - 4.33: 17893 4.33 - 4.90: 30160 Nonbonded interactions: 67904 Sorted by model distance: nonbonded pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " model vdw 2.034 3.760 nonbonded pdb=" OE1 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.235 3.040 nonbonded pdb=" O ARG D 692 " pdb=" OG SER D 696 " model vdw 2.265 3.040 nonbonded pdb=" O ARG B 692 " pdb=" OG SER B 696 " model vdw 2.266 3.040 ... (remaining 67899 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } 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: 1.940 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.060 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 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 8549 Z= 0.726 Angle : 0.757 9.755 11534 Z= 0.332 Chirality : 0.062 0.422 1284 Planarity : 0.003 0.037 1422 Dihedral : 15.953 114.786 3296 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.67 % Allowed : 0.45 % Favored : 98.88 % 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: -0.58 (0.25), residues: 1044 helix: 0.66 (0.26), residues: 380 sheet: -0.24 (0.38), residues: 190 loop : -1.29 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 767 HIS 0.002 0.001 HIS C 412 PHE 0.013 0.001 PHE A 438 TYR 0.014 0.001 TYR A 647 ARG 0.009 0.000 ARG D 660 Details of bonding type rmsd hydrogen bonds : bond 0.19513 ( 308) hydrogen bonds : angle 6.31505 ( 912) SS BOND : bond 0.00173 ( 3) SS BOND : angle 0.23286 ( 6) covalent geometry : bond 0.01456 ( 8546) covalent geometry : angle 0.75727 (11528) *********************** 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 146 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.948 Fit side-chains REVERT: D 503 MET cc_start: 0.6505 (ttm) cc_final: 0.6265 (ttm) REVERT: B 503 MET cc_start: 0.6510 (ttm) cc_final: 0.6256 (ttm) outliers start: 6 outliers final: 2 residues processed: 143 average time/residue: 0.2286 time to fit residues: 43.5402 Evaluate side-chains 125 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain B residue 644 GLU 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: 8.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.190720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.171706 restraints weight = 11219.689| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.87 r_work: 0.3964 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8549 Z= 0.175 Angle : 0.620 9.312 11534 Z= 0.308 Chirality : 0.048 0.204 1284 Planarity : 0.004 0.027 1422 Dihedral : 10.992 98.492 1272 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.45 % Allowed : 7.48 % Favored : 91.07 % 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: -0.78 (0.25), residues: 1044 helix: 0.48 (0.25), residues: 410 sheet: -0.53 (0.39), residues: 168 loop : -1.38 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 767 HIS 0.001 0.001 HIS D 435 PHE 0.014 0.002 PHE C 491 TYR 0.017 0.002 TYR C 405 ARG 0.004 0.001 ARG D 660 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 308) hydrogen bonds : angle 5.01623 ( 912) SS BOND : bond 0.00221 ( 3) SS BOND : angle 0.71162 ( 6) covalent geometry : bond 0.00419 ( 8546) covalent geometry : angle 0.62025 (11528) *********************** 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 132 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.6274 (ttp) cc_final: 0.6058 (ttm) REVERT: A 710 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: D 407 MET cc_start: 0.7167 (mtt) cc_final: 0.6655 (mtt) REVERT: B 407 MET cc_start: 0.7126 (mtt) cc_final: 0.6633 (mtt) REVERT: C 463 MET cc_start: 0.6099 (ttt) cc_final: 0.5803 (ttm) REVERT: C 710 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7312 (mp0) outliers start: 13 outliers final: 9 residues processed: 130 average time/residue: 0.2196 time to fit residues: 38.2061 Evaluate side-chains 117 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 723 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 86 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.191778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172813 restraints weight = 11443.240| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.90 r_work: 0.3966 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8549 Z= 0.141 Angle : 0.564 9.872 11534 Z= 0.278 Chirality : 0.045 0.161 1284 Planarity : 0.004 0.045 1422 Dihedral : 10.737 95.537 1266 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.67 % Allowed : 11.61 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1044 helix: 0.47 (0.25), residues: 410 sheet: -0.52 (0.41), residues: 148 loop : -1.50 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 767 HIS 0.002 0.001 HIS B 412 PHE 0.011 0.002 PHE A 491 TYR 0.013 0.001 TYR C 405 ARG 0.003 0.000 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 308) hydrogen bonds : angle 4.81244 ( 912) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.65382 ( 6) covalent geometry : bond 0.00337 ( 8546) covalent geometry : angle 0.56425 (11528) *********************** 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 122 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 1.035 Fit side-chains REVERT: A 463 MET cc_start: 0.6317 (ttp) cc_final: 0.6012 (ttm) REVERT: C 463 MET cc_start: 0.6152 (ttt) cc_final: 0.5841 (ttm) outliers start: 6 outliers final: 4 residues processed: 119 average time/residue: 0.2377 time to fit residues: 37.2778 Evaluate side-chains 114 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 447 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 77 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 412 HIS A 714 GLN C 411 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.187268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.168466 restraints weight = 11416.924| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.89 r_work: 0.3928 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8549 Z= 0.185 Angle : 0.617 10.990 11534 Z= 0.305 Chirality : 0.047 0.166 1284 Planarity : 0.004 0.053 1422 Dihedral : 11.042 96.464 1266 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.46 % Allowed : 13.06 % Favored : 84.49 % 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: -1.25 (0.25), residues: 1044 helix: 0.18 (0.25), residues: 412 sheet: -0.95 (0.40), residues: 158 loop : -1.66 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 767 HIS 0.002 0.001 HIS B 412 PHE 0.013 0.002 PHE B 438 TYR 0.013 0.002 TYR C 405 ARG 0.005 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 308) hydrogen bonds : angle 4.92829 ( 912) SS BOND : bond 0.00127 ( 3) SS BOND : angle 0.68559 ( 6) covalent geometry : bond 0.00442 ( 8546) covalent geometry : angle 0.61692 (11528) *********************** 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 140 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.6480 (ttp) cc_final: 0.6159 (ttm) REVERT: A 710 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: A 752 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8174 (tttt) REVERT: C 407 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.5481 (mmt) REVERT: C 413 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.5838 (mm-30) REVERT: C 463 MET cc_start: 0.6224 (ttt) cc_final: 0.5966 (ttm) REVERT: C 710 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7277 (mp0) outliers start: 22 outliers final: 8 residues processed: 133 average time/residue: 0.2424 time to fit residues: 42.4502 Evaluate side-chains 122 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 710 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 27 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 412 HIS ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.189403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.170945 restraints weight = 11348.557| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.87 r_work: 0.3946 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8549 Z= 0.138 Angle : 0.565 10.074 11534 Z= 0.279 Chirality : 0.045 0.135 1284 Planarity : 0.004 0.050 1422 Dihedral : 10.700 93.692 1266 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.90 % Allowed : 16.41 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.25), residues: 1044 helix: 0.25 (0.25), residues: 412 sheet: -0.87 (0.41), residues: 146 loop : -1.61 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 767 HIS 0.001 0.001 HIS B 412 PHE 0.010 0.002 PHE A 491 TYR 0.011 0.001 TYR A 405 ARG 0.005 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 308) hydrogen bonds : angle 4.77692 ( 912) SS BOND : bond 0.00152 ( 3) SS BOND : angle 0.53129 ( 6) covalent geometry : bond 0.00329 ( 8546) covalent geometry : angle 0.56484 (11528) *********************** 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 134 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.008 Fit side-chains REVERT: A 463 MET cc_start: 0.6386 (ttp) cc_final: 0.6165 (ttm) REVERT: A 710 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: C 407 MET cc_start: 0.6166 (OUTLIER) cc_final: 0.5251 (mmt) REVERT: C 463 MET cc_start: 0.6289 (ttt) cc_final: 0.6052 (ttm) REVERT: C 710 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7356 (mp0) outliers start: 17 outliers final: 9 residues processed: 127 average time/residue: 0.2435 time to fit residues: 41.0166 Evaluate side-chains 123 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 713 GLU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 710 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 15 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 412 HIS C 411 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.190698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.171900 restraints weight = 11355.989| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.89 r_work: 0.3954 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8549 Z= 0.125 Angle : 0.562 10.194 11534 Z= 0.275 Chirality : 0.044 0.134 1284 Planarity : 0.004 0.042 1422 Dihedral : 10.478 91.771 1266 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.90 % Allowed : 17.08 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.16 (0.25), residues: 1044 helix: 0.27 (0.25), residues: 416 sheet: -0.93 (0.41), residues: 146 loop : -1.63 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 767 HIS 0.001 0.001 HIS B 412 PHE 0.012 0.002 PHE D 438 TYR 0.010 0.001 TYR A 405 ARG 0.006 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 308) hydrogen bonds : angle 4.70642 ( 912) SS BOND : bond 0.00110 ( 3) SS BOND : angle 0.49438 ( 6) covalent geometry : bond 0.00299 ( 8546) covalent geometry : angle 0.56208 (11528) *********************** 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 129 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 1.001 Fit side-chains REVERT: A 710 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: C 407 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.5262 (mmt) REVERT: C 710 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7318 (mp0) outliers start: 17 outliers final: 10 residues processed: 122 average time/residue: 0.2320 time to fit residues: 37.7726 Evaluate side-chains 121 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 713 GLU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 710 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.0020 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN C 411 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.189781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.170847 restraints weight = 11507.844| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 1.91 r_work: 0.3942 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8549 Z= 0.141 Angle : 0.589 10.751 11534 Z= 0.287 Chirality : 0.045 0.155 1284 Planarity : 0.004 0.060 1422 Dihedral : 10.519 91.585 1266 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.34 % Allowed : 18.19 % Favored : 79.46 % 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: 0.21 (0.25), residues: 416 sheet: -1.00 (0.41), residues: 146 loop : -1.68 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 767 HIS 0.001 0.001 HIS B 412 PHE 0.010 0.002 PHE A 491 TYR 0.011 0.001 TYR A 405 ARG 0.006 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 308) hydrogen bonds : angle 4.74607 ( 912) SS BOND : bond 0.00109 ( 3) SS BOND : angle 0.49698 ( 6) covalent geometry : bond 0.00338 ( 8546) covalent geometry : angle 0.58894 (11528) *********************** 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 134 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.895 Fit side-chains REVERT: A 413 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.5450 (mm-30) REVERT: A 710 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: C 407 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5168 (mmt) REVERT: C 710 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7315 (mp0) outliers start: 21 outliers final: 11 residues processed: 125 average time/residue: 0.2328 time to fit residues: 38.7034 Evaluate side-chains 124 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 487 GLU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 710 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN C 411 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.185596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.166577 restraints weight = 11579.617| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.90 r_work: 0.3898 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8549 Z= 0.223 Angle : 0.678 11.174 11534 Z= 0.336 Chirality : 0.049 0.228 1284 Planarity : 0.005 0.068 1422 Dihedral : 11.271 97.656 1266 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.90 % Allowed : 18.30 % Favored : 78.79 % 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: -1.49 (0.24), residues: 1044 helix: -0.01 (0.25), residues: 410 sheet: -1.17 (0.44), residues: 118 loop : -1.76 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 767 HIS 0.002 0.001 HIS A 412 PHE 0.014 0.003 PHE D 438 TYR 0.014 0.002 TYR A 424 ARG 0.006 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 308) hydrogen bonds : angle 5.08676 ( 912) SS BOND : bond 0.00085 ( 3) SS BOND : angle 0.56040 ( 6) covalent geometry : bond 0.00535 ( 8546) covalent geometry : angle 0.67782 (11528) *********************** 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 137 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5412 (mm-30) REVERT: A 710 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: C 407 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5246 (mmt) REVERT: C 637 GLU cc_start: 0.7916 (tp30) cc_final: 0.7644 (tp30) REVERT: C 710 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7289 (mp0) outliers start: 26 outliers final: 11 residues processed: 126 average time/residue: 0.2342 time to fit residues: 39.2476 Evaluate side-chains 126 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 713 GLU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 723 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 26 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 412 HIS C 411 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.190241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.171553 restraints weight = 11666.178| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 1.91 r_work: 0.3953 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8549 Z= 0.116 Angle : 0.587 9.998 11534 Z= 0.289 Chirality : 0.044 0.135 1284 Planarity : 0.004 0.065 1422 Dihedral : 10.496 91.712 1266 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.45 % Allowed : 20.09 % Favored : 78.46 % 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: -1.30 (0.25), residues: 1044 helix: 0.21 (0.25), residues: 414 sheet: -1.16 (0.41), residues: 146 loop : -1.71 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 671 HIS 0.002 0.001 HIS D 435 PHE 0.009 0.001 PHE A 491 TYR 0.011 0.001 TYR C 440 ARG 0.008 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 308) hydrogen bonds : angle 4.80212 ( 912) SS BOND : bond 0.00086 ( 3) SS BOND : angle 0.42723 ( 6) covalent geometry : bond 0.00273 ( 8546) covalent geometry : angle 0.58740 (11528) *********************** 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 132 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.897 Fit side-chains REVERT: A 710 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: C 407 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5125 (mmt) REVERT: C 637 GLU cc_start: 0.7833 (tp30) cc_final: 0.7562 (tp30) REVERT: C 710 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7337 (mp0) outliers start: 13 outliers final: 8 residues processed: 126 average time/residue: 0.2365 time to fit residues: 39.5385 Evaluate side-chains 123 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 710 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 66 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 412 HIS C 411 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.190024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171651 restraints weight = 11465.521| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 1.89 r_work: 0.3961 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8549 Z= 0.114 Angle : 0.586 9.566 11534 Z= 0.291 Chirality : 0.044 0.142 1284 Planarity : 0.004 0.062 1422 Dihedral : 10.280 90.166 1266 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.45 % Allowed : 20.76 % Favored : 77.79 % 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: -1.17 (0.25), residues: 1044 helix: 0.36 (0.25), residues: 412 sheet: -1.10 (0.40), residues: 146 loop : -1.67 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 671 HIS 0.002 0.001 HIS C 412 PHE 0.009 0.001 PHE A 491 TYR 0.008 0.001 TYR C 405 ARG 0.008 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 308) hydrogen bonds : angle 4.75726 ( 912) SS BOND : bond 0.00062 ( 3) SS BOND : angle 0.46938 ( 6) covalent geometry : bond 0.00268 ( 8546) covalent geometry : angle 0.58572 (11528) ********************** 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 126 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.990 Fit side-chains REVERT: A 710 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: C 407 MET cc_start: 0.5969 (OUTLIER) cc_final: 0.5046 (mmt) REVERT: C 637 GLU cc_start: 0.7764 (tp30) cc_final: 0.7528 (tp30) REVERT: C 710 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7344 (mp0) outliers start: 13 outliers final: 7 residues processed: 120 average time/residue: 0.2478 time to fit residues: 39.2668 Evaluate side-chains 123 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 718 CYS Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 710 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 60 optimal weight: 0.0770 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 412 HIS C 411 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.189633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.170798 restraints weight = 11535.494| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 1.97 r_work: 0.3954 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8549 Z= 0.120 Angle : 0.601 9.492 11534 Z= 0.299 Chirality : 0.044 0.155 1284 Planarity : 0.004 0.059 1422 Dihedral : 10.240 89.261 1266 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.34 % Allowed : 20.76 % Favored : 77.90 % 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: -1.03 (0.25), residues: 1044 helix: 0.51 (0.26), residues: 398 sheet: -1.09 (0.40), residues: 146 loop : -1.54 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 671 HIS 0.004 0.001 HIS C 412 PHE 0.012 0.002 PHE D 438 TYR 0.009 0.001 TYR A 405 ARG 0.008 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03121 ( 308) hydrogen bonds : angle 4.76907 ( 912) SS BOND : bond 0.00051 ( 3) SS BOND : angle 0.48984 ( 6) covalent geometry : bond 0.00284 ( 8546) covalent geometry : angle 0.60062 (11528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4665.26 seconds wall clock time: 81 minutes 53.50 seconds (4913.50 seconds total)