Starting phenix.real_space_refine on Fri Aug 22 22:52:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fq2_29375/08_2025/8fq2_29375.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fq2_29375/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fq2_29375/08_2025/8fq2_29375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fq2_29375/08_2025/8fq2_29375.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fq2_29375/08_2025/8fq2_29375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fq2_29375/08_2025/8fq2_29375.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: "D" 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: "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} Restraints were copied for chains: C, B Time building chain proxies: 2.20, per 1000 atoms: 0.26 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=4, 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 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 355.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 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: 0.21 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: 0.85 Time building geometry restraints manager: 0.93 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: 4880 22.96 - 45.91: 314 45.91 - 68.87: 32 68.87 - 91.83: 20 91.83 - 114.79: 10 Dihedral angle restraints: 5256 sinusoidal: 2204 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 5253 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: 2.24 - 2.77: 1390 2.77 - 3.30: 7876 3.30 - 3.83: 13806 3.83 - 4.37: 16351 4.37 - 4.90: 28478 Nonbonded interactions: 67901 Sorted by model distance: 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 nonbonded pdb=" OG SER C 497 " pdb=" O2 CYZ C1302 " model vdw 2.273 3.040 ... (remaining 67896 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'B' } 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: 2.850 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.190 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.350 ------------------------------------------------------------------------------- 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 8550 Z= 0.725 Angle : 0.757 9.755 11536 Z= 0.332 Chirality : 0.062 0.422 1284 Planarity : 0.003 0.037 1422 Dihedral : 15.953 114.786 3296 Min Nonbonded Distance : 2.235 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (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 ARG 0.009 0.000 ARG D 660 TYR 0.014 0.001 TYR A 647 PHE 0.013 0.001 PHE A 438 TRP 0.015 0.001 TRP B 767 HIS 0.002 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.01456 ( 8546) covalent geometry : angle 0.75727 (11528) SS BOND : bond 0.00228 ( 4) SS BOND : angle 0.23715 ( 8) hydrogen bonds : bond 0.19513 ( 308) hydrogen bonds : angle 6.31505 ( 912) *********************** 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 : 0.306 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: 0.0944 time to fit residues: 18.1015 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 : 0.212 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.193943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175679 restraints weight = 11200.134| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.83 r_work: 0.4000 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8550 Z= 0.147 Angle : 0.578 8.847 11536 Z= 0.287 Chirality : 0.046 0.158 1284 Planarity : 0.004 0.027 1422 Dihedral : 10.875 98.647 1272 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.67 % Allowed : 7.92 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.25), residues: 1044 helix: 0.65 (0.26), residues: 400 sheet: -0.10 (0.42), residues: 148 loop : -1.36 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 660 TYR 0.015 0.002 TYR C 405 PHE 0.013 0.002 PHE C 491 TRP 0.007 0.001 TRP A 767 HIS 0.001 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8546) covalent geometry : angle 0.57766 (11528) SS BOND : bond 0.00369 ( 4) SS BOND : angle 0.59491 ( 8) hydrogen bonds : bond 0.03674 ( 308) hydrogen bonds : angle 4.92634 ( 912) *********************** 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 134 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.308 Fit side-chains REVERT: A 463 MET cc_start: 0.6180 (ttp) cc_final: 0.5967 (ttm) REVERT: B 407 MET cc_start: 0.7061 (mtt) cc_final: 0.6437 (mtt) outliers start: 6 outliers final: 4 residues processed: 132 average time/residue: 0.1006 time to fit residues: 17.7096 Evaluate side-chains 122 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 644 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 714 GLN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.192996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.174227 restraints weight = 11284.683| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 1.88 r_work: 0.3985 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8550 Z= 0.133 Angle : 0.552 9.243 11536 Z= 0.272 Chirality : 0.044 0.137 1284 Planarity : 0.003 0.026 1422 Dihedral : 10.631 95.085 1269 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.23 % Allowed : 10.27 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.25), residues: 1044 helix: 0.67 (0.26), residues: 398 sheet: -0.43 (0.41), residues: 148 loop : -1.39 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 661 TYR 0.013 0.001 TYR C 405 PHE 0.011 0.002 PHE A 491 TRP 0.007 0.001 TRP C 767 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8546) covalent geometry : angle 0.55215 (11528) SS BOND : bond 0.00248 ( 4) SS BOND : angle 0.53873 ( 8) hydrogen bonds : bond 0.03446 ( 308) hydrogen bonds : angle 4.73900 ( 912) *********************** 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 131 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.349 Fit side-chains REVERT: A 710 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: D 407 MET cc_start: 0.7250 (mtt) cc_final: 0.6882 (mtt) REVERT: B 407 MET cc_start: 0.7216 (mtt) cc_final: 0.6847 (mtt) REVERT: C 407 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5566 (mmt) REVERT: C 710 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: C 721 MET cc_start: 0.7327 (pmm) cc_final: 0.7122 (pmm) outliers start: 11 outliers final: 5 residues processed: 127 average time/residue: 0.0982 time to fit residues: 16.9267 Evaluate side-chains 124 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 772 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.0000 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 chunk 36 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 7 optimal weight: 0.0770 overall best weight: 0.3100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 411 ASN ** 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 = 0.4335 r_free = 0.4335 target = 0.198214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.179473 restraints weight = 11471.905| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.91 r_work: 0.4038 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3916 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8550 Z= 0.085 Angle : 0.498 8.132 11536 Z= 0.243 Chirality : 0.042 0.138 1284 Planarity : 0.003 0.029 1422 Dihedral : 9.774 89.868 1266 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.90 % Allowed : 11.27 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.25), residues: 1044 helix: 0.87 (0.26), residues: 402 sheet: -0.30 (0.42), residues: 148 loop : -1.29 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 694 TYR 0.007 0.001 TYR C 405 PHE 0.011 0.001 PHE B 438 TRP 0.005 0.001 TRP A 766 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 8546) covalent geometry : angle 0.49842 (11528) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.33890 ( 8) hydrogen bonds : bond 0.02564 ( 308) hydrogen bonds : angle 4.50119 ( 912) *********************** 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 134 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.333 Fit side-chains REVERT: A 710 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: D 407 MET cc_start: 0.7322 (mtt) cc_final: 0.6917 (mtt) REVERT: B 407 MET cc_start: 0.7342 (mtt) cc_final: 0.6917 (mtt) REVERT: C 407 MET cc_start: 0.6240 (OUTLIER) cc_final: 0.5575 (mmt) REVERT: C 710 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: C 721 MET cc_start: 0.7289 (pmm) cc_final: 0.7075 (pmm) outliers start: 17 outliers final: 4 residues processed: 130 average time/residue: 0.1077 time to fit residues: 18.9025 Evaluate side-chains 117 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 412 HIS 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 97 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 92 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.196204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.177799 restraints weight = 11441.057| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.88 r_work: 0.4019 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8550 Z= 0.097 Angle : 0.514 8.251 11536 Z= 0.252 Chirality : 0.043 0.152 1284 Planarity : 0.003 0.029 1422 Dihedral : 9.654 89.979 1266 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.45 % Allowed : 13.50 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.25), residues: 1044 helix: 0.91 (0.26), residues: 402 sheet: -0.38 (0.42), residues: 148 loop : -1.30 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 694 TYR 0.011 0.001 TYR C 405 PHE 0.008 0.001 PHE A 491 TRP 0.005 0.001 TRP A 767 HIS 0.001 0.000 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8546) covalent geometry : angle 0.51459 (11528) SS BOND : bond 0.00136 ( 4) SS BOND : angle 0.32541 ( 8) hydrogen bonds : bond 0.02763 ( 308) hydrogen bonds : angle 4.50859 ( 912) *********************** 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 129 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.365 Fit side-chains REVERT: A 710 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: D 407 MET cc_start: 0.7361 (mtt) cc_final: 0.7020 (mtt) REVERT: B 407 MET cc_start: 0.7396 (mtt) cc_final: 0.7047 (mtt) REVERT: C 407 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5666 (mmt) REVERT: C 710 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: C 721 MET cc_start: 0.7293 (pmm) cc_final: 0.7069 (pmm) outliers start: 13 outliers final: 6 residues processed: 124 average time/residue: 0.1293 time to fit residues: 20.8543 Evaluate side-chains 123 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 644 GLU Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 407 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 99 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** 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 = 0.4249 r_free = 0.4249 target = 0.188788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.169150 restraints weight = 11264.209| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 1.97 r_work: 0.3944 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8550 Z= 0.178 Angle : 0.609 10.514 11536 Z= 0.304 Chirality : 0.046 0.168 1284 Planarity : 0.004 0.030 1422 Dihedral : 10.892 94.595 1266 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.34 % Allowed : 14.17 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.25), residues: 1044 helix: 0.52 (0.25), residues: 408 sheet: -0.77 (0.41), residues: 156 loop : -1.52 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 684 TYR 0.014 0.002 TYR C 405 PHE 0.012 0.002 PHE A 491 TRP 0.009 0.001 TRP A 767 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8546) covalent geometry : angle 0.60916 (11528) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.52922 ( 8) hydrogen bonds : bond 0.03819 ( 308) hydrogen bonds : angle 4.86280 ( 912) *********************** 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 138 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.263 Fit side-chains REVERT: A 710 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: C 413 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.5926 (mm-30) REVERT: C 710 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: C 721 MET cc_start: 0.7147 (pmm) cc_final: 0.6912 (pmm) outliers start: 21 outliers final: 14 residues processed: 134 average time/residue: 0.1117 time to fit residues: 19.8473 Evaluate side-chains 125 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 447 ASP 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 36 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.189441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.170615 restraints weight = 11505.324| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 1.90 r_work: 0.3951 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8550 Z= 0.144 Angle : 0.576 10.237 11536 Z= 0.286 Chirality : 0.045 0.147 1284 Planarity : 0.004 0.031 1422 Dihedral : 10.626 93.393 1266 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.34 % Allowed : 14.84 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.25), residues: 1044 helix: 0.51 (0.25), residues: 398 sheet: -0.78 (0.41), residues: 146 loop : -1.46 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 684 TYR 0.012 0.001 TYR C 405 PHE 0.011 0.002 PHE C 491 TRP 0.007 0.001 TRP A 767 HIS 0.001 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8546) covalent geometry : angle 0.57584 (11528) SS BOND : bond 0.00133 ( 4) SS BOND : angle 0.44108 ( 8) hydrogen bonds : bond 0.03400 ( 308) hydrogen bonds : angle 4.79666 ( 912) *********************** 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 138 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 710 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: C 407 MET cc_start: 0.6369 (OUTLIER) cc_final: 0.5855 (mmt) REVERT: C 413 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.5884 (mm-30) REVERT: C 710 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: C 721 MET cc_start: 0.7217 (pmm) cc_final: 0.6989 (pmm) outliers start: 21 outliers final: 11 residues processed: 131 average time/residue: 0.1014 time to fit residues: 18.0601 Evaluate side-chains 130 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 644 GLU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 413 GLU 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 38 optimal weight: 0.0000 chunk 77 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 102 optimal weight: 0.0770 chunk 28 optimal weight: 5.9990 overall best weight: 0.4142 ------------------------------------------------------------------------------- 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 = 0.4308 r_free = 0.4308 target = 0.195194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.176757 restraints weight = 11306.955| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 1.87 r_work: 0.4014 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8550 Z= 0.092 Angle : 0.532 8.341 11536 Z= 0.262 Chirality : 0.042 0.138 1284 Planarity : 0.004 0.031 1422 Dihedral : 9.683 87.187 1266 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.12 % Allowed : 16.74 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.25), residues: 1044 helix: 0.81 (0.26), residues: 400 sheet: -0.59 (0.42), residues: 146 loop : -1.42 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 684 TYR 0.010 0.001 TYR C 405 PHE 0.008 0.001 PHE D 438 TRP 0.007 0.001 TRP A 766 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8546) covalent geometry : angle 0.53236 (11528) SS BOND : bond 0.00123 ( 4) SS BOND : angle 0.33023 ( 8) hydrogen bonds : bond 0.02555 ( 308) hydrogen bonds : angle 4.59664 ( 912) *********************** 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 126 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 710 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: C 407 MET cc_start: 0.6345 (OUTLIER) cc_final: 0.5616 (mmt) REVERT: C 710 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: C 721 MET cc_start: 0.7174 (pmm) cc_final: 0.6917 (pmm) REVERT: D 1301 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7371 (tm-30) REVERT: B 1301 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7342 (tm-30) outliers start: 10 outliers final: 3 residues processed: 122 average time/residue: 0.1069 time to fit residues: 17.5931 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 : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 710 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.0000 chunk 34 optimal weight: 0.5980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.193606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.175380 restraints weight = 11281.046| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.87 r_work: 0.4002 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8550 Z= 0.097 Angle : 0.531 8.116 11536 Z= 0.262 Chirality : 0.043 0.158 1284 Planarity : 0.003 0.033 1422 Dihedral : 9.468 86.390 1266 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.45 % Allowed : 16.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.25), residues: 1044 helix: 0.94 (0.26), residues: 400 sheet: -0.55 (0.42), residues: 146 loop : -1.40 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 684 TYR 0.010 0.001 TYR C 405 PHE 0.008 0.001 PHE C 491 TRP 0.006 0.001 TRP A 767 HIS 0.001 0.000 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8546) covalent geometry : angle 0.53061 (11528) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.34389 ( 8) hydrogen bonds : bond 0.02725 ( 308) hydrogen bonds : angle 4.51570 ( 912) *********************** 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 130 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 710 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: C 407 MET cc_start: 0.6308 (OUTLIER) cc_final: 0.5603 (mmt) REVERT: C 463 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.6102 (ttm) REVERT: C 710 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: C 721 MET cc_start: 0.7170 (pmm) cc_final: 0.6930 (pmm) outliers start: 13 outliers final: 5 residues processed: 125 average time/residue: 0.1147 time to fit residues: 19.2157 Evaluate side-chains 121 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 463 MET 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: 3.9990 chunk 103 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.191993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172956 restraints weight = 11363.445| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.91 r_work: 0.3963 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8550 Z= 0.129 Angle : 0.572 9.112 11536 Z= 0.284 Chirality : 0.045 0.186 1284 Planarity : 0.004 0.032 1422 Dihedral : 9.980 89.135 1266 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.45 % Allowed : 16.74 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.25), residues: 1044 helix: 0.79 (0.26), residues: 398 sheet: -0.70 (0.41), residues: 146 loop : -1.47 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 684 TYR 0.011 0.001 TYR C 405 PHE 0.011 0.002 PHE B 438 TRP 0.007 0.001 TRP A 767 HIS 0.001 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8546) covalent geometry : angle 0.57194 (11528) SS BOND : bond 0.00091 ( 4) SS BOND : angle 0.40115 ( 8) hydrogen bonds : bond 0.03159 ( 308) hydrogen bonds : angle 4.65749 ( 912) ********************** 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 128 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.328 Fit side-chains REVERT: A 710 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: C 407 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5462 (mmt) REVERT: C 463 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.6188 (ttm) REVERT: C 710 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: C 721 MET cc_start: 0.7189 (pmm) cc_final: 0.6946 (pmm) outliers start: 13 outliers final: 7 residues processed: 125 average time/residue: 0.1101 time to fit residues: 18.6504 Evaluate side-chains 122 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 720 THR 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 772 GLU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 463 MET 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 85 optimal weight: 4.9990 chunk 89 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 82 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 0.0980 chunk 69 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.195131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.176480 restraints weight = 11267.104| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.93 r_work: 0.4019 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8550 Z= 0.094 Angle : 0.543 8.070 11536 Z= 0.268 Chirality : 0.043 0.184 1284 Planarity : 0.004 0.034 1422 Dihedral : 9.119 83.659 1266 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.34 % Allowed : 16.85 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.25), residues: 1044 helix: 0.97 (0.26), residues: 400 sheet: -0.53 (0.42), residues: 146 loop : -1.42 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 684 TYR 0.009 0.001 TYR A 405 PHE 0.011 0.001 PHE A 667 TRP 0.006 0.001 TRP C 766 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8546) covalent geometry : angle 0.54276 (11528) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.37802 ( 8) hydrogen bonds : bond 0.02507 ( 308) hydrogen bonds : angle 4.52461 ( 912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2375.84 seconds wall clock time: 41 minutes 30.73 seconds (2490.73 seconds total)