Starting phenix.real_space_refine on Sat Jun 7 03:24:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fq2_29375/06_2025/8fq2_29375.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fq2_29375/06_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_29375/06_2025/8fq2_29375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fq2_29375/06_2025/8fq2_29375.map" model { file = "/net/cci-nas-00/data/ceres_data/8fq2_29375/06_2025/8fq2_29375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fq2_29375/06_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-5710/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: 6.30, per 1000 atoms: 0.75 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 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: 0.98 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: 2.16 Time building geometry restraints manager: 2.19 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: 3.130 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: 0.060 Set scattering table: 0.070 Process input model: 22.120 Find NCS groups from input model: 0.130 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- 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 : 0.973 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: 0.2334 time to fit residues: 44.5110 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 : 1.007 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.171675 restraints weight = 11219.684| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.88 r_work: 0.3968 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.6279 (ttp) cc_final: 0.6065 (ttm) REVERT: A 710 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: D 407 MET cc_start: 0.7170 (mtt) cc_final: 0.6664 (mtt) REVERT: B 407 MET cc_start: 0.7128 (mtt) cc_final: 0.6636 (mtt) REVERT: C 463 MET cc_start: 0.6103 (ttt) cc_final: 0.5812 (ttm) REVERT: C 710 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7314 (mp0) outliers start: 13 outliers final: 9 residues processed: 130 average time/residue: 0.2257 time to fit residues: 39.5065 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 : 0.867 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.190838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.171985 restraints weight = 11370.943| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 1.90 r_work: 0.3967 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2129 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 : 0.561 9.777 11534 Z= 0.277 Chirality : 0.045 0.156 1284 Planarity : 0.004 0.045 1422 Dihedral : 10.700 95.180 1266 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.67 % Allowed : 11.50 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1044 helix: 0.47 (0.25), residues: 410 sheet: -0.52 (0.41), residues: 148 loop : -1.49 (0.27), 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 0.012 0.001 TYR C 405 ARG 0.003 0.000 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 308) hydrogen bonds : angle 4.79444 ( 912) SS BOND : bond 0.00230 ( 3) SS BOND : angle 0.65786 ( 6) covalent geometry : bond 0.00335 ( 8546) covalent geometry : angle 0.56085 (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 123 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.992 Fit side-chains REVERT: A 463 MET cc_start: 0.6326 (ttp) cc_final: 0.6024 (ttm) REVERT: C 463 MET cc_start: 0.6145 (ttt) cc_final: 0.5842 (ttm) outliers start: 6 outliers final: 4 residues processed: 120 average time/residue: 0.2414 time to fit residues: 38.2137 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 : 0.872 ------------------------------------------------------------------------------- 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: 4.9990 chunk 105 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 5 optimal weight: 0.0670 chunk 74 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- 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 = 0.4244 r_free = 0.4244 target = 0.188778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.170107 restraints weight = 11469.144| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.87 r_work: 0.3939 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8549 Z= 0.169 Angle : 0.598 10.457 11534 Z= 0.296 Chirality : 0.046 0.164 1284 Planarity : 0.004 0.049 1422 Dihedral : 10.899 95.464 1266 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.57 % Allowed : 12.83 % Favored : 84.60 % 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: 0.25 (0.25), residues: 412 sheet: -0.91 (0.40), residues: 158 loop : -1.62 (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 D 412 PHE 0.012 0.002 PHE A 491 TYR 0.013 0.002 TYR A 405 ARG 0.005 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 308) hydrogen bonds : angle 4.84443 ( 912) SS BOND : bond 0.00170 ( 3) SS BOND : angle 0.66019 ( 6) covalent geometry : bond 0.00404 ( 8546) covalent geometry : angle 0.59833 (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 141 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.6431 (ttp) cc_final: 0.6151 (ttm) REVERT: A 710 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: A 752 LYS cc_start: 0.8383 (ttpt) cc_final: 0.8135 (tttt) REVERT: C 407 MET cc_start: 0.6275 (OUTLIER) cc_final: 0.5322 (mmt) REVERT: C 413 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.5769 (mm-30) REVERT: C 463 MET cc_start: 0.6291 (ttt) cc_final: 0.6041 (ttm) REVERT: C 710 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7321 (mp0) outliers start: 23 outliers final: 9 residues processed: 133 average time/residue: 0.2440 time to fit residues: 42.6906 Evaluate side-chains 125 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 102 optimal weight: 0.0470 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 overall best weight: 0.7882 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.192502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.174345 restraints weight = 11290.199| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 1.84 r_work: 0.3982 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8549 Z= 0.104 Angle : 0.529 9.149 11534 Z= 0.260 Chirality : 0.043 0.135 1284 Planarity : 0.004 0.048 1422 Dihedral : 10.254 91.065 1266 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.67 % Allowed : 15.62 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1044 helix: 0.44 (0.25), residues: 416 sheet: -0.73 (0.42), residues: 148 loop : -1.57 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 767 HIS 0.001 0.001 HIS B 412 PHE 0.012 0.001 PHE B 438 TYR 0.009 0.001 TYR A 405 ARG 0.005 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.02963 ( 308) hydrogen bonds : angle 4.63277 ( 912) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.47349 ( 6) covalent geometry : bond 0.00244 ( 8546) covalent geometry : angle 0.52860 (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 136 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.970 Fit side-chains REVERT: A 710 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: C 407 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.5654 (mmt) REVERT: C 710 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7298 (mp0) outliers start: 15 outliers final: 5 residues processed: 132 average time/residue: 0.2457 time to fit residues: 42.7229 Evaluate side-chains 121 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 666 VAL 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 65 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.192205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.173832 restraints weight = 11343.570| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 1.85 r_work: 0.3975 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3855 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2611 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= 0.111 Angle : 0.534 9.101 11534 Z= 0.264 Chirality : 0.043 0.135 1284 Planarity : 0.004 0.041 1422 Dihedral : 10.205 90.245 1266 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.12 % Allowed : 16.74 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1044 helix: 0.58 (0.25), residues: 412 sheet: -0.72 (0.42), residues: 146 loop : -1.58 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 767 HIS 0.004 0.001 HIS A 412 PHE 0.009 0.001 PHE A 491 TYR 0.011 0.001 TYR A 405 ARG 0.006 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 308) hydrogen bonds : angle 4.60216 ( 912) SS BOND : bond 0.00105 ( 3) SS BOND : angle 0.47333 ( 6) covalent geometry : bond 0.00264 ( 8546) covalent geometry : angle 0.53417 (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 136 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.965 Fit side-chains REVERT: A 413 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5383 (mm-30) REVERT: A 710 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: C 407 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.5323 (mmt) REVERT: C 710 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7315 (mp0) outliers start: 19 outliers final: 10 residues processed: 127 average time/residue: 0.2514 time to fit residues: 42.0918 Evaluate side-chains 126 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 102 optimal weight: 0.0370 chunk 100 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.195136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.176360 restraints weight = 11444.311| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 1.91 r_work: 0.3997 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8549 Z= 0.094 Angle : 0.519 8.631 11534 Z= 0.255 Chirality : 0.042 0.133 1284 Planarity : 0.004 0.056 1422 Dihedral : 9.812 86.813 1266 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.67 % Allowed : 17.30 % 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: -0.74 (0.25), residues: 1044 helix: 0.75 (0.26), residues: 400 sheet: -0.62 (0.42), residues: 146 loop : -1.49 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 671 HIS 0.001 0.000 HIS B 412 PHE 0.011 0.001 PHE B 438 TYR 0.008 0.001 TYR A 405 ARG 0.006 0.000 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.02721 ( 308) hydrogen bonds : angle 4.52494 ( 912) SS BOND : bond 0.00124 ( 3) SS BOND : angle 0.40606 ( 6) covalent geometry : bond 0.00220 ( 8546) covalent geometry : angle 0.51888 (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 131 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.973 Fit side-chains REVERT: A 413 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.5468 (mm-30) REVERT: A 710 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: C 637 GLU cc_start: 0.7764 (tp30) cc_final: 0.7491 (tp30) REVERT: C 710 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7241 (mp0) outliers start: 15 outliers final: 10 residues processed: 125 average time/residue: 0.2394 time to fit residues: 39.8426 Evaluate side-chains 122 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 634 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 B residue 713 GLU 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: 4.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 55 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.187974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.168508 restraints weight = 11451.381| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 1.98 r_work: 0.3926 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8549 Z= 0.168 Angle : 0.593 9.724 11534 Z= 0.297 Chirality : 0.046 0.184 1284 Planarity : 0.004 0.056 1422 Dihedral : 10.729 93.740 1266 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.23 % Allowed : 17.41 % Favored : 80.36 % 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: -1.10 (0.25), residues: 1044 helix: 0.41 (0.25), residues: 410 sheet: -0.86 (0.41), residues: 146 loop : -1.68 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 767 HIS 0.006 0.001 HIS A 412 PHE 0.012 0.002 PHE A 491 TYR 0.013 0.002 TYR A 424 ARG 0.006 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 308) hydrogen bonds : angle 4.78929 ( 912) SS BOND : bond 0.00117 ( 3) SS BOND : angle 0.50125 ( 6) covalent geometry : bond 0.00403 ( 8546) covalent geometry : angle 0.59284 (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 131 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 413 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5457 (mm-30) REVERT: A 710 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: C 637 GLU cc_start: 0.7871 (tp30) cc_final: 0.7637 (tp30) REVERT: C 710 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7295 (mp0) outliers start: 20 outliers final: 11 residues processed: 123 average time/residue: 0.2521 time to fit residues: 41.4270 Evaluate side-chains 124 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 B residue 713 GLU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 412 HIS 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 26 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 79 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4279 r_free = 0.4279 target = 0.192380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.173255 restraints weight = 11517.335| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.97 r_work: 0.3974 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8549 Z= 0.100 Angle : 0.557 9.970 11534 Z= 0.273 Chirality : 0.043 0.135 1284 Planarity : 0.004 0.055 1422 Dihedral : 10.076 88.352 1266 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.56 % Allowed : 18.30 % Favored : 80.13 % 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: -0.92 (0.25), residues: 1044 helix: 0.62 (0.26), residues: 400 sheet: -0.78 (0.41), residues: 146 loop : -1.58 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 671 HIS 0.001 0.000 HIS D 435 PHE 0.011 0.001 PHE D 438 TYR 0.009 0.001 TYR A 405 ARG 0.007 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.02856 ( 308) hydrogen bonds : angle 4.64466 ( 912) SS BOND : bond 0.00126 ( 3) SS BOND : angle 0.40537 ( 6) covalent geometry : bond 0.00235 ( 8546) covalent geometry : angle 0.55729 (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 127 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 710 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: C 637 GLU cc_start: 0.7742 (tp30) cc_final: 0.7483 (tp30) REVERT: C 710 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7321 (mp0) outliers start: 14 outliers final: 8 residues processed: 120 average time/residue: 0.2732 time to fit residues: 43.9621 Evaluate side-chains 118 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 66 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.0370 chunk 50 optimal weight: 0.9980 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS 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 = 0.4256 r_free = 0.4256 target = 0.189741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.170459 restraints weight = 11417.864| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 1.97 r_work: 0.3945 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8549 Z= 0.144 Angle : 0.605 10.054 11534 Z= 0.299 Chirality : 0.045 0.170 1284 Planarity : 0.004 0.056 1422 Dihedral : 10.421 90.984 1266 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.23 % Allowed : 18.75 % Favored : 80.02 % 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 (0.25), residues: 410 sheet: -0.88 (0.40), residues: 146 loop : -1.67 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 767 HIS 0.004 0.001 HIS A 412 PHE 0.011 0.002 PHE A 491 TYR 0.011 0.001 TYR A 424 ARG 0.007 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 308) hydrogen bonds : angle 4.74129 ( 912) SS BOND : bond 0.00053 ( 3) SS BOND : angle 0.48607 ( 6) covalent geometry : bond 0.00344 ( 8546) covalent geometry : angle 0.60482 (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 122 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.885 Fit side-chains REVERT: A 710 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: C 407 MET cc_start: 0.6149 (OUTLIER) cc_final: 0.5174 (mmt) REVERT: C 637 GLU cc_start: 0.7808 (tp30) cc_final: 0.7554 (tp30) REVERT: C 710 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7368 (mp0) outliers start: 11 outliers final: 6 residues processed: 118 average time/residue: 0.2368 time to fit residues: 37.1968 Evaluate side-chains 119 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 407 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: 5.9990 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4217 r_free = 0.4217 target = 0.185756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.167022 restraints weight = 11552.372| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.87 r_work: 0.3909 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3223 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= 0.228 Angle : 0.692 11.357 11534 Z= 0.347 Chirality : 0.050 0.226 1284 Planarity : 0.005 0.069 1422 Dihedral : 11.343 99.308 1266 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.45 % Allowed : 18.97 % Favored : 79.58 % 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: -1.36 (0.24), residues: 1044 helix: 0.12 (0.25), residues: 406 sheet: -1.04 (0.44), residues: 118 loop : -1.70 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 766 HIS 0.006 0.001 HIS C 412 PHE 0.014 0.003 PHE D 682 TYR 0.016 0.002 TYR A 424 ARG 0.007 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 308) hydrogen bonds : angle 5.10317 ( 912) SS BOND : bond 0.00081 ( 3) SS BOND : angle 0.51406 ( 6) covalent geometry : bond 0.00543 ( 8546) covalent geometry : angle 0.69205 (11528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4702.40 seconds wall clock time: 82 minutes 34.80 seconds (4954.80 seconds total)