Starting phenix.real_space_refine on Fri Nov 15 06:21:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq2_29375/11_2024/8fq2_29375.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq2_29375/11_2024/8fq2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq2_29375/11_2024/8fq2_29375.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq2_29375/11_2024/8fq2_29375.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq2_29375/11_2024/8fq2_29375.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fq2_29375/11_2024/8fq2_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.48, per 1000 atoms: 0.77 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=2, 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 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: 1.06 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: 2.32 Time building geometry restraints manager: 2.56 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: 4876 22.96 - 45.91: 313 45.91 - 68.87: 31 68.87 - 91.83: 20 91.83 - 114.79: 10 Dihedral angle restraints: 5250 sinusoidal: 2198 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 5247 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 - 2.60: 68 2.60 - 3.18: 6979 3.18 - 3.75: 12770 3.75 - 4.33: 17896 4.33 - 4.90: 30194 Nonbonded interactions: 67907 Sorted by model distance: nonbonded pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " model vdw 2.031 3.760 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 ... (remaining 67902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 715 or (resid 716 and (name N or name CA \ or name C or name O or name CB )) or resid 717 through 773 or resid 1301 or resi \ d 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 715 or (resid 716 and (name N or name CA \ or name C or name O or name CB )) or resid 717 through 773 or resid 1301 or resi \ d 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.470 Find NCS groups from input model: 0.450 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.840 ------------------------------------------------------------------------------- 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 8546 Z= 0.934 Angle : 0.757 9.755 11528 Z= 0.332 Chirality : 0.062 0.422 1284 Planarity : 0.003 0.037 1422 Dihedral : 15.953 114.786 3296 Min Nonbonded Distance : 2.031 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 *********************** 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 : 1.048 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: 0.2407 time to fit residues: 45.7585 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 : 0.988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8546 Z= 0.271 Angle : 0.615 9.502 11528 Z= 0.305 Chirality : 0.047 0.198 1284 Planarity : 0.004 0.027 1422 Dihedral : 11.042 98.758 1272 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.12 % Allowed : 7.48 % 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 (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: -0.75 (0.25), residues: 1044 helix: 0.51 (0.25), residues: 410 sheet: -0.50 (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 0.002 0.001 HIS D 412 PHE 0.014 0.002 PHE C 491 TYR 0.016 0.002 TYR C 405 ARG 0.005 0.001 ARG D 660 *********************** 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 131 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.5978 (ttp) cc_final: 0.5728 (ttm) REVERT: D 407 MET cc_start: 0.6773 (mtt) cc_final: 0.6291 (mtt) REVERT: B 407 MET cc_start: 0.6735 (mtt) cc_final: 0.6236 (mtt) outliers start: 10 outliers final: 6 residues processed: 129 average time/residue: 0.2408 time to fit residues: 41.7420 Evaluate side-chains 117 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 723 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 65 optimal weight: 0.4980 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 0.0010 chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.2992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8546 Z= 0.210 Angle : 0.557 9.776 11528 Z= 0.274 Chirality : 0.045 0.137 1284 Planarity : 0.004 0.045 1422 Dihedral : 10.688 95.036 1266 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.45 % Allowed : 11.27 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.25), residues: 1044 helix: 0.51 (0.25), residues: 410 sheet: -0.50 (0.41), residues: 148 loop : -1.46 (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 B 660 *********************** 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: 13 poor density : 118 time to evaluate : 0.937 Fit side-chains REVERT: A 710 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: C 710 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: C 721 MET cc_start: 0.6889 (pmm) cc_final: 0.6616 (pmm) outliers start: 13 outliers final: 5 residues processed: 126 average time/residue: 0.2580 time to fit residues: 42.8657 Evaluate side-chains 119 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 95 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 85 optimal weight: 0.0570 overall best weight: 1.5102 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8546 Z= 0.233 Angle : 0.575 10.105 11528 Z= 0.284 Chirality : 0.045 0.141 1284 Planarity : 0.004 0.051 1422 Dihedral : 10.714 94.013 1266 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.46 % Allowed : 12.50 % 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 (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: -1.09 (0.25), residues: 1044 helix: 0.33 (0.25), residues: 414 sheet: -0.82 (0.41), residues: 158 loop : -1.62 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 767 HIS 0.002 0.001 HIS B 412 PHE 0.011 0.002 PHE C 491 TYR 0.013 0.001 TYR A 405 ARG 0.005 0.001 ARG A 684 *********************** 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 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.987 Fit side-chains REVERT: A 710 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: C 413 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.5657 (mm-30) REVERT: C 710 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: C 721 MET cc_start: 0.6828 (pmm) cc_final: 0.6520 (pmm) outliers start: 22 outliers final: 9 residues processed: 134 average time/residue: 0.2511 time to fit residues: 44.5225 Evaluate side-chains 130 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 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 413 GLU 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 58 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8546 Z= 0.371 Angle : 0.680 11.575 11528 Z= 0.340 Chirality : 0.049 0.204 1284 Planarity : 0.005 0.056 1422 Dihedral : 11.498 99.362 1266 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.90 % Allowed : 16.29 % Favored : 80.80 % 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: -1.54 (0.24), residues: 1044 helix: -0.08 (0.25), residues: 410 sheet: -1.18 (0.43), residues: 128 loop : -1.76 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 767 HIS 0.003 0.001 HIS A 435 PHE 0.015 0.003 PHE B 682 TYR 0.016 0.002 TYR A 424 ARG 0.005 0.001 ARG C 684 *********************** 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 144 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5257 (mm-30) REVERT: A 710 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: C 710 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: C 721 MET cc_start: 0.6718 (pmm) cc_final: 0.6458 (pmm) outliers start: 26 outliers final: 15 residues processed: 133 average time/residue: 0.2473 time to fit residues: 44.0455 Evaluate side-chains 129 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 A residue 747 ASN Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 713 GLU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain 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 408 MET Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 747 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8546 Z= 0.182 Angle : 0.561 9.821 11528 Z= 0.278 Chirality : 0.044 0.134 1284 Planarity : 0.004 0.053 1422 Dihedral : 10.625 92.813 1266 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.67 % Allowed : 18.75 % 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: -1.31 (0.24), residues: 1044 helix: 0.15 (0.25), residues: 412 sheet: -1.09 (0.41), residues: 146 loop : -1.68 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 767 HIS 0.001 0.001 HIS B 435 PHE 0.009 0.001 PHE A 491 TYR 0.011 0.001 TYR C 405 ARG 0.006 0.001 ARG C 684 *********************** 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 134 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.899 Fit side-chains REVERT: A 710 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: C 710 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: C 721 MET cc_start: 0.6701 (pmm) cc_final: 0.6447 (pmm) outliers start: 15 outliers final: 8 residues processed: 129 average time/residue: 0.2434 time to fit residues: 41.5998 Evaluate side-chains 124 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 772 GLU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 713 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 102 optimal weight: 0.0470 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8546 Z= 0.164 Angle : 0.566 10.894 11528 Z= 0.274 Chirality : 0.043 0.134 1284 Planarity : 0.004 0.051 1422 Dihedral : 10.189 89.463 1266 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.23 % Allowed : 19.08 % Favored : 78.68 % 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: -1.19 (0.25), residues: 1044 helix: 0.32 (0.25), residues: 416 sheet: -0.98 (0.41), residues: 146 loop : -1.72 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 671 HIS 0.001 0.001 HIS A 435 PHE 0.011 0.001 PHE B 438 TYR 0.010 0.001 TYR C 405 ARG 0.006 0.000 ARG C 684 *********************** 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 137 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.971 Fit side-chains REVERT: A 710 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: C 413 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.5811 (mm-30) REVERT: C 710 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7094 (mp0) outliers start: 20 outliers final: 8 residues processed: 130 average time/residue: 0.2436 time to fit residues: 42.3985 Evaluate side-chains 126 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 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 666 VAL 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 30 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8546 Z= 0.324 Angle : 0.661 10.714 11528 Z= 0.328 Chirality : 0.049 0.227 1284 Planarity : 0.004 0.049 1422 Dihedral : 11.078 95.749 1266 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.46 % Allowed : 20.09 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1044 helix: 0.09 (0.25), residues: 412 sheet: -1.24 (0.39), residues: 156 loop : -1.74 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 767 HIS 0.003 0.001 HIS A 412 PHE 0.013 0.002 PHE D 438 TYR 0.017 0.002 TYR A 440 ARG 0.007 0.001 ARG C 684 *********************** 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 134 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 710 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: C 413 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.5670 (mm-30) REVERT: C 637 GLU cc_start: 0.7653 (tp30) cc_final: 0.7392 (tp30) REVERT: C 710 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7076 (mp0) outliers start: 22 outliers final: 11 residues processed: 126 average time/residue: 0.2459 time to fit residues: 41.6493 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 : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 718 CYS 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 487 GLU 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 413 GLU 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 95 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 0.0030 overall best weight: 1.0194 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8546 Z= 0.186 Angle : 0.588 9.716 11528 Z= 0.291 Chirality : 0.044 0.135 1284 Planarity : 0.004 0.059 1422 Dihedral : 10.450 90.763 1266 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.45 % Allowed : 21.43 % Favored : 77.12 % 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: -1.33 (0.25), residues: 1044 helix: 0.21 (0.25), residues: 414 sheet: -1.20 (0.40), residues: 146 loop : -1.74 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 671 HIS 0.004 0.001 HIS C 412 PHE 0.012 0.002 PHE B 438 TYR 0.012 0.001 TYR C 440 ARG 0.007 0.001 ARG A 684 *********************** 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 128 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.029 Fit side-chains REVERT: A 710 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: C 637 GLU cc_start: 0.7546 (tp30) cc_final: 0.7281 (tp30) REVERT: C 710 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7115 (mp0) outliers start: 13 outliers final: 8 residues processed: 124 average time/residue: 0.2483 time to fit residues: 40.9781 Evaluate side-chains 125 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 718 CYS 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 61 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8546 Z= 0.158 Angle : 0.573 9.534 11528 Z= 0.282 Chirality : 0.043 0.141 1284 Planarity : 0.004 0.052 1422 Dihedral : 9.923 86.856 1266 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.34 % Allowed : 21.54 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.25), residues: 1044 helix: 0.50 (0.26), residues: 400 sheet: -1.13 (0.40), residues: 146 loop : -1.60 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 671 HIS 0.001 0.001 HIS B 412 PHE 0.010 0.001 PHE D 438 TYR 0.010 0.001 TYR C 405 ARG 0.008 0.001 ARG A 684 ********************** 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: 12 poor density : 116 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 710 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: C 637 GLU cc_start: 0.7488 (tp30) cc_final: 0.7242 (tp30) REVERT: C 710 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7049 (mp0) outliers start: 12 outliers final: 7 residues processed: 124 average time/residue: 0.2609 time to fit residues: 42.5690 Evaluate side-chains 124 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 718 CYS 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 25 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 84 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 0.0270 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.194247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.175915 restraints weight = 11367.389| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.88 r_work: 0.3996 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8546 Z= 0.148 Angle : 0.566 9.193 11528 Z= 0.279 Chirality : 0.043 0.152 1284 Planarity : 0.004 0.052 1422 Dihedral : 9.560 84.971 1266 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.45 % Allowed : 21.54 % Favored : 77.01 % 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: -0.98 (0.25), residues: 1044 helix: 0.62 (0.26), residues: 400 sheet: -1.01 (0.40), residues: 146 loop : -1.60 (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 C 412 PHE 0.009 0.001 PHE D 495 TYR 0.015 0.001 TYR A 440 ARG 0.008 0.001 ARG A 684 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.19 seconds wall clock time: 39 minutes 45.01 seconds (2385.01 seconds total)