Starting phenix.real_space_refine on Thu Mar 5 01:25:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n5e_24187/03_2026/7n5e_24187.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n5e_24187/03_2026/7n5e_24187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n5e_24187/03_2026/7n5e_24187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n5e_24187/03_2026/7n5e_24187.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n5e_24187/03_2026/7n5e_24187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n5e_24187/03_2026/7n5e_24187.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 11784 2.51 5 N 2960 2.21 5 O 3094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17915 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2579 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 7, 'TRANS': 308} Chain breaks: 2 Chain: "B" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "C" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "E" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "F" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "G" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2535 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 7, 'TRANS': 302} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.50, per 1000 atoms: 0.25 Number of scatterers: 17915 At special positions: 0 Unit cell: (147.29, 144.2, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 3094 8.00 N 2960 7.00 C 11784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.74 Conformation dependent library (CDL) restraints added in 912.5 milliseconds 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 9 sheets defined 59.3% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 295 through 333 removed outlier: 4.266A pdb=" N HIS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 504 through 552 Processing helix chain 'A' and resid 556 through 574 removed outlier: 3.585A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 661 through 678 Processing helix chain 'A' and resid 714 through 737 Processing helix chain 'B' and resid 295 through 329 removed outlier: 3.824A pdb=" N LEU B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 331 No H-bonds generated for 'chain 'B' and resid 330 through 331' Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 349 Processing helix chain 'B' and resid 508 through 524 Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 556 through 590 removed outlier: 5.467A pdb=" N ASN B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 661 through 678 Processing helix chain 'B' and resid 714 through 737 Processing helix chain 'C' and resid 295 through 329 removed outlier: 3.892A pdb=" N SER C 329 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 331 No H-bonds generated for 'chain 'C' and resid 330 through 331' Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 352 removed outlier: 3.519A pdb=" N GLN C 350 " --> pdb=" O HIS C 346 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR C 351 " --> pdb=" O SER C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 524 Processing helix chain 'C' and resid 526 through 552 Processing helix chain 'C' and resid 556 through 590 removed outlier: 5.551A pdb=" N ASN C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 635 Processing helix chain 'C' and resid 661 through 678 Processing helix chain 'C' and resid 714 through 737 Processing helix chain 'D' and resid 295 through 327 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 352 removed outlier: 3.541A pdb=" N GLN D 350 " --> pdb=" O HIS D 346 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR D 351 " --> pdb=" O SER D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 524 Processing helix chain 'D' and resid 526 through 552 Processing helix chain 'D' and resid 556 through 590 removed outlier: 5.586A pdb=" N ASN D 576 " --> pdb=" O PHE D 572 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 635 Processing helix chain 'D' and resid 661 through 678 Processing helix chain 'D' and resid 714 through 737 Processing helix chain 'E' and resid 295 through 327 Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 332 through 334 No H-bonds generated for 'chain 'E' and resid 332 through 334' Processing helix chain 'E' and resid 335 through 352 removed outlier: 3.661A pdb=" N GLN E 350 " --> pdb=" O HIS E 346 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR E 351 " --> pdb=" O SER E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 524 Processing helix chain 'E' and resid 526 through 552 Processing helix chain 'E' and resid 556 through 590 removed outlier: 5.669A pdb=" N ASN E 576 " --> pdb=" O PHE E 572 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR E 577 " --> pdb=" O ILE E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 635 Processing helix chain 'E' and resid 661 through 678 Processing helix chain 'E' and resid 714 through 736 Processing helix chain 'F' and resid 295 through 329 removed outlier: 3.985A pdb=" N SER F 329 " --> pdb=" O ILE F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 331 No H-bonds generated for 'chain 'F' and resid 330 through 331' Processing helix chain 'F' and resid 332 through 334 No H-bonds generated for 'chain 'F' and resid 332 through 334' Processing helix chain 'F' and resid 335 through 352 Processing helix chain 'F' and resid 508 through 524 Processing helix chain 'F' and resid 526 through 552 Processing helix chain 'F' and resid 556 through 590 removed outlier: 5.688A pdb=" N ASN F 576 " --> pdb=" O PHE F 572 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR F 577 " --> pdb=" O ILE F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 635 Processing helix chain 'F' and resid 661 through 678 Processing helix chain 'F' and resid 714 through 737 Processing helix chain 'G' and resid 295 through 329 removed outlier: 3.906A pdb=" N SER G 329 " --> pdb=" O ILE G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 331 No H-bonds generated for 'chain 'G' and resid 330 through 331' Processing helix chain 'G' and resid 332 through 334 No H-bonds generated for 'chain 'G' and resid 332 through 334' Processing helix chain 'G' and resid 335 through 352 Processing helix chain 'G' and resid 508 through 524 Processing helix chain 'G' and resid 526 through 552 Processing helix chain 'G' and resid 556 through 590 removed outlier: 5.688A pdb=" N ASN G 576 " --> pdb=" O PHE G 572 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR G 577 " --> pdb=" O ILE G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 635 Processing helix chain 'G' and resid 661 through 678 Processing helix chain 'G' and resid 714 through 737 Processing sheet with id=AA1, first strand: chain 'A' and resid 599 through 602 removed outlier: 6.640A pdb=" N VAL A 618 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET A 612 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A 626 " --> pdb=" O ASN B 641 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 618 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N MET B 612 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 626 " --> pdb=" O ASN C 641 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 618 " --> pdb=" O GLU C 610 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N MET C 612 " --> pdb=" O THR C 616 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR C 616 " --> pdb=" O MET C 612 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 626 " --> pdb=" O ASN D 641 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 618 " --> pdb=" O GLU D 610 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N MET D 612 " --> pdb=" O THR D 616 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR D 616 " --> pdb=" O MET D 612 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS D 626 " --> pdb=" O ASN E 641 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL E 618 " --> pdb=" O GLU E 610 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET E 612 " --> pdb=" O THR E 616 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR E 616 " --> pdb=" O MET E 612 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS E 626 " --> pdb=" O ASN F 641 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL F 618 " --> pdb=" O GLU F 610 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS F 626 " --> pdb=" O ASN G 641 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL G 618 " --> pdb=" O GLU G 610 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N MET G 612 " --> pdb=" O THR G 616 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR G 616 " --> pdb=" O MET G 612 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS G 626 " --> pdb=" O ASN A 641 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 649 through 657 removed outlier: 6.531A pdb=" N LYS A 699 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A 694 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS A 701 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 707 " --> pdb=" O GLN A 686 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN A 686 " --> pdb=" O ASN A 707 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 745 through 750 removed outlier: 6.485A pdb=" N GLN A 745 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG B 750 " --> pdb=" O GLN A 745 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE A 747 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE G 749 " --> pdb=" O ARG A 750 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 649 through 657 removed outlier: 6.484A pdb=" N LYS B 699 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 694 " --> pdb=" O LYS B 699 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS B 701 " --> pdb=" O LYS B 692 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 649 through 657 removed outlier: 6.416A pdb=" N LYS C 699 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE C 694 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS C 701 " --> pdb=" O LYS C 692 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN C 707 " --> pdb=" O GLN C 686 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN C 686 " --> pdb=" O ASN C 707 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 649 through 657 removed outlier: 6.507A pdb=" N LYS D 699 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE D 694 " --> pdb=" O LYS D 699 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS D 701 " --> pdb=" O LYS D 692 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 649 through 657 removed outlier: 6.465A pdb=" N LYS E 699 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE E 694 " --> pdb=" O LYS E 699 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS E 701 " --> pdb=" O LYS E 692 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 649 through 657 removed outlier: 6.506A pdb=" N LYS F 699 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE F 694 " --> pdb=" O LYS F 699 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS F 701 " --> pdb=" O LYS F 692 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN F 707 " --> pdb=" O GLN F 686 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN F 686 " --> pdb=" O ASN F 707 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 649 through 657 removed outlier: 6.330A pdb=" N LYS G 699 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE G 694 " --> pdb=" O LYS G 699 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS G 701 " --> pdb=" O LYS G 692 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN G 707 " --> pdb=" O GLN G 686 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN G 686 " --> pdb=" O ASN G 707 " (cutoff:3.500A) 1231 hydrogen bonds defined for protein. 3618 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: 3.02 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3350 1.31 - 1.44: 4632 1.44 - 1.56: 10105 1.56 - 1.69: 59 1.69 - 1.81: 133 Bond restraints: 18279 Sorted by residual: bond pdb=" CB HIS A 331 " pdb=" CG HIS A 331 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.47e+01 bond pdb=" CD2 TRP D 507 " pdb=" CE3 TRP D 507 " ideal model delta sigma weight residual 1.398 1.505 -0.107 1.60e-02 3.91e+03 4.46e+01 bond pdb=" CD2 TRP B 507 " pdb=" CE3 TRP B 507 " ideal model delta sigma weight residual 1.398 1.503 -0.105 1.60e-02 3.91e+03 4.28e+01 bond pdb=" CZ2 TRP C 507 " pdb=" CH2 TRP C 507 " ideal model delta sigma weight residual 1.368 1.486 -0.118 1.90e-02 2.77e+03 3.82e+01 bond pdb=" CZ2 TRP E 507 " pdb=" CH2 TRP E 507 " ideal model delta sigma weight residual 1.368 1.483 -0.115 1.90e-02 2.77e+03 3.64e+01 ... (remaining 18274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 19782 1.77 - 3.54: 3936 3.54 - 5.31: 804 5.31 - 7.07: 171 7.07 - 8.84: 23 Bond angle restraints: 24716 Sorted by residual: angle pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " pdb=" CG PHE A 335 " ideal model delta sigma weight residual 113.80 122.08 -8.28 1.00e+00 1.00e+00 6.86e+01 angle pdb=" C GLN G 291 " pdb=" N PRO G 292 " pdb=" CA PRO G 292 " ideal model delta sigma weight residual 119.47 128.27 -8.80 1.16e+00 7.43e-01 5.76e+01 angle pdb=" C GLN C 291 " pdb=" N PRO C 292 " pdb=" CA PRO C 292 " ideal model delta sigma weight residual 119.56 127.00 -7.44 1.02e+00 9.61e-01 5.32e+01 angle pdb=" N THR C 557 " pdb=" CA THR C 557 " pdb=" C THR C 557 " ideal model delta sigma weight residual 112.89 121.73 -8.84 1.24e+00 6.50e-01 5.08e+01 angle pdb=" C HIS E 592 " pdb=" N PRO E 593 " pdb=" CA PRO E 593 " ideal model delta sigma weight residual 119.56 126.71 -7.15 1.01e+00 9.80e-01 5.02e+01 ... (remaining 24711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 10586 17.71 - 35.42: 253 35.42 - 53.13: 50 53.13 - 70.84: 30 70.84 - 88.54: 12 Dihedral angle restraints: 10931 sinusoidal: 4511 harmonic: 6420 Sorted by residual: dihedral pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " ideal model delta harmonic sigma weight residual 122.80 130.99 -8.19 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" N ARG A 296 " pdb=" C ARG A 296 " pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " ideal model delta harmonic sigma weight residual 122.80 114.64 8.16 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CB GLU A 611 " pdb=" CG GLU A 611 " pdb=" CD GLU A 611 " pdb=" OE1 GLU A 611 " ideal model delta sinusoidal sigma weight residual 0.00 -88.54 88.54 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 10928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2091 0.092 - 0.185: 712 0.185 - 0.277: 110 0.277 - 0.370: 17 0.370 - 0.462: 1 Chirality restraints: 2931 Sorted by residual: chirality pdb=" CA THR C 557 " pdb=" N THR C 557 " pdb=" C THR C 557 " pdb=" CB THR C 557 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CA TRP B 304 " pdb=" N TRP B 304 " pdb=" C TRP B 304 " pdb=" CB TRP B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA THR G 557 " pdb=" N THR G 557 " pdb=" C THR G 557 " pdb=" CB THR G 557 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 2928 not shown) Planarity restraints: 3023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 335 " -0.059 2.00e-02 2.50e+03 3.66e-02 2.35e+01 pdb=" CG PHE A 335 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 335 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 335 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A 335 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 335 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 335 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 291 " 0.022 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C GLN E 291 " -0.074 2.00e-02 2.50e+03 pdb=" O GLN E 291 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO E 292 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 675 " 0.044 2.00e-02 2.50e+03 2.53e-02 1.28e+01 pdb=" CG TYR E 675 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR E 675 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 675 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR E 675 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR E 675 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR E 675 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 675 " 0.042 2.00e-02 2.50e+03 ... (remaining 3020 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 6714 2.88 - 3.39: 18129 3.39 - 3.89: 30327 3.89 - 4.40: 34802 4.40 - 4.90: 56059 Nonbonded interactions: 146031 Sorted by model distance: nonbonded pdb=" OD1 ASP F 737 " pdb=" NZ LYS F 739 " model vdw 2.378 3.120 nonbonded pdb=" OD1 ASP G 737 " pdb=" NZ LYS G 739 " model vdw 2.385 3.120 nonbonded pdb=" OD1 ASP B 737 " pdb=" NZ LYS B 739 " model vdw 2.386 3.120 nonbonded pdb=" OD1 ASP D 737 " pdb=" NZ LYS D 739 " model vdw 2.399 3.120 nonbonded pdb=" OD1 ASP E 737 " pdb=" NZ LYS E 739 " model vdw 2.399 3.120 ... (remaining 146026 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 294 through 354 or resid 507 through 801)) selection = (chain 'B' and resid 294 through 801) selection = (chain 'C' and resid 294 through 801) selection = (chain 'D' and resid 294 through 801) selection = (chain 'E' and resid 294 through 801) selection = (chain 'F' and resid 294 through 801) selection = (chain 'G' and resid 294 through 801) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.360 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.023 0.132 18279 Z= 1.207 Angle : 1.544 8.842 24716 Z= 1.056 Chirality : 0.090 0.462 2931 Planarity : 0.008 0.043 3023 Dihedral : 10.255 88.544 6707 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 0.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.17), residues: 2146 helix: 1.62 (0.13), residues: 1206 sheet: 0.56 (0.31), residues: 290 loop : 1.09 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 334 TYR 0.044 0.009 TYR E 675 PHE 0.059 0.006 PHE A 335 TRP 0.036 0.010 TRP E 683 HIS 0.010 0.002 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.02280 (18279) covalent geometry : angle 1.54442 (24716) hydrogen bonds : bond 0.14397 ( 1231) hydrogen bonds : angle 6.18949 ( 3618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 585 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 541 ILE cc_start: 0.8735 (mt) cc_final: 0.8435 (mt) REVERT: B 563 LEU cc_start: 0.8000 (tp) cc_final: 0.7773 (mm) REVERT: B 624 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7783 (mmtm) REVERT: C 526 LYS cc_start: 0.6893 (mttt) cc_final: 0.5990 (tptp) REVERT: C 595 ASP cc_start: 0.7265 (m-30) cc_final: 0.7002 (m-30) REVERT: D 701 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8330 (mmtp) REVERT: E 632 SER cc_start: 0.8136 (p) cc_final: 0.7909 (p) REVERT: E 717 GLU cc_start: 0.7571 (tp30) cc_final: 0.7356 (tp30) REVERT: E 737 ASP cc_start: 0.7125 (t0) cc_final: 0.6892 (t0) REVERT: G 324 LYS cc_start: 0.8490 (mttm) cc_final: 0.8270 (mttm) REVERT: G 525 ASN cc_start: 0.6814 (m-40) cc_final: 0.6601 (t0) REVERT: G 581 ILE cc_start: 0.8434 (mt) cc_final: 0.8105 (mt) REVERT: G 748 SER cc_start: 0.8818 (t) cc_final: 0.8614 (p) outliers start: 0 outliers final: 1 residues processed: 585 average time/residue: 0.6589 time to fit residues: 425.7015 Evaluate side-chains 508 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 507 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 547 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS A 605 ASN A 741 ASN C 345 HIS C 531 GLN C 648 GLN C 688 ASN C 698 ASN D 533 ASN D 698 ASN D 713 GLN E 531 GLN E 648 GLN E 698 ASN F 345 HIS ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 576 ASN G 719 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.165195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.130327 restraints weight = 25312.789| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.68 r_work: 0.3429 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18279 Z= 0.169 Angle : 0.562 7.000 24716 Z= 0.307 Chirality : 0.044 0.173 2931 Planarity : 0.004 0.045 3023 Dihedral : 7.501 59.194 2367 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.49 % Allowed : 9.68 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.18), residues: 2146 helix: 3.01 (0.14), residues: 1202 sheet: 0.36 (0.29), residues: 311 loop : 1.24 (0.29), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 599 TYR 0.009 0.001 TYR D 740 PHE 0.020 0.002 PHE A 335 TRP 0.015 0.002 TRP B 316 HIS 0.007 0.001 HIS A 331 Details of bonding type rmsd covalent geometry : bond 0.00359 (18279) covalent geometry : angle 0.56223 (24716) hydrogen bonds : bond 0.06020 ( 1231) hydrogen bonds : angle 4.42865 ( 3618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 530 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LYS cc_start: 0.7703 (tttm) cc_final: 0.7387 (tttm) REVERT: A 621 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8242 (mtpp) REVERT: A 680 LEU cc_start: 0.8734 (mt) cc_final: 0.8531 (mp) REVERT: B 624 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8263 (mmtm) REVERT: B 669 LYS cc_start: 0.8274 (mtpm) cc_final: 0.7984 (ttmm) REVERT: B 673 LYS cc_start: 0.8593 (tttm) cc_final: 0.8362 (tttm) REVERT: B 748 SER cc_start: 0.8600 (t) cc_final: 0.8260 (p) REVERT: C 322 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8022 (mt) REVERT: C 526 LYS cc_start: 0.6893 (mttt) cc_final: 0.6365 (ttpp) REVERT: C 536 VAL cc_start: 0.8513 (t) cc_final: 0.8284 (m) REVERT: C 544 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.5860 (mmp) REVERT: C 657 ASP cc_start: 0.7961 (t70) cc_final: 0.7759 (t70) REVERT: C 669 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7886 (mttm) REVERT: D 322 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8448 (mp) REVERT: D 650 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8230 (t0) REVERT: D 653 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7780 (mt-10) REVERT: D 709 THR cc_start: 0.8429 (p) cc_final: 0.8110 (m) REVERT: E 530 LYS cc_start: 0.8463 (mttt) cc_final: 0.8247 (mttt) REVERT: E 720 ARG cc_start: 0.7753 (ttp-110) cc_final: 0.7494 (ttm-80) REVERT: E 737 ASP cc_start: 0.7255 (t0) cc_final: 0.6946 (t0) REVERT: F 322 LEU cc_start: 0.8055 (mp) cc_final: 0.7777 (tt) REVERT: F 653 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: F 717 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8310 (mm-30) REVERT: G 324 LYS cc_start: 0.8392 (mttm) cc_final: 0.8082 (mttm) REVERT: G 525 ASN cc_start: 0.7207 (m-40) cc_final: 0.6954 (t0) REVERT: G 534 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8562 (mtpt) REVERT: G 545 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7990 (mm) REVERT: G 577 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7992 (p) REVERT: G 581 ILE cc_start: 0.8562 (mt) cc_final: 0.8198 (mt) REVERT: G 717 GLU cc_start: 0.8213 (tp30) cc_final: 0.7767 (tm-30) REVERT: G 748 SER cc_start: 0.8822 (t) cc_final: 0.8586 (p) outliers start: 50 outliers final: 21 residues processed: 542 average time/residue: 0.6056 time to fit residues: 365.9031 Evaluate side-chains 532 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 503 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 534 LYS Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 568 VAL Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 680 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 167 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 ASN A 686 GLN C 531 GLN ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 ASN F 688 ASN G 531 GLN G 681 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.164672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129338 restraints weight = 25302.151| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.66 r_work: 0.3431 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18279 Z= 0.153 Angle : 0.491 7.039 24716 Z= 0.266 Chirality : 0.042 0.143 2931 Planarity : 0.003 0.045 3023 Dihedral : 7.441 59.480 2367 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.04 % Allowed : 11.62 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.19), residues: 2146 helix: 3.30 (0.14), residues: 1202 sheet: 0.60 (0.29), residues: 299 loop : 0.82 (0.28), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 599 TYR 0.013 0.001 TYR E 740 PHE 0.019 0.002 PHE G 582 TRP 0.013 0.001 TRP E 304 HIS 0.006 0.001 HIS F 684 Details of bonding type rmsd covalent geometry : bond 0.00343 (18279) covalent geometry : angle 0.49128 (24716) hydrogen bonds : bond 0.05015 ( 1231) hydrogen bonds : angle 4.16649 ( 3618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 513 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 544 MET cc_start: 0.7968 (ppp) cc_final: 0.7658 (ppp) REVERT: A 579 LYS cc_start: 0.7822 (tttm) cc_final: 0.7492 (tttm) REVERT: A 621 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8283 (mtpp) REVERT: B 624 LYS cc_start: 0.8575 (mmtm) cc_final: 0.8317 (mmtm) REVERT: B 669 LYS cc_start: 0.8259 (mtpm) cc_final: 0.7991 (ttmm) REVERT: B 748 SER cc_start: 0.8539 (t) cc_final: 0.8279 (p) REVERT: C 536 VAL cc_start: 0.8565 (t) cc_final: 0.8331 (m) REVERT: C 544 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.5995 (mmp) REVERT: C 669 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7849 (mttm) REVERT: D 531 GLN cc_start: 0.7529 (mt0) cc_final: 0.7323 (mt0) REVERT: D 650 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8194 (t0) REVERT: D 664 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7519 (tptm) REVERT: E 671 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.8279 (mmm-85) REVERT: E 717 GLU cc_start: 0.7899 (tp30) cc_final: 0.7646 (tp30) REVERT: E 720 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7517 (mtm-85) REVERT: E 737 ASP cc_start: 0.7261 (t0) cc_final: 0.6971 (t70) REVERT: F 322 LEU cc_start: 0.8000 (mp) cc_final: 0.7731 (tt) REVERT: F 653 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: F 671 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.8102 (mmm-85) REVERT: G 324 LYS cc_start: 0.8413 (mttm) cc_final: 0.8109 (mttm) REVERT: G 525 ASN cc_start: 0.7299 (m-40) cc_final: 0.7073 (t0) REVERT: G 534 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8467 (mtpt) REVERT: G 748 SER cc_start: 0.8758 (t) cc_final: 0.8545 (p) outliers start: 61 outliers final: 28 residues processed: 528 average time/residue: 0.6219 time to fit residues: 365.0917 Evaluate side-chains 522 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 489 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain E residue 720 ARG Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 722 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 0.9990 chunk 131 optimal weight: 50.0000 chunk 96 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 142 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 100 optimal weight: 50.0000 chunk 53 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 ASN A 686 GLN A 688 ASN A 741 ASN B 613 ASN C 648 GLN D 613 ASN ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 576 ASN E 648 GLN F 688 ASN G 531 GLN G 681 ASN G 688 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.163985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128322 restraints weight = 25353.092| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.73 r_work: 0.3398 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18279 Z= 0.179 Angle : 0.505 8.819 24716 Z= 0.270 Chirality : 0.042 0.166 2931 Planarity : 0.003 0.042 3023 Dihedral : 7.229 57.851 2367 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.54 % Allowed : 12.12 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.19), residues: 2146 helix: 3.33 (0.14), residues: 1202 sheet: 0.30 (0.29), residues: 311 loop : 0.68 (0.28), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 599 TYR 0.012 0.002 TYR E 740 PHE 0.022 0.002 PHE G 574 TRP 0.014 0.001 TRP C 304 HIS 0.006 0.001 HIS F 684 Details of bonding type rmsd covalent geometry : bond 0.00419 (18279) covalent geometry : angle 0.50511 (24716) hydrogen bonds : bond 0.04910 ( 1231) hydrogen bonds : angle 4.13854 ( 3618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 505 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7973 (ppp) cc_final: 0.7646 (ppp) REVERT: A 579 LYS cc_start: 0.7774 (tttm) cc_final: 0.7482 (tttm) REVERT: A 621 LYS cc_start: 0.8544 (mtpp) cc_final: 0.8342 (mtpp) REVERT: B 624 LYS cc_start: 0.8632 (mmtm) cc_final: 0.8365 (mmtm) REVERT: B 629 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8097 (t80) REVERT: B 662 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.8051 (t) REVERT: B 669 LYS cc_start: 0.8201 (mtpm) cc_final: 0.7927 (ttmm) REVERT: B 701 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8219 (mtmm) REVERT: B 748 SER cc_start: 0.8567 (t) cc_final: 0.8313 (p) REVERT: C 301 PHE cc_start: 0.7049 (t80) cc_final: 0.6688 (t80) REVERT: C 536 VAL cc_start: 0.8617 (t) cc_final: 0.8384 (m) REVERT: C 547 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.7056 (mm) REVERT: C 664 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7577 (mttt) REVERT: C 669 LYS cc_start: 0.8218 (ttmm) cc_final: 0.7770 (mttm) REVERT: D 531 GLN cc_start: 0.7665 (mt0) cc_final: 0.7462 (mt0) REVERT: E 737 ASP cc_start: 0.7439 (t0) cc_final: 0.7127 (t70) REVERT: F 322 LEU cc_start: 0.7996 (mp) cc_final: 0.7726 (tt) REVERT: F 579 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7934 (ttpp) REVERT: F 653 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: F 667 ASP cc_start: 0.7720 (m-30) cc_final: 0.7471 (t0) REVERT: G 305 THR cc_start: 0.8000 (t) cc_final: 0.7799 (p) REVERT: G 324 LYS cc_start: 0.8445 (mttm) cc_final: 0.8104 (mttm) REVERT: G 525 ASN cc_start: 0.7386 (m-40) cc_final: 0.7118 (t0) REVERT: G 534 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8447 (mtpt) REVERT: G 577 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8080 (p) REVERT: G 748 SER cc_start: 0.8774 (t) cc_final: 0.8563 (p) outliers start: 71 outliers final: 36 residues processed: 519 average time/residue: 0.6077 time to fit residues: 350.4498 Evaluate side-chains 542 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 498 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 635 CYS Chi-restraints excluded: chain C residue 664 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 718 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 534 LYS Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 128 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 174 optimal weight: 0.5980 chunk 142 optimal weight: 0.3980 chunk 168 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 688 ASN D 576 ASN ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 648 GLN F 688 ASN G 291 GLN G 531 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.164288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129388 restraints weight = 25327.964| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.65 r_work: 0.3411 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18279 Z= 0.141 Angle : 0.464 7.926 24716 Z= 0.250 Chirality : 0.041 0.202 2931 Planarity : 0.003 0.041 3023 Dihedral : 7.085 59.092 2367 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.14 % Allowed : 13.52 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.26 (0.19), residues: 2146 helix: 3.44 (0.14), residues: 1202 sheet: 0.22 (0.28), residues: 311 loop : 0.67 (0.28), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 722 TYR 0.010 0.001 TYR E 740 PHE 0.019 0.001 PHE D 301 TRP 0.014 0.001 TRP C 304 HIS 0.004 0.001 HIS E 708 Details of bonding type rmsd covalent geometry : bond 0.00315 (18279) covalent geometry : angle 0.46385 (24716) hydrogen bonds : bond 0.04492 ( 1231) hydrogen bonds : angle 4.03627 ( 3618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 514 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7920 (ppp) cc_final: 0.7634 (ppp) REVERT: A 579 LYS cc_start: 0.7740 (tttm) cc_final: 0.7488 (tttm) REVERT: A 670 ASP cc_start: 0.7557 (t0) cc_final: 0.7337 (t0) REVERT: A 717 GLU cc_start: 0.7528 (tp30) cc_final: 0.7057 (tp30) REVERT: A 737 ASP cc_start: 0.7906 (t0) cc_final: 0.7610 (t0) REVERT: B 624 LYS cc_start: 0.8606 (mmtm) cc_final: 0.8326 (mmtm) REVERT: B 629 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8070 (t80) REVERT: B 662 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.8035 (t) REVERT: B 669 LYS cc_start: 0.8264 (mtpm) cc_final: 0.7989 (ttmm) REVERT: B 748 SER cc_start: 0.8525 (t) cc_final: 0.8297 (p) REVERT: C 301 PHE cc_start: 0.7028 (t80) cc_final: 0.6684 (t80) REVERT: C 536 VAL cc_start: 0.8634 (t) cc_final: 0.8404 (m) REVERT: C 669 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7775 (mttm) REVERT: C 670 ASP cc_start: 0.7752 (m-30) cc_final: 0.7449 (m-30) REVERT: D 531 GLN cc_start: 0.7629 (mt0) cc_final: 0.7412 (mt0) REVERT: E 737 ASP cc_start: 0.7465 (t0) cc_final: 0.7156 (t70) REVERT: F 322 LEU cc_start: 0.8062 (mp) cc_final: 0.7784 (tt) REVERT: F 579 LYS cc_start: 0.8206 (ttpp) cc_final: 0.7920 (ttpp) REVERT: F 653 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: F 667 ASP cc_start: 0.7723 (m-30) cc_final: 0.7451 (t0) REVERT: F 671 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.8046 (mmm-85) REVERT: F 717 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7778 (tp30) REVERT: G 324 LYS cc_start: 0.8445 (mttm) cc_final: 0.8136 (mttm) REVERT: G 525 ASN cc_start: 0.7311 (m-40) cc_final: 0.7105 (m-40) REVERT: G 534 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8412 (mtpt) outliers start: 63 outliers final: 30 residues processed: 527 average time/residue: 0.5940 time to fit residues: 348.0276 Evaluate side-chains 539 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 505 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 534 LYS Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 80 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 171 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 179 optimal weight: 0.7980 chunk 201 optimal weight: 0.2980 chunk 41 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 688 ASN E 531 GLN E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.164509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129621 restraints weight = 25244.921| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.64 r_work: 0.3418 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18279 Z= 0.137 Angle : 0.473 8.961 24716 Z= 0.250 Chirality : 0.041 0.181 2931 Planarity : 0.003 0.038 3023 Dihedral : 7.090 59.523 2365 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.69 % Allowed : 14.46 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.19), residues: 2146 helix: 3.51 (0.14), residues: 1202 sheet: 0.15 (0.28), residues: 311 loop : 0.64 (0.29), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 722 TYR 0.012 0.001 TYR E 675 PHE 0.018 0.001 PHE D 301 TRP 0.013 0.001 TRP C 304 HIS 0.004 0.001 HIS F 684 Details of bonding type rmsd covalent geometry : bond 0.00306 (18279) covalent geometry : angle 0.47280 (24716) hydrogen bonds : bond 0.04342 ( 1231) hydrogen bonds : angle 3.99191 ( 3618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 507 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7888 (ppp) cc_final: 0.7641 (ppp) REVERT: A 607 MET cc_start: 0.8547 (mtm) cc_final: 0.8296 (mtm) REVERT: A 670 ASP cc_start: 0.7588 (t0) cc_final: 0.7356 (t0) REVERT: A 737 ASP cc_start: 0.7885 (t0) cc_final: 0.7534 (t0) REVERT: B 574 PHE cc_start: 0.6645 (m-10) cc_final: 0.6379 (m-10) REVERT: B 624 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8324 (mmtm) REVERT: B 629 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8089 (t80) REVERT: B 669 LYS cc_start: 0.8257 (mtpm) cc_final: 0.7984 (ttmm) REVERT: B 731 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8262 (ttpp) REVERT: B 748 SER cc_start: 0.8521 (t) cc_final: 0.8291 (p) REVERT: C 301 PHE cc_start: 0.6990 (t80) cc_final: 0.6665 (t80) REVERT: C 532 LEU cc_start: 0.8598 (tp) cc_final: 0.8277 (tt) REVERT: C 536 VAL cc_start: 0.8643 (t) cc_final: 0.8421 (m) REVERT: C 669 LYS cc_start: 0.8205 (ttmm) cc_final: 0.7782 (mttm) REVERT: C 670 ASP cc_start: 0.7760 (m-30) cc_final: 0.7453 (m-30) REVERT: D 531 GLN cc_start: 0.7611 (mt0) cc_final: 0.7387 (mt0) REVERT: E 701 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8452 (mtpp) REVERT: E 717 GLU cc_start: 0.7712 (tp30) cc_final: 0.7291 (tp30) REVERT: E 737 ASP cc_start: 0.7531 (t0) cc_final: 0.7221 (t70) REVERT: F 322 LEU cc_start: 0.8114 (mp) cc_final: 0.7819 (tt) REVERT: F 569 VAL cc_start: 0.8435 (t) cc_final: 0.8187 (p) REVERT: F 579 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7923 (ttpp) REVERT: F 612 MET cc_start: 0.8605 (mtp) cc_final: 0.8319 (ttm) REVERT: F 653 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: F 667 ASP cc_start: 0.7724 (m-30) cc_final: 0.7467 (t0) REVERT: F 671 ARG cc_start: 0.8455 (mmm-85) cc_final: 0.8110 (mmm160) REVERT: F 717 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7748 (tp30) REVERT: G 324 LYS cc_start: 0.8395 (mttm) cc_final: 0.8083 (mttm) REVERT: G 525 ASN cc_start: 0.7323 (m-40) cc_final: 0.7117 (m-40) REVERT: G 534 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8401 (mtpt) outliers start: 54 outliers final: 35 residues processed: 519 average time/residue: 0.6247 time to fit residues: 360.4072 Evaluate side-chains 541 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 504 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 539 ILE Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 31 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 ASN A 686 GLN A 688 ASN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 648 GLN F 531 GLN F 688 ASN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 ASN G 681 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.164418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129236 restraints weight = 25350.024| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.65 r_work: 0.3413 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18279 Z= 0.146 Angle : 0.469 8.574 24716 Z= 0.250 Chirality : 0.041 0.179 2931 Planarity : 0.003 0.036 3023 Dihedral : 7.024 59.239 2365 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.94 % Allowed : 14.36 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.19), residues: 2146 helix: 3.54 (0.14), residues: 1202 sheet: 0.15 (0.28), residues: 311 loop : 0.61 (0.28), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 599 TYR 0.012 0.001 TYR D 740 PHE 0.021 0.001 PHE A 574 TRP 0.013 0.001 TRP C 304 HIS 0.005 0.001 HIS E 708 Details of bonding type rmsd covalent geometry : bond 0.00334 (18279) covalent geometry : angle 0.46886 (24716) hydrogen bonds : bond 0.04326 ( 1231) hydrogen bonds : angle 3.97494 ( 3618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 503 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7848 (ppp) cc_final: 0.7620 (ppp) REVERT: A 670 ASP cc_start: 0.7582 (t0) cc_final: 0.7362 (t0) REVERT: A 737 ASP cc_start: 0.7903 (t0) cc_final: 0.7555 (t0) REVERT: B 624 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8319 (mmtm) REVERT: B 629 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8105 (t80) REVERT: B 662 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8082 (m) REVERT: B 669 LYS cc_start: 0.8263 (mtpm) cc_final: 0.7993 (ttmm) REVERT: B 697 VAL cc_start: 0.8044 (m) cc_final: 0.7819 (t) REVERT: B 701 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8174 (mtmm) REVERT: C 301 PHE cc_start: 0.6975 (t80) cc_final: 0.6666 (t80) REVERT: C 536 VAL cc_start: 0.8655 (t) cc_final: 0.8428 (m) REVERT: C 670 ASP cc_start: 0.7764 (m-30) cc_final: 0.7460 (m-30) REVERT: D 531 GLN cc_start: 0.7615 (mt0) cc_final: 0.7392 (mt0) REVERT: D 572 PHE cc_start: 0.7738 (t80) cc_final: 0.7472 (t80) REVERT: E 574 PHE cc_start: 0.6819 (m-10) cc_final: 0.6241 (m-10) REVERT: E 717 GLU cc_start: 0.7704 (tp30) cc_final: 0.7156 (tp30) REVERT: E 720 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.7294 (mtm-85) REVERT: E 737 ASP cc_start: 0.7596 (t0) cc_final: 0.7345 (t70) REVERT: F 322 LEU cc_start: 0.8115 (mp) cc_final: 0.7820 (tt) REVERT: F 569 VAL cc_start: 0.8472 (t) cc_final: 0.8229 (p) REVERT: F 579 LYS cc_start: 0.8173 (ttpp) cc_final: 0.7919 (ttpp) REVERT: F 653 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: F 667 ASP cc_start: 0.7740 (m-30) cc_final: 0.7476 (t0) REVERT: F 671 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.8138 (mmm160) REVERT: F 717 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7844 (tp30) REVERT: G 324 LYS cc_start: 0.8391 (mttm) cc_final: 0.8083 (mttm) REVERT: G 533 ASN cc_start: 0.8111 (t0) cc_final: 0.7889 (OUTLIER) REVERT: G 534 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8427 (mtpt) REVERT: G 701 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7686 (mttt) outliers start: 59 outliers final: 37 residues processed: 516 average time/residue: 0.5828 time to fit residues: 334.2228 Evaluate side-chains 542 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 500 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 605 ASN Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 653 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 534 LYS Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 701 LYS Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 8 optimal weight: 7.9990 chunk 214 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 166 optimal weight: 0.7980 chunk 155 optimal weight: 0.0570 chunk 106 optimal weight: 0.7980 chunk 204 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 15 optimal weight: 0.0670 chunk 93 optimal weight: 5.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 688 ASN E 531 GLN E 648 GLN E 688 ASN F 531 GLN F 688 ASN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.165410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130244 restraints weight = 25180.332| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.65 r_work: 0.3426 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18279 Z= 0.113 Angle : 0.463 9.285 24716 Z= 0.243 Chirality : 0.040 0.192 2931 Planarity : 0.003 0.035 3023 Dihedral : 6.985 59.630 2365 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.64 % Allowed : 15.41 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.41 (0.19), residues: 2146 helix: 3.62 (0.14), residues: 1202 sheet: 0.17 (0.28), residues: 311 loop : 0.65 (0.29), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 599 TYR 0.012 0.001 TYR D 740 PHE 0.018 0.001 PHE D 301 TRP 0.012 0.001 TRP C 304 HIS 0.004 0.001 HIS E 708 Details of bonding type rmsd covalent geometry : bond 0.00239 (18279) covalent geometry : angle 0.46324 (24716) hydrogen bonds : bond 0.04026 ( 1231) hydrogen bonds : angle 3.90010 ( 3618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 502 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 544 MET cc_start: 0.7857 (ppp) cc_final: 0.7618 (ppp) REVERT: A 673 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8227 (ttpp) REVERT: A 717 GLU cc_start: 0.7256 (tp30) cc_final: 0.6843 (tp30) REVERT: A 737 ASP cc_start: 0.7875 (t0) cc_final: 0.7246 (t0) REVERT: B 624 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8320 (mmtm) REVERT: B 629 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.8120 (t80) REVERT: B 662 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.8060 (m) REVERT: B 669 LYS cc_start: 0.8309 (mtpm) cc_final: 0.8046 (ttmm) REVERT: B 697 VAL cc_start: 0.8025 (m) cc_final: 0.7805 (t) REVERT: B 701 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8164 (mtmm) REVERT: B 717 GLU cc_start: 0.7618 (tp30) cc_final: 0.7171 (tp30) REVERT: C 301 PHE cc_start: 0.6944 (t80) cc_final: 0.6645 (t80) REVERT: C 532 LEU cc_start: 0.8572 (tp) cc_final: 0.8274 (tt) REVERT: C 536 VAL cc_start: 0.8651 (t) cc_final: 0.8425 (m) REVERT: C 669 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7817 (mttm) REVERT: C 698 ASN cc_start: 0.7414 (t0) cc_final: 0.6998 (t0) REVERT: D 531 GLN cc_start: 0.7617 (mt0) cc_final: 0.7372 (mt0) REVERT: D 572 PHE cc_start: 0.7731 (t80) cc_final: 0.7433 (t80) REVERT: E 717 GLU cc_start: 0.7648 (tp30) cc_final: 0.7240 (tp30) REVERT: E 737 ASP cc_start: 0.7588 (t0) cc_final: 0.7334 (t70) REVERT: F 322 LEU cc_start: 0.8094 (mp) cc_final: 0.7812 (tt) REVERT: F 569 VAL cc_start: 0.8466 (t) cc_final: 0.8226 (p) REVERT: F 579 LYS cc_start: 0.8127 (ttpp) cc_final: 0.7856 (ttpp) REVERT: F 667 ASP cc_start: 0.7669 (m-30) cc_final: 0.7432 (t0) REVERT: F 671 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8148 (mmm160) REVERT: F 717 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7802 (tp30) REVERT: G 324 LYS cc_start: 0.8399 (mttm) cc_final: 0.8094 (mttm) REVERT: G 533 ASN cc_start: 0.8193 (t0) cc_final: 0.7919 (m-40) REVERT: G 534 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8425 (mtpt) REVERT: G 701 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7672 (mttt) outliers start: 53 outliers final: 36 residues processed: 517 average time/residue: 0.5694 time to fit residues: 327.1013 Evaluate side-chains 541 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 500 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 701 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 534 LYS Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 701 LYS Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 28 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 206 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 204 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 158 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 688 ASN C 648 GLN ** E 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 531 GLN F 648 GLN F 688 ASN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.164648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129661 restraints weight = 25203.372| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.64 r_work: 0.3421 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18279 Z= 0.143 Angle : 0.481 9.427 24716 Z= 0.253 Chirality : 0.041 0.191 2931 Planarity : 0.003 0.036 3023 Dihedral : 6.936 59.808 2365 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.59 % Allowed : 15.61 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.35 (0.19), residues: 2146 helix: 3.58 (0.14), residues: 1202 sheet: 0.13 (0.28), residues: 311 loop : 0.61 (0.29), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 720 TYR 0.013 0.001 TYR D 740 PHE 0.019 0.001 PHE D 301 TRP 0.012 0.001 TRP C 304 HIS 0.005 0.001 HIS E 708 Details of bonding type rmsd covalent geometry : bond 0.00328 (18279) covalent geometry : angle 0.48145 (24716) hydrogen bonds : bond 0.04177 ( 1231) hydrogen bonds : angle 3.93442 ( 3618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 494 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 544 MET cc_start: 0.7829 (ppp) cc_final: 0.7596 (ppp) REVERT: A 717 GLU cc_start: 0.7320 (tp30) cc_final: 0.6881 (tp30) REVERT: A 737 ASP cc_start: 0.7923 (t0) cc_final: 0.7456 (t0) REVERT: B 624 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8331 (mmtm) REVERT: B 629 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.8118 (t80) REVERT: B 662 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.8065 (m) REVERT: B 669 LYS cc_start: 0.8262 (mtpm) cc_final: 0.7994 (ttmm) REVERT: B 697 VAL cc_start: 0.8065 (m) cc_final: 0.7846 (t) REVERT: B 701 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8173 (mtmm) REVERT: C 301 PHE cc_start: 0.6987 (t80) cc_final: 0.6692 (t80) REVERT: C 532 LEU cc_start: 0.8590 (tp) cc_final: 0.8302 (tt) REVERT: C 536 VAL cc_start: 0.8652 (t) cc_final: 0.8432 (m) REVERT: C 669 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7792 (mttm) REVERT: C 698 ASN cc_start: 0.7408 (t0) cc_final: 0.7014 (t0) REVERT: D 531 GLN cc_start: 0.7628 (mt0) cc_final: 0.7395 (mt0) REVERT: D 572 PHE cc_start: 0.7747 (t80) cc_final: 0.7447 (t80) REVERT: E 717 GLU cc_start: 0.7674 (tp30) cc_final: 0.7306 (tp30) REVERT: E 737 ASP cc_start: 0.7626 (t0) cc_final: 0.7360 (t70) REVERT: F 322 LEU cc_start: 0.8106 (mp) cc_final: 0.7830 (tt) REVERT: F 569 VAL cc_start: 0.8512 (t) cc_final: 0.8269 (p) REVERT: F 579 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7875 (ttpp) REVERT: F 667 ASP cc_start: 0.7689 (m-30) cc_final: 0.7454 (t0) REVERT: F 671 ARG cc_start: 0.8479 (mmm-85) cc_final: 0.8141 (mmm160) REVERT: F 717 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7733 (tp30) REVERT: G 324 LYS cc_start: 0.8430 (mttm) cc_final: 0.8130 (mttm) REVERT: G 533 ASN cc_start: 0.8198 (t0) cc_final: 0.7952 (m-40) REVERT: G 534 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8436 (mtpt) REVERT: G 701 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7663 (mttt) outliers start: 52 outliers final: 37 residues processed: 508 average time/residue: 0.6205 time to fit residues: 350.0552 Evaluate side-chains 531 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 489 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 701 LYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 534 LYS Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 701 LYS Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 178 optimal weight: 0.0050 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 50.0000 chunk 119 optimal weight: 0.0570 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 chunk 173 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 overall best weight: 0.3312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 688 ASN D 576 ASN ** E 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 688 ASN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.165666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130882 restraints weight = 25209.476| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.65 r_work: 0.3439 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18279 Z= 0.105 Angle : 0.473 11.322 24716 Z= 0.249 Chirality : 0.041 0.197 2931 Planarity : 0.003 0.035 3023 Dihedral : 6.754 57.690 2365 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.04 % Allowed : 16.46 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.42 (0.19), residues: 2146 helix: 3.64 (0.14), residues: 1202 sheet: 0.09 (0.28), residues: 311 loop : 0.68 (0.29), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 671 TYR 0.012 0.001 TYR D 740 PHE 0.020 0.001 PHE D 301 TRP 0.011 0.001 TRP C 304 HIS 0.003 0.001 HIS E 708 Details of bonding type rmsd covalent geometry : bond 0.00217 (18279) covalent geometry : angle 0.47269 (24716) hydrogen bonds : bond 0.03884 ( 1231) hydrogen bonds : angle 3.88115 ( 3618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 493 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 544 MET cc_start: 0.7767 (ppp) cc_final: 0.7534 (ppp) REVERT: A 717 GLU cc_start: 0.7209 (tp30) cc_final: 0.6666 (tp30) REVERT: A 737 ASP cc_start: 0.7904 (t0) cc_final: 0.7447 (t0) REVERT: B 624 LYS cc_start: 0.8559 (mmtm) cc_final: 0.8330 (mmtm) REVERT: B 629 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8108 (t80) REVERT: B 662 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.8026 (m) REVERT: B 669 LYS cc_start: 0.8295 (mtpm) cc_final: 0.8033 (ttmm) REVERT: B 697 VAL cc_start: 0.8033 (m) cc_final: 0.7819 (t) REVERT: B 701 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8163 (mtmm) REVERT: C 301 PHE cc_start: 0.6955 (t80) cc_final: 0.6658 (t80) REVERT: C 532 LEU cc_start: 0.8553 (tp) cc_final: 0.8274 (tt) REVERT: C 536 VAL cc_start: 0.8651 (t) cc_final: 0.8438 (m) REVERT: C 669 LYS cc_start: 0.8181 (ttmm) cc_final: 0.7812 (mttm) REVERT: C 698 ASN cc_start: 0.7348 (t0) cc_final: 0.6927 (t0) REVERT: D 531 GLN cc_start: 0.7601 (mt0) cc_final: 0.7350 (mt0) REVERT: E 717 GLU cc_start: 0.7612 (tp30) cc_final: 0.7149 (tp30) REVERT: E 720 ARG cc_start: 0.7550 (mtm-85) cc_final: 0.7040 (mtm-85) REVERT: E 737 ASP cc_start: 0.7630 (t0) cc_final: 0.7370 (t70) REVERT: F 322 LEU cc_start: 0.8087 (mp) cc_final: 0.7808 (tt) REVERT: F 569 VAL cc_start: 0.8508 (t) cc_final: 0.8280 (p) REVERT: F 579 LYS cc_start: 0.8119 (ttpp) cc_final: 0.7837 (ttpp) REVERT: F 667 ASP cc_start: 0.7707 (m-30) cc_final: 0.7463 (t0) REVERT: F 671 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.8129 (mmm160) REVERT: F 717 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7687 (tp30) REVERT: G 324 LYS cc_start: 0.8411 (mttm) cc_final: 0.8112 (mttm) REVERT: G 533 ASN cc_start: 0.8159 (t0) cc_final: 0.7943 (m-40) REVERT: G 534 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8362 (mttp) REVERT: G 701 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7624 (mttt) outliers start: 41 outliers final: 29 residues processed: 505 average time/residue: 0.6101 time to fit residues: 342.5250 Evaluate side-chains 521 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 488 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 606 LYS Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 545 ILE Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 701 LYS Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 189 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 200 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN A 688 ASN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN ** E 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN F 531 GLN F 688 ASN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.165108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129963 restraints weight = 25291.136| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.65 r_work: 0.3424 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18279 Z= 0.138 Angle : 0.496 12.062 24716 Z= 0.261 Chirality : 0.042 0.231 2931 Planarity : 0.003 0.042 3023 Dihedral : 6.802 56.655 2365 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.14 % Allowed : 16.86 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.35 (0.19), residues: 2146 helix: 3.59 (0.14), residues: 1202 sheet: 0.09 (0.28), residues: 311 loop : 0.63 (0.29), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 671 TYR 0.013 0.001 TYR D 740 PHE 0.021 0.001 PHE D 574 TRP 0.010 0.001 TRP C 304 HIS 0.005 0.001 HIS E 708 Details of bonding type rmsd covalent geometry : bond 0.00313 (18279) covalent geometry : angle 0.49620 (24716) hydrogen bonds : bond 0.04083 ( 1231) hydrogen bonds : angle 3.91785 ( 3618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9104.65 seconds wall clock time: 155 minutes 3.46 seconds (9303.46 seconds total)