Starting phenix.real_space_refine on Mon Jun 16 01:31:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n5e_24187/06_2025/7n5e_24187.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n5e_24187/06_2025/7n5e_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7n5e_24187/06_2025/7n5e_24187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n5e_24187/06_2025/7n5e_24187.map" model { file = "/net/cci-nas-00/data/ceres_data/7n5e_24187/06_2025/7n5e_24187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n5e_24187/06_2025/7n5e_24187.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.48, per 1000 atoms: 0.58 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: 4.41 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.88 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: 5.65 Time building geometry restraints manager: 5.21 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 751 or resid 801)) selection = (chain 'B' and (resid 294 through 751 or resid 801)) selection = (chain 'C' and (resid 294 through 751 or resid 801)) selection = (chain 'D' and (resid 294 through 751 or resid 801)) selection = (chain 'E' and (resid 294 through 751 or resid 801)) selection = (chain 'F' and (resid 294 through 751 or resid 801)) selection = (chain 'G' and (resid 294 through 751 or resid 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: 1.220 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 39.530 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.070 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:14.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (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 TRP 0.036 0.010 TRP E 683 HIS 0.010 0.002 HIS A 331 PHE 0.059 0.006 PHE A 335 TYR 0.044 0.009 TYR E 675 ARG 0.006 0.001 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.14397 ( 1231) hydrogen bonds : angle 6.18949 ( 3618) covalent geometry : bond 0.02280 (18279) covalent geometry : angle 1.54442 (24716) *********************** 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 : 1.791 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: 0.7001 (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: 0.8271 (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: 1.4615 time to fit residues: 943.9886 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 : 2.035 ------------------------------------------------------------------------------- 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 183 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 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 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.164991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.130337 restraints weight = 25302.019| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.63 r_work: 0.3433 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18279 Z= 0.184 Angle : 0.564 6.283 24716 Z= 0.312 Chirality : 0.044 0.178 2931 Planarity : 0.004 0.042 3023 Dihedral : 7.451 59.222 2367 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.54 % Allowed : 9.73 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.18), residues: 2146 helix: 3.06 (0.14), residues: 1202 sheet: 0.40 (0.29), residues: 306 loop : 1.24 (0.28), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 304 HIS 0.007 0.001 HIS A 331 PHE 0.021 0.002 PHE A 335 TYR 0.010 0.002 TYR D 740 ARG 0.004 0.000 ARG F 599 Details of bonding type rmsd hydrogen bonds : bond 0.06224 ( 1231) hydrogen bonds : angle 4.46240 ( 3618) covalent geometry : bond 0.00384 (18279) covalent geometry : angle 0.56422 (24716) *********************** 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 586 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 535 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ILE cc_start: 0.8453 (mt) cc_final: 0.8166 (mt) REVERT: A 544 MET cc_start: 0.8046 (ppp) cc_final: 0.7698 (ppp) REVERT: A 579 LYS cc_start: 0.7712 (tttm) cc_final: 0.7390 (tttm) REVERT: A 673 LYS cc_start: 0.8622 (ttpp) cc_final: 0.8267 (ttmm) REVERT: B 624 LYS cc_start: 0.8563 (mmtm) cc_final: 0.8255 (mmtm) REVERT: B 669 LYS cc_start: 0.8282 (mtpm) cc_final: 0.7987 (ttmm) REVERT: B 673 LYS cc_start: 0.8599 (tttm) cc_final: 0.8360 (tttm) REVERT: B 748 SER cc_start: 0.8616 (t) cc_final: 0.8264 (p) REVERT: C 322 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7992 (mt) REVERT: C 526 LYS cc_start: 0.6908 (mttt) cc_final: 0.6401 (ttpp) REVERT: C 536 VAL cc_start: 0.8511 (t) cc_final: 0.8276 (m) REVERT: C 544 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.5856 (mmp) REVERT: C 669 LYS cc_start: 0.8288 (ttmm) cc_final: 0.7894 (mttm) REVERT: D 322 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8448 (mp) REVERT: D 650 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8234 (t0) REVERT: D 709 THR cc_start: 0.8422 (p) cc_final: 0.8110 (m) REVERT: E 530 LYS cc_start: 0.8457 (mttt) cc_final: 0.8238 (mttt) REVERT: E 720 ARG cc_start: 0.7740 (ttp-110) cc_final: 0.7487 (ttm-80) REVERT: E 737 ASP cc_start: 0.7230 (t0) cc_final: 0.6929 (t0) REVERT: F 322 LEU cc_start: 0.8048 (mp) cc_final: 0.7763 (tt) REVERT: F 717 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8366 (mm-30) REVERT: G 324 LYS cc_start: 0.8337 (mttm) cc_final: 0.8025 (mttm) REVERT: G 525 ASN cc_start: 0.7198 (m-40) cc_final: 0.6957 (t0) REVERT: G 534 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8487 (mtpt) REVERT: G 577 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7973 (p) REVERT: G 581 ILE cc_start: 0.8553 (mt) cc_final: 0.8198 (mt) REVERT: G 717 GLU cc_start: 0.8211 (tp30) cc_final: 0.7747 (tm-30) REVERT: G 748 SER cc_start: 0.8827 (t) cc_final: 0.8585 (p) outliers start: 51 outliers final: 23 residues processed: 547 average time/residue: 1.4891 time to fit residues: 911.2313 Evaluate side-chains 542 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 513 time to evaluate : 2.083 ------------------------------------------------------------------------------- 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 541 ILE 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 693 GLU 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 607 MET 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 G residue 534 LYS 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 180 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 190 optimal weight: 0.0170 chunk 31 optimal weight: 40.0000 chunk 64 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 chunk 109 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- 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 686 GLN C 531 GLN C 713 GLN ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 HIS E 531 GLN E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN G 531 GLN G 681 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.164993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130055 restraints weight = 25297.819| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.65 r_work: 0.3435 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18279 Z= 0.138 Angle : 0.482 7.426 24716 Z= 0.262 Chirality : 0.041 0.142 2931 Planarity : 0.003 0.043 3023 Dihedral : 7.408 58.235 2367 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.79 % Allowed : 11.62 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.19), residues: 2146 helix: 3.33 (0.14), residues: 1202 sheet: 0.59 (0.29), residues: 299 loop : 0.88 (0.28), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 304 HIS 0.004 0.001 HIS A 346 PHE 0.021 0.001 PHE G 301 TYR 0.010 0.001 TYR E 740 ARG 0.004 0.000 ARG F 599 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 1231) hydrogen bonds : angle 4.16760 ( 3618) covalent geometry : bond 0.00298 (18279) covalent geometry : angle 0.48218 (24716) *********************** 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 575 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 519 time to evaluate : 1.853 Fit side-chains revert: symmetry clash REVERT: A 541 ILE cc_start: 0.8467 (mt) cc_final: 0.8069 (mm) REVERT: A 544 MET cc_start: 0.7991 (ppp) cc_final: 0.7683 (ppp) REVERT: A 579 LYS cc_start: 0.7756 (tttm) cc_final: 0.7430 (tttm) REVERT: A 605 ASN cc_start: 0.8404 (m110) cc_final: 0.8194 (m-40) REVERT: A 621 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8266 (mttp) REVERT: B 624 LYS cc_start: 0.8566 (mmtm) cc_final: 0.8285 (mmtm) REVERT: B 669 LYS cc_start: 0.8264 (mtpm) cc_final: 0.8008 (ttmm) REVERT: B 748 SER cc_start: 0.8568 (t) cc_final: 0.8300 (p) REVERT: C 322 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8067 (mt) REVERT: C 536 VAL cc_start: 0.8558 (t) cc_final: 0.8328 (m) REVERT: C 544 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.5917 (mmp) REVERT: C 669 LYS cc_start: 0.8252 (ttmm) cc_final: 0.7857 (mttm) REVERT: C 713 GLN cc_start: 0.8141 (tp40) cc_final: 0.7630 (tp40) REVERT: D 650 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8188 (t0) REVERT: D 664 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7510 (tptm) REVERT: E 702 MET cc_start: 0.8525 (mtp) cc_final: 0.8325 (mtt) REVERT: E 737 ASP cc_start: 0.7346 (t0) cc_final: 0.7060 (t70) REVERT: F 322 LEU cc_start: 0.8020 (mp) cc_final: 0.7747 (tt) REVERT: F 671 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8218 (mmm160) REVERT: F 715 PHE cc_start: 0.8342 (t80) cc_final: 0.8142 (t80) REVERT: G 324 LYS cc_start: 0.8426 (mttm) cc_final: 0.8128 (mttm) REVERT: G 525 ASN cc_start: 0.7264 (m-40) cc_final: 0.7039 (t0) REVERT: G 534 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8458 (mtpt) outliers start: 56 outliers final: 28 residues processed: 535 average time/residue: 1.3101 time to fit residues: 783.3023 Evaluate side-chains 535 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 503 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 663 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 322 LEU 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 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 319 LYS Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 722 ARG Chi-restraints excluded: chain G residue 739 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 211 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 130 optimal weight: 50.0000 chunk 84 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 648 GLN ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 GLN G 681 ASN G 688 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 = 0.164180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128361 restraints weight = 25238.280| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.73 r_work: 0.3411 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18279 Z= 0.157 Angle : 0.492 9.040 24716 Z= 0.263 Chirality : 0.042 0.194 2931 Planarity : 0.003 0.040 3023 Dihedral : 7.149 58.652 2367 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.29 % Allowed : 12.02 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.19), residues: 2146 helix: 3.38 (0.14), residues: 1202 sheet: 0.22 (0.27), residues: 341 loop : 0.78 (0.29), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 304 HIS 0.005 0.001 HIS F 684 PHE 0.022 0.002 PHE G 574 TYR 0.012 0.001 TYR E 740 ARG 0.006 0.000 ARG F 599 Details of bonding type rmsd hydrogen bonds : bond 0.04813 ( 1231) hydrogen bonds : angle 4.10832 ( 3618) covalent geometry : bond 0.00359 (18279) covalent geometry : angle 0.49189 (24716) *********************** 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 565 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 499 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ILE cc_start: 0.8435 (mt) cc_final: 0.7974 (mm) REVERT: A 544 MET cc_start: 0.7923 (ppp) cc_final: 0.7579 (ppp) REVERT: A 579 LYS cc_start: 0.7745 (tttm) cc_final: 0.7403 (tttm) REVERT: A 605 ASN cc_start: 0.8457 (m110) cc_final: 0.8232 (m-40) REVERT: A 717 GLU cc_start: 0.7604 (tp30) cc_final: 0.7130 (tp30) REVERT: B 624 LYS cc_start: 0.8584 (mmtm) cc_final: 0.8350 (mmtm) REVERT: B 662 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.8030 (t) REVERT: B 669 LYS cc_start: 0.8239 (mtpm) cc_final: 0.7966 (ttmm) REVERT: B 689 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8334 (ttp) REVERT: B 748 SER cc_start: 0.8563 (t) cc_final: 0.8296 (p) REVERT: C 322 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8079 (mt) REVERT: C 536 VAL cc_start: 0.8561 (t) cc_final: 0.8325 (m) REVERT: C 547 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.7011 (mm) REVERT: C 669 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7779 (mttm) REVERT: C 713 GLN cc_start: 0.8106 (tp40) cc_final: 0.7645 (tp40) REVERT: D 322 LEU cc_start: 0.8642 (mt) cc_final: 0.8393 (mp) REVERT: D 664 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7495 (tptm) REVERT: E 701 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8482 (mtpp) REVERT: E 737 ASP cc_start: 0.7350 (t0) cc_final: 0.7047 (t70) REVERT: F 322 LEU cc_start: 0.7987 (mp) cc_final: 0.7706 (tt) REVERT: F 579 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7897 (ttpp) REVERT: F 603 ASP cc_start: 0.8050 (m-30) cc_final: 0.7832 (m-30) REVERT: F 667 ASP cc_start: 0.7714 (m-30) cc_final: 0.7442 (t0) REVERT: F 715 PHE cc_start: 0.8324 (t80) cc_final: 0.8109 (t80) REVERT: G 324 LYS cc_start: 0.8409 (mttm) cc_final: 0.8079 (mttm) REVERT: G 525 ASN cc_start: 0.7347 (m-40) cc_final: 0.7077 (t0) REVERT: G 534 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8449 (mtpt) REVERT: G 577 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.8073 (p) REVERT: G 689 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8252 (ttp) REVERT: G 701 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7793 (mtpt) outliers start: 66 outliers final: 31 residues processed: 517 average time/residue: 1.3953 time to fit residues: 801.9607 Evaluate side-chains 538 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 499 time to evaluate : 1.942 ------------------------------------------------------------------------------- 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 B residue 662 VAL Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 739 LYS 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 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 586 ILE Chi-restraints excluded: chain D residue 616 THR 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 546 VAL Chi-restraints excluded: chain E residue 567 LEU 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 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 545 ILE Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 577 THR Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 689 MET Chi-restraints excluded: chain G residue 701 LYS Chi-restraints excluded: chain G residue 722 ARG 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 136 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 191 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 185 optimal weight: 0.0970 chunk 138 optimal weight: 0.8980 chunk 199 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 A 741 ASN B 613 ASN D 576 ASN E 531 GLN E 576 ASN E 648 GLN F 688 ASN G 291 GLN G 531 GLN G 681 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.164524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129383 restraints weight = 25363.312| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.69 r_work: 0.3415 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3143 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= 0.141 Angle : 0.465 8.067 24716 Z= 0.250 Chirality : 0.041 0.216 2931 Planarity : 0.003 0.036 3023 Dihedral : 7.011 58.152 2367 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.09 % Allowed : 13.02 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.19), residues: 2146 helix: 3.44 (0.14), residues: 1202 sheet: 0.21 (0.27), residues: 341 loop : 0.75 (0.29), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 304 HIS 0.004 0.001 HIS E 708 PHE 0.020 0.001 PHE D 301 TYR 0.009 0.001 TYR E 740 ARG 0.003 0.000 ARG D 722 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 1231) hydrogen bonds : angle 4.03011 ( 3618) covalent geometry : bond 0.00315 (18279) covalent geometry : angle 0.46537 (24716) *********************** 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: 62 poor density : 515 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7896 (ppp) cc_final: 0.7636 (ppp) REVERT: A 579 LYS cc_start: 0.7745 (tttm) cc_final: 0.7463 (tttm) REVERT: A 673 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8325 (ttpp) REVERT: B 574 PHE cc_start: 0.6730 (m-10) cc_final: 0.6469 (m-10) REVERT: B 624 LYS cc_start: 0.8590 (mmtm) cc_final: 0.8336 (mmtm) REVERT: B 629 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8053 (t80) REVERT: B 662 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8039 (t) REVERT: B 669 LYS cc_start: 0.8273 (mtpm) cc_final: 0.8006 (ttmm) REVERT: B 748 SER cc_start: 0.8521 (t) cc_final: 0.8296 (p) REVERT: C 301 PHE cc_start: 0.7046 (t80) cc_final: 0.6703 (t80) REVERT: C 322 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8085 (mt) REVERT: C 536 VAL cc_start: 0.8624 (t) cc_final: 0.8396 (m) REVERT: C 669 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7821 (mttm) REVERT: C 713 GLN cc_start: 0.8066 (tp40) cc_final: 0.7658 (tp40) REVERT: D 322 LEU cc_start: 0.8620 (mt) cc_final: 0.8400 (mp) REVERT: D 664 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7553 (tptm) REVERT: E 701 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8454 (mtpp) REVERT: E 717 GLU cc_start: 0.7707 (tp30) cc_final: 0.7290 (tp30) REVERT: E 737 ASP cc_start: 0.7430 (t0) cc_final: 0.7138 (t70) REVERT: F 322 LEU cc_start: 0.8047 (mp) cc_final: 0.7776 (tt) REVERT: F 579 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7967 (ttpp) REVERT: F 667 ASP cc_start: 0.7723 (m-30) cc_final: 0.7469 (t0) REVERT: F 671 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.8049 (mmm-85) REVERT: F 717 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7957 (tp30) REVERT: G 324 LYS cc_start: 0.8413 (mttm) cc_final: 0.8100 (mttm) REVERT: G 525 ASN cc_start: 0.7273 (m-40) cc_final: 0.7028 (t0) REVERT: G 534 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8418 (mtpt) REVERT: G 577 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.8059 (p) REVERT: G 701 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7727 (mtpt) outliers start: 62 outliers final: 30 residues processed: 529 average time/residue: 1.2963 time to fit residues: 762.6668 Evaluate side-chains 538 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 501 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 718 LYS 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 739 LYS Chi-restraints excluded: chain C residue 322 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 534 LYS Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 664 LYS 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 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 678 GLN Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 534 LYS 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 701 LYS Chi-restraints excluded: chain G residue 722 ARG 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 102 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 85 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 137 optimal weight: 0.7980 chunk 24 optimal weight: 0.0470 chunk 51 optimal weight: 0.5980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 E 531 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4073 r_free = 0.4073 target = 0.165548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130680 restraints weight = 25527.667| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.66 r_work: 0.3438 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3340 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= 0.109 Angle : 0.458 9.448 24716 Z= 0.241 Chirality : 0.040 0.216 2931 Planarity : 0.003 0.034 3023 Dihedral : 6.868 59.882 2365 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.09 % Allowed : 13.77 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.19), residues: 2146 helix: 3.56 (0.14), residues: 1202 sheet: 0.30 (0.29), residues: 305 loop : 0.65 (0.28), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 304 HIS 0.003 0.001 HIS E 708 PHE 0.017 0.001 PHE D 301 TYR 0.007 0.001 TYR D 740 ARG 0.004 0.000 ARG F 599 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 1231) hydrogen bonds : angle 3.92859 ( 3618) covalent geometry : bond 0.00222 (18279) covalent geometry : angle 0.45834 (24716) *********************** 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 560 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 498 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7837 (ppp) cc_final: 0.7557 (ppp) REVERT: A 579 LYS cc_start: 0.7715 (tttm) cc_final: 0.7428 (tttm) REVERT: A 673 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8312 (ttpp) REVERT: A 717 GLU cc_start: 0.7405 (tp30) cc_final: 0.7076 (tp30) REVERT: A 737 ASP cc_start: 0.7878 (t0) cc_final: 0.7510 (t0) REVERT: B 531 GLN cc_start: 0.8177 (mt0) cc_final: 0.7965 (mt0) REVERT: B 574 PHE cc_start: 0.6533 (m-10) cc_final: 0.5926 (m-10) REVERT: B 624 LYS cc_start: 0.8594 (mmtm) cc_final: 0.8341 (mmtm) REVERT: B 629 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.8090 (t80) REVERT: B 662 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7983 (t) REVERT: B 669 LYS cc_start: 0.8297 (mtpm) cc_final: 0.8033 (ttmm) REVERT: B 717 GLU cc_start: 0.7652 (tp30) cc_final: 0.7209 (tp30) REVERT: B 731 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8262 (ttpp) REVERT: B 748 SER cc_start: 0.8534 (t) cc_final: 0.8292 (p) REVERT: C 301 PHE cc_start: 0.6962 (t80) cc_final: 0.6624 (t80) REVERT: C 322 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8090 (mt) REVERT: C 532 LEU cc_start: 0.8559 (tp) cc_final: 0.8282 (tt) REVERT: C 536 VAL cc_start: 0.8639 (t) cc_final: 0.8413 (m) REVERT: C 669 LYS cc_start: 0.8200 (ttmm) cc_final: 0.7807 (mttm) REVERT: C 670 ASP cc_start: 0.7770 (m-30) cc_final: 0.7448 (m-30) REVERT: C 713 GLN cc_start: 0.8053 (tp40) cc_final: 0.7581 (tp40) REVERT: D 322 LEU cc_start: 0.8598 (mt) cc_final: 0.8366 (mp) REVERT: D 572 PHE cc_start: 0.7691 (t80) cc_final: 0.7418 (t80) REVERT: E 574 PHE cc_start: 0.6506 (m-10) cc_final: 0.5953 (m-10) REVERT: E 701 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8432 (mtpp) REVERT: E 717 GLU cc_start: 0.7676 (tp30) cc_final: 0.7306 (tp30) REVERT: E 737 ASP cc_start: 0.7448 (t0) cc_final: 0.7140 (t70) REVERT: F 322 LEU cc_start: 0.8103 (mp) cc_final: 0.7815 (tt) REVERT: F 579 LYS cc_start: 0.8178 (ttpp) cc_final: 0.7952 (ttpp) REVERT: F 667 ASP cc_start: 0.7720 (m-30) cc_final: 0.7446 (t0) REVERT: F 671 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8119 (mmm160) REVERT: G 324 LYS cc_start: 0.8400 (mttm) cc_final: 0.8089 (mttm) REVERT: G 525 ASN cc_start: 0.7291 (m-40) cc_final: 0.7038 (t0) REVERT: G 534 LYS cc_start: 0.8624 (ttmm) cc_final: 0.8401 (mtpt) REVERT: G 701 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7707 (mtpt) outliers start: 62 outliers final: 29 residues processed: 513 average time/residue: 1.3478 time to fit residues: 766.2717 Evaluate side-chains 525 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 492 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 563 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 322 LEU 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 629 TYR Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 534 LYS 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 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 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 621 LYS Chi-restraints excluded: chain G residue 701 LYS Chi-restraints excluded: chain G residue 722 ARG 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 77 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 160 optimal weight: 40.0000 chunk 40 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 648 GLN E 531 GLN E 648 GLN E 688 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4053 r_free = 0.4053 target = 0.163984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.128685 restraints weight = 25240.842| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.66 r_work: 0.3407 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18279 Z= 0.167 Angle : 0.491 8.455 24716 Z= 0.261 Chirality : 0.042 0.175 2931 Planarity : 0.003 0.037 3023 Dihedral : 7.049 59.809 2365 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.04 % Allowed : 13.92 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.19), residues: 2146 helix: 3.49 (0.14), residues: 1202 sheet: 0.23 (0.29), residues: 311 loop : 0.58 (0.28), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 304 HIS 0.006 0.001 HIS F 684 PHE 0.019 0.002 PHE D 301 TYR 0.012 0.002 TYR D 740 ARG 0.003 0.000 ARG E 599 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 1231) hydrogen bonds : angle 4.00645 ( 3618) covalent geometry : bond 0.00389 (18279) covalent geometry : angle 0.49142 (24716) *********************** 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 573 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 512 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7853 (ppp) cc_final: 0.7619 (ppp) REVERT: A 737 ASP cc_start: 0.7909 (t0) cc_final: 0.7580 (t0) REVERT: B 624 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8339 (mmtm) REVERT: B 629 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.8129 (t80) REVERT: B 669 LYS cc_start: 0.8275 (mtpm) cc_final: 0.8004 (ttmm) REVERT: B 731 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8247 (ttpp) REVERT: C 301 PHE cc_start: 0.6983 (t80) cc_final: 0.6667 (t80) REVERT: C 322 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8080 (mt) REVERT: C 532 LEU cc_start: 0.8594 (tp) cc_final: 0.8302 (tt) REVERT: C 536 VAL cc_start: 0.8650 (t) cc_final: 0.8436 (m) REVERT: C 670 ASP cc_start: 0.7767 (m-30) cc_final: 0.7451 (m-30) REVERT: C 713 GLN cc_start: 0.8064 (tp40) cc_final: 0.7637 (tp40) REVERT: D 322 LEU cc_start: 0.8621 (mt) cc_final: 0.8418 (mp) REVERT: D 572 PHE cc_start: 0.7739 (t80) cc_final: 0.7466 (t80) REVERT: D 695 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7451 (mt-10) REVERT: E 717 GLU cc_start: 0.7680 (tp30) cc_final: 0.7274 (tp30) REVERT: E 737 ASP cc_start: 0.7534 (t0) cc_final: 0.7268 (t70) REVERT: F 322 LEU cc_start: 0.8108 (mp) cc_final: 0.7829 (tt) REVERT: F 579 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7947 (ttpp) REVERT: F 667 ASP cc_start: 0.7710 (m-30) cc_final: 0.7464 (t0) REVERT: F 671 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8141 (mmm160) REVERT: F 717 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7802 (tp30) REVERT: G 324 LYS cc_start: 0.8409 (mttm) cc_final: 0.8098 (mttm) REVERT: G 525 ASN cc_start: 0.7354 (m-40) cc_final: 0.7136 (m-40) REVERT: G 533 ASN cc_start: 0.8091 (t0) cc_final: 0.7881 (OUTLIER) REVERT: G 534 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8426 (mtpt) REVERT: G 701 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7695 (mtpt) outliers start: 61 outliers final: 42 residues processed: 526 average time/residue: 1.3168 time to fit residues: 770.3163 Evaluate side-chains 560 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 515 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 655 SER 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 563 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 322 LEU 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 635 CYS 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 534 LYS 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 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 567 LEU Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 695 GLU Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 701 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 37 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 172 optimal weight: 0.0170 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 158 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 648 GLN ** 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 = 0.4061 r_free = 0.4061 target = 0.164659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129437 restraints weight = 25261.359| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.65 r_work: 0.3422 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3527 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= 0.137 Angle : 0.478 9.218 24716 Z= 0.252 Chirality : 0.041 0.188 2931 Planarity : 0.003 0.035 3023 Dihedral : 7.014 59.929 2365 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.89 % Allowed : 15.21 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.19), residues: 2146 helix: 3.54 (0.14), residues: 1202 sheet: 0.17 (0.28), residues: 311 loop : 0.56 (0.29), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 304 HIS 0.005 0.001 HIS E 708 PHE 0.017 0.001 PHE D 301 TYR 0.012 0.001 TYR D 740 ARG 0.003 0.000 ARG D 722 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 1231) hydrogen bonds : angle 3.95835 ( 3618) covalent geometry : bond 0.00309 (18279) covalent geometry : angle 0.47843 (24716) *********************** 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 566 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 508 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7847 (ppp) cc_final: 0.7622 (ppp) REVERT: A 737 ASP cc_start: 0.7908 (t0) cc_final: 0.7526 (t0) REVERT: B 624 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8327 (mmtm) REVERT: B 629 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.8115 (t80) REVERT: B 669 LYS cc_start: 0.8276 (mtpm) cc_final: 0.7996 (ttmm) REVERT: B 697 VAL cc_start: 0.8014 (m) cc_final: 0.7794 (t) REVERT: B 701 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8146 (mtmm) REVERT: C 301 PHE cc_start: 0.6950 (t80) cc_final: 0.6648 (t80) REVERT: C 322 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8089 (mt) REVERT: C 532 LEU cc_start: 0.8597 (tp) cc_final: 0.8301 (tt) REVERT: C 536 VAL cc_start: 0.8637 (t) cc_final: 0.8425 (m) REVERT: C 669 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7811 (mttm) REVERT: C 713 GLN cc_start: 0.8044 (tp40) cc_final: 0.7592 (tp40) REVERT: D 572 PHE cc_start: 0.7742 (t80) cc_final: 0.7443 (t80) REVERT: D 701 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8162 (mmtm) REVERT: E 717 GLU cc_start: 0.7676 (tp30) cc_final: 0.7359 (tp30) REVERT: E 737 ASP cc_start: 0.7538 (t0) cc_final: 0.7275 (t70) REVERT: F 322 LEU cc_start: 0.8105 (mp) cc_final: 0.7815 (tt) REVERT: F 569 VAL cc_start: 0.8462 (t) cc_final: 0.8234 (p) REVERT: F 579 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7885 (ttpp) REVERT: F 667 ASP cc_start: 0.7699 (m-30) cc_final: 0.7448 (t0) REVERT: F 671 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.8158 (mmm160) REVERT: F 717 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7761 (tp30) REVERT: G 324 LYS cc_start: 0.8385 (mttm) cc_final: 0.8071 (mttm) REVERT: G 525 ASN cc_start: 0.7305 (m-40) cc_final: 0.7080 (m-40) REVERT: G 533 ASN cc_start: 0.8054 (t0) cc_final: 0.7830 (m-40) REVERT: G 701 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7679 (mtpt) REVERT: G 718 LYS cc_start: 0.8660 (tttm) cc_final: 0.8419 (tttt) outliers start: 58 outliers final: 35 residues processed: 528 average time/residue: 1.3266 time to fit residues: 778.6815 Evaluate side-chains 546 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 507 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 563 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 322 LEU 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 629 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 534 LYS 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 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 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 614 ILE 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 545 ILE Chi-restraints excluded: chain G residue 583 GLU Chi-restraints excluded: chain G residue 695 GLU Chi-restraints excluded: chain G residue 701 LYS Chi-restraints excluded: chain G residue 722 ARG 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 119 optimal weight: 1.9990 chunk 159 optimal weight: 0.0050 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 54 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 204 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 174 optimal weight: 0.7980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 E 531 GLN F 531 GLN ** 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 = 0.4071 r_free = 0.4071 target = 0.165479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130324 restraints weight = 25486.232| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.66 r_work: 0.3434 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3660 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= 0.110 Angle : 0.466 8.988 24716 Z= 0.247 Chirality : 0.041 0.194 2931 Planarity : 0.003 0.035 3023 Dihedral : 6.870 59.235 2365 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.59 % Allowed : 15.86 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.19), residues: 2146 helix: 3.58 (0.14), residues: 1202 sheet: 0.10 (0.28), residues: 311 loop : 0.62 (0.29), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 304 HIS 0.004 0.001 HIS E 708 PHE 0.020 0.001 PHE D 301 TYR 0.013 0.001 TYR E 675 ARG 0.005 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 1231) hydrogen bonds : angle 3.89701 ( 3618) covalent geometry : bond 0.00231 (18279) covalent geometry : angle 0.46607 (24716) *********************** 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 550 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 498 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7826 (ppp) cc_final: 0.7584 (ppp) REVERT: A 717 GLU cc_start: 0.7175 (tp30) cc_final: 0.6759 (tp30) REVERT: A 737 ASP cc_start: 0.7884 (t0) cc_final: 0.7227 (t70) REVERT: B 624 LYS cc_start: 0.8570 (mmtm) cc_final: 0.8323 (mmtm) REVERT: B 629 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.8131 (t80) REVERT: B 669 LYS cc_start: 0.8305 (mtpm) cc_final: 0.8034 (ttmm) REVERT: C 301 PHE cc_start: 0.6903 (t80) cc_final: 0.6600 (t80) REVERT: C 322 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8071 (mt) REVERT: C 532 LEU cc_start: 0.8565 (tp) cc_final: 0.8272 (tt) REVERT: C 536 VAL cc_start: 0.8652 (t) cc_final: 0.8424 (m) REVERT: C 669 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7834 (mttm) REVERT: C 698 ASN cc_start: 0.7415 (t0) cc_final: 0.6987 (t0) REVERT: C 713 GLN cc_start: 0.8019 (tp40) cc_final: 0.7518 (tp40) REVERT: E 717 GLU cc_start: 0.7589 (tp30) cc_final: 0.7153 (tp30) REVERT: E 720 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7008 (mtm-85) REVERT: E 737 ASP cc_start: 0.7610 (t0) cc_final: 0.7347 (t70) REVERT: F 322 LEU cc_start: 0.8098 (mp) cc_final: 0.7808 (tt) REVERT: F 579 LYS cc_start: 0.8123 (ttpp) cc_final: 0.7858 (ttpp) REVERT: F 667 ASP cc_start: 0.7705 (m-30) cc_final: 0.7453 (t0) REVERT: F 671 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8149 (mmm160) REVERT: F 717 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7726 (tp30) REVERT: G 324 LYS cc_start: 0.8386 (mttm) cc_final: 0.8075 (mttm) REVERT: G 525 ASN cc_start: 0.7312 (m-40) cc_final: 0.7030 (m-40) REVERT: G 533 ASN cc_start: 0.8179 (t0) cc_final: 0.7948 (m-40) REVERT: G 701 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7628 (mtpt) REVERT: G 718 LYS cc_start: 0.8622 (tttm) cc_final: 0.8364 (tttt) outliers start: 52 outliers final: 32 residues processed: 514 average time/residue: 1.3537 time to fit residues: 771.6600 Evaluate side-chains 524 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 488 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 739 LYS Chi-restraints excluded: chain C residue 322 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 534 LYS 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 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 577 THR Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 720 ARG 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 701 LYS Chi-restraints excluded: chain G residue 722 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 184 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 199 optimal weight: 0.6980 chunk 162 optimal weight: 50.0000 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 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 ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN D 576 ASN ** E 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4062 r_free = 0.4062 target = 0.164645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129621 restraints weight = 25330.107| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.65 r_work: 0.3425 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18279 Z= 0.141 Angle : 0.495 10.342 24716 Z= 0.261 Chirality : 0.041 0.194 2931 Planarity : 0.003 0.035 3023 Dihedral : 6.864 58.135 2365 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.24 % Allowed : 16.56 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.19), residues: 2146 helix: 3.56 (0.14), residues: 1202 sheet: 0.08 (0.28), residues: 311 loop : 0.58 (0.29), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 304 HIS 0.005 0.001 HIS E 708 PHE 0.024 0.001 PHE D 574 TYR 0.015 0.001 TYR D 740 ARG 0.002 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 1231) hydrogen bonds : angle 3.93077 ( 3618) covalent geometry : bond 0.00322 (18279) covalent geometry : angle 0.49522 (24716) ********************** 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 549 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 504 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7834 (ppp) cc_final: 0.7591 (ppp) REVERT: A 621 LYS cc_start: 0.8447 (mtpp) cc_final: 0.8233 (mtpp) REVERT: A 731 LYS cc_start: 0.9036 (ttmm) cc_final: 0.8770 (ttpt) REVERT: A 737 ASP cc_start: 0.7927 (t0) cc_final: 0.7487 (t0) REVERT: B 624 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8356 (mmtm) REVERT: B 629 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.8123 (t80) REVERT: B 662 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.8048 (m) REVERT: B 669 LYS cc_start: 0.8312 (mtpm) cc_final: 0.8039 (ttmm) REVERT: B 697 VAL cc_start: 0.8057 (m) cc_final: 0.7833 (t) REVERT: C 301 PHE cc_start: 0.6923 (t80) cc_final: 0.6633 (t80) REVERT: C 322 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8052 (mt) REVERT: C 669 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7852 (mttm) REVERT: C 698 ASN cc_start: 0.7401 (t0) cc_final: 0.6996 (t0) REVERT: C 713 GLN cc_start: 0.8036 (tp40) cc_final: 0.7561 (tp40) REVERT: E 717 GLU cc_start: 0.7620 (tp30) cc_final: 0.7182 (tp30) REVERT: E 720 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6998 (mtm-85) REVERT: E 737 ASP cc_start: 0.7631 (t0) cc_final: 0.7369 (t70) REVERT: F 322 LEU cc_start: 0.8114 (mp) cc_final: 0.7826 (tt) REVERT: F 569 VAL cc_start: 0.8499 (t) cc_final: 0.8275 (p) REVERT: F 579 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7862 (ttpp) REVERT: F 667 ASP cc_start: 0.7710 (m-30) cc_final: 0.7477 (t0) REVERT: F 671 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.8150 (mmm160) REVERT: F 717 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7696 (tp30) REVERT: G 324 LYS cc_start: 0.8394 (mttm) cc_final: 0.8085 (mttm) REVERT: G 525 ASN cc_start: 0.7324 (m-40) cc_final: 0.7085 (m-40) REVERT: G 533 ASN cc_start: 0.8171 (t0) cc_final: 0.7935 (m-40) REVERT: G 637 LYS cc_start: 0.8598 (mttp) cc_final: 0.8396 (mttt) REVERT: G 701 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7623 (mtpt) REVERT: G 718 LYS cc_start: 0.8644 (tttm) cc_final: 0.8389 (tttt) outliers start: 45 outliers final: 34 residues processed: 521 average time/residue: 1.3373 time to fit residues: 774.7842 Evaluate side-chains 539 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 500 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 563 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 322 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 534 LYS 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 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 607 MET Chi-restraints excluded: chain E residue 632 SER Chi-restraints excluded: chain E residue 720 ARG Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 531 GLN 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 722 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 13 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 174 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 GLN F 648 GLN ** G 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN G 698 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.163779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128948 restraints weight = 25305.647| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.64 r_work: 0.3411 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18279 Z= 0.193 Angle : 0.538 12.080 24716 Z= 0.281 Chirality : 0.043 0.242 2931 Planarity : 0.003 0.038 3023 Dihedral : 6.878 59.507 2365 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.29 % Allowed : 16.76 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.19), residues: 2146 helix: 3.45 (0.14), residues: 1202 sheet: 0.04 (0.26), residues: 341 loop : 0.59 (0.30), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 316 HIS 0.006 0.001 HIS E 708 PHE 0.023 0.002 PHE D 574 TYR 0.016 0.002 TYR D 740 ARG 0.004 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 1231) hydrogen bonds : angle 4.01651 ( 3618) covalent geometry : bond 0.00459 (18279) covalent geometry : angle 0.53809 (24716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20686.55 seconds wall clock time: 356 minutes 17.41 seconds (21377.41 seconds total)