Starting phenix.real_space_refine on Sat Aug 8 16:24:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vjn_65116/08_2026/9vjn_65116.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vjn_65116/08_2026/9vjn_65116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vjn_65116/08_2026/9vjn_65116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vjn_65116/08_2026/9vjn_65116.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vjn_65116/08_2026/9vjn_65116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vjn_65116/08_2026/9vjn_65116.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 120 5.16 5 C 18648 2.51 5 N 4604 2.21 5 O 4944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28320 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6927 Classifications: {'peptide': 845} Link IDs: {'PTRANS': 18, 'TRANS': 826} Chain breaks: 11 Chain: "D" Number of atoms: 6927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6927 Classifications: {'peptide': 845} Link IDs: {'PTRANS': 18, 'TRANS': 826} Chain breaks: 11 Chain: "C" Number of atoms: 6927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6927 Classifications: {'peptide': 845} Link IDs: {'PTRANS': 18, 'TRANS': 826} Chain breaks: 11 Chain: "B" Number of atoms: 6927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6927 Classifications: {'peptide': 845} Link IDs: {'PTRANS': 18, 'TRANS': 826} Chain breaks: 11 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 153 Unusual residues: {'POV': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 153 Unusual residues: {'POV': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 153 Unusual residues: {'POV': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 153 Unusual residues: {'POV': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 6.26, per 1000 atoms: 0.22 Number of scatterers: 28320 At special positions: 0 Unit cell: (142.545, 142.545, 146.965, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 4 15.00 O 4944 8.00 N 4604 7.00 C 18648 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: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 8 sheets defined 77.0% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.678A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.714A pdb=" N LYS A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 309 through 322 removed outlier: 4.354A pdb=" N SER A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.523A pdb=" N ALA A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'A' and resid 370 through 387 removed outlier: 4.102A pdb=" N SER A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 425 through 437 removed outlier: 3.998A pdb=" N GLN A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 454 through 468 removed outlier: 4.866A pdb=" N GLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 removed outlier: 3.643A pdb=" N ASN A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.540A pdb=" N PHE A 487 " --> pdb=" O ASN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 533 removed outlier: 3.517A pdb=" N ARG A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.768A pdb=" N GLU A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 584 " --> pdb=" O ILE A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 removed outlier: 4.029A pdb=" N LEU A 592 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 636 removed outlier: 3.583A pdb=" N ALA A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 645 removed outlier: 3.530A pdb=" N VAL A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 723 through 733 removed outlier: 3.659A pdb=" N SER A 733 " --> pdb=" O ALA A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 758 removed outlier: 3.584A pdb=" N VAL A 743 " --> pdb=" O SER A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 790 Processing helix chain 'A' and resid 791 through 795 Processing helix chain 'A' and resid 796 through 818 removed outlier: 3.604A pdb=" N VAL A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 852 removed outlier: 3.520A pdb=" N LEU A 825 " --> pdb=" O ASN A 821 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 837 " --> pdb=" O CYS A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 890 removed outlier: 3.530A pdb=" N ALA A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 912 removed outlier: 3.541A pdb=" N TYR A 905 " --> pdb=" O ARG A 901 " (cutoff:3.500A) Proline residue: A 907 - end of helix Processing helix chain 'A' and resid 955 through 984 removed outlier: 5.138A pdb=" N TYR A 981 " --> pdb=" O ALA A 977 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR A 982 " --> pdb=" O MET A 978 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A 983 " --> pdb=" O PHE A 979 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY A 984 " --> pdb=" O GLY A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1008 removed outlier: 3.503A pdb=" N VAL A 993 " --> pdb=" O ASN A 989 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1014 No H-bonds generated for 'chain 'A' and resid 1012 through 1014' Processing helix chain 'A' and resid 1015 through 1028 removed outlier: 4.055A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1070 removed outlier: 3.504A pdb=" N TRP A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A1070 " --> pdb=" O LYS A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1104 removed outlier: 4.021A pdb=" N LYS A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 137 removed outlier: 3.682A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 202 removed outlier: 3.636A pdb=" N TYR D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 287 Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.520A pdb=" N LYS D 321 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.526A pdb=" N ALA D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'D' and resid 370 through 387 removed outlier: 4.090A pdb=" N SER D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 419 Processing helix chain 'D' and resid 425 through 437 removed outlier: 3.948A pdb=" N GLN D 429 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 454 through 468 removed outlier: 4.870A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE D 463 " --> pdb=" O GLN D 459 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 removed outlier: 3.634A pdb=" N ASN D 480 " --> pdb=" O LEU D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 488 removed outlier: 3.541A pdb=" N PHE D 487 " --> pdb=" O ASN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 500 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 533 removed outlier: 3.508A pdb=" N ARG D 533 " --> pdb=" O ALA D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 570 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.765A pdb=" N GLU D 582 " --> pdb=" O LYS D 578 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR D 584 " --> pdb=" O ILE D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 602 removed outlier: 4.042A pdb=" N LEU D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 636 removed outlier: 3.597A pdb=" N ALA D 611 " --> pdb=" O ASP D 607 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 645 removed outlier: 3.554A pdb=" N VAL D 645 " --> pdb=" O GLU D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 663 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 Processing helix chain 'D' and resid 703 through 708 Processing helix chain 'D' and resid 723 through 733 removed outlier: 3.657A pdb=" N SER D 733 " --> pdb=" O ALA D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 758 removed outlier: 3.583A pdb=" N VAL D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 790 Processing helix chain 'D' and resid 791 through 795 Processing helix chain 'D' and resid 796 through 818 removed outlier: 3.622A pdb=" N VAL D 800 " --> pdb=" O ASP D 796 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 852 removed outlier: 3.514A pdb=" N LEU D 825 " --> pdb=" O ASN D 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 837 " --> pdb=" O CYS D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 890 removed outlier: 3.530A pdb=" N ALA D 880 " --> pdb=" O VAL D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 912 removed outlier: 3.533A pdb=" N TYR D 905 " --> pdb=" O ARG D 901 " (cutoff:3.500A) Proline residue: D 907 - end of helix Processing helix chain 'D' and resid 955 through 984 removed outlier: 5.142A pdb=" N TYR D 981 " --> pdb=" O ALA D 977 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N THR D 982 " --> pdb=" O MET D 978 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL D 983 " --> pdb=" O PHE D 979 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY D 984 " --> pdb=" O GLY D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1008 removed outlier: 3.968A pdb=" N ARG D1008 " --> pdb=" O GLU D1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1014 No H-bonds generated for 'chain 'D' and resid 1012 through 1014' Processing helix chain 'D' and resid 1015 through 1028 removed outlier: 4.058A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1070 removed outlier: 3.562A pdb=" N TRP D1055 " --> pdb=" O GLU D1051 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D1067 " --> pdb=" O TYR D1063 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D1070 " --> pdb=" O LYS D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1080 through 1104 removed outlier: 4.047A pdb=" N LYS D1104 " --> pdb=" O ALA D1100 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 137 removed outlier: 3.682A pdb=" N LEU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.632A pdb=" N TYR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.519A pdb=" N LYS C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.526A pdb=" N ALA C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 370 through 387 removed outlier: 4.090A pdb=" N SER C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 419 Processing helix chain 'C' and resid 425 through 437 removed outlier: 3.951A pdb=" N GLN C 429 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 454 through 468 removed outlier: 4.871A pdb=" N GLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 463 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 464 " --> pdb=" O GLU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 removed outlier: 3.634A pdb=" N ASN C 480 " --> pdb=" O LEU C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 488 removed outlier: 3.540A pdb=" N PHE C 487 " --> pdb=" O ASN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 500 Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 533 removed outlier: 3.507A pdb=" N ARG C 533 " --> pdb=" O ALA C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 570 Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.763A pdb=" N GLU C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR C 584 " --> pdb=" O ILE C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 602 removed outlier: 4.042A pdb=" N LEU C 592 " --> pdb=" O THR C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 636 removed outlier: 3.597A pdb=" N ALA C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 645 removed outlier: 3.554A pdb=" N VAL C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 663 Processing helix chain 'C' and resid 665 through 670 Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 Processing helix chain 'C' and resid 703 through 708 Processing helix chain 'C' and resid 723 through 733 removed outlier: 3.659A pdb=" N SER C 733 " --> pdb=" O ALA C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 758 removed outlier: 3.582A pdb=" N VAL C 743 " --> pdb=" O SER C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 765 through 790 Processing helix chain 'C' and resid 791 through 795 Processing helix chain 'C' and resid 796 through 818 removed outlier: 3.607A pdb=" N VAL C 800 " --> pdb=" O ASP C 796 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 852 removed outlier: 3.513A pdb=" N LEU C 825 " --> pdb=" O ASN C 821 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 837 " --> pdb=" O CYS C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 890 removed outlier: 3.530A pdb=" N ALA C 880 " --> pdb=" O VAL C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 912 removed outlier: 3.533A pdb=" N TYR C 905 " --> pdb=" O ARG C 901 " (cutoff:3.500A) Proline residue: C 907 - end of helix Processing helix chain 'C' and resid 955 through 984 removed outlier: 5.145A pdb=" N TYR C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N THR C 982 " --> pdb=" O MET C 978 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 983 " --> pdb=" O PHE C 979 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY C 984 " --> pdb=" O GLY C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1008 removed outlier: 3.501A pdb=" N VAL C 993 " --> pdb=" O ASN C 989 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG C1008 " --> pdb=" O GLU C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1014 No H-bonds generated for 'chain 'C' and resid 1012 through 1014' Processing helix chain 'C' and resid 1015 through 1028 removed outlier: 4.058A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1070 removed outlier: 3.563A pdb=" N TRP C1055 " --> pdb=" O GLU C1051 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS C1070 " --> pdb=" O LYS C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1104 removed outlier: 4.029A pdb=" N LYS C1104 " --> pdb=" O ALA C1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.682A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 186 through 201 removed outlier: 3.702A pdb=" N LYS B 190 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.519A pdb=" N LYS B 321 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.526A pdb=" N ALA B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 370 through 387 removed outlier: 4.092A pdb=" N SER B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 Processing helix chain 'B' and resid 425 through 437 removed outlier: 3.955A pdb=" N GLN B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 454 through 468 removed outlier: 4.865A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 removed outlier: 3.635A pdb=" N ASN B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 488 removed outlier: 3.541A pdb=" N PHE B 487 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 500 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 533 removed outlier: 3.508A pdb=" N ARG B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 570 Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.762A pdb=" N GLU B 582 " --> pdb=" O LYS B 578 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 602 removed outlier: 4.044A pdb=" N LEU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 636 removed outlier: 3.598A pdb=" N ALA B 611 " --> pdb=" O ASP B 607 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 645 removed outlier: 3.553A pdb=" N VAL B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 Processing helix chain 'B' and resid 703 through 708 Processing helix chain 'B' and resid 723 through 733 removed outlier: 3.653A pdb=" N SER B 733 " --> pdb=" O ALA B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 758 removed outlier: 3.584A pdb=" N VAL B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 790 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 796 through 818 removed outlier: 3.598A pdb=" N VAL B 800 " --> pdb=" O ASP B 796 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 852 removed outlier: 3.513A pdb=" N LEU B 825 " --> pdb=" O ASN B 821 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 837 " --> pdb=" O CYS B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 890 removed outlier: 3.531A pdb=" N ALA B 880 " --> pdb=" O VAL B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 912 removed outlier: 3.533A pdb=" N TYR B 905 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Proline residue: B 907 - end of helix Processing helix chain 'B' and resid 955 through 984 removed outlier: 5.142A pdb=" N TYR B 981 " --> pdb=" O ALA B 977 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N THR B 982 " --> pdb=" O MET B 978 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL B 983 " --> pdb=" O PHE B 979 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY B 984 " --> pdb=" O GLY B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1008 removed outlier: 3.501A pdb=" N VAL B 993 " --> pdb=" O ASN B 989 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG B1008 " --> pdb=" O GLU B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1014 No H-bonds generated for 'chain 'B' and resid 1012 through 1014' Processing helix chain 'B' and resid 1015 through 1028 removed outlier: 4.054A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1070 removed outlier: 3.555A pdb=" N TRP B1055 " --> pdb=" O GLU B1051 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B1067 " --> pdb=" O TYR B1063 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B1070 " --> pdb=" O LYS B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1104 removed outlier: 4.040A pdb=" N LYS B1104 " --> pdb=" O ALA B1100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 120 removed outlier: 6.209A pdb=" N LYS A 116 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU A 262 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 118 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 210 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 179 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 328 through 329 Processing sheet with id=AA3, first strand: chain 'D' and resid 116 through 120 removed outlier: 6.203A pdb=" N LYS D 116 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU D 262 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU D 118 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL D 210 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 179 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 329 Processing sheet with id=AA5, first strand: chain 'C' and resid 116 through 120 removed outlier: 6.203A pdb=" N LYS C 116 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU C 262 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU C 118 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 210 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 179 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 328 through 329 Processing sheet with id=AA7, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.202A pdb=" N LYS B 116 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU B 262 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 118 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B 210 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 179 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 328 through 329 1818 hydrogen bonds defined for protein. 5418 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: 5.87 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4792 1.33 - 1.45: 7742 1.45 - 1.57: 16250 1.57 - 1.70: 8 1.70 - 1.82: 184 Bond restraints: 28976 Sorted by residual: bond pdb=" N GLY C 115 " pdb=" CA GLY C 115 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.20e+00 bond pdb=" N GLY D 115 " pdb=" CA GLY D 115 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.20e+00 bond pdb=" N GLY B 115 " pdb=" CA GLY B 115 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.20e+00 bond pdb=" N GLY A 115 " pdb=" CA GLY A 115 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.08e+00 bond pdb=" CB GLN C 173 " pdb=" CG GLN C 173 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.25e+00 ... (remaining 28971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 38948 2.07 - 4.13: 276 4.13 - 6.20: 18 6.20 - 8.26: 6 8.26 - 10.33: 4 Bond angle restraints: 39252 Sorted by residual: angle pdb=" CB MET C 161 " pdb=" CG MET C 161 " pdb=" SD MET C 161 " ideal model delta sigma weight residual 112.70 123.03 -10.33 3.00e+00 1.11e-01 1.18e+01 angle pdb=" CB MET B 161 " pdb=" CG MET B 161 " pdb=" SD MET B 161 " ideal model delta sigma weight residual 112.70 123.01 -10.31 3.00e+00 1.11e-01 1.18e+01 angle pdb=" CB MET A 161 " pdb=" CG MET A 161 " pdb=" SD MET A 161 " ideal model delta sigma weight residual 112.70 122.81 -10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CA GLU B 491 " pdb=" CB GLU B 491 " pdb=" CG GLU B 491 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CB MET D 161 " pdb=" CG MET D 161 " pdb=" SD MET D 161 " ideal model delta sigma weight residual 112.70 122.59 -9.89 3.00e+00 1.11e-01 1.09e+01 ... (remaining 39247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 15217 17.69 - 35.38: 1828 35.38 - 53.07: 439 53.07 - 70.75: 125 70.75 - 88.44: 47 Dihedral angle restraints: 17656 sinusoidal: 7728 harmonic: 9928 Sorted by residual: dihedral pdb=" CA ASP C 469 " pdb=" CB ASP C 469 " pdb=" CG ASP C 469 " pdb=" OD1 ASP C 469 " ideal model delta sinusoidal sigma weight residual -30.00 -84.53 54.53 1 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA ASP A 469 " pdb=" CB ASP A 469 " pdb=" CG ASP A 469 " pdb=" OD1 ASP A 469 " ideal model delta sinusoidal sigma weight residual -30.00 -84.53 54.53 1 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA ASP D 469 " pdb=" CB ASP D 469 " pdb=" CG ASP D 469 " pdb=" OD1 ASP D 469 " ideal model delta sinusoidal sigma weight residual -30.00 -84.50 54.50 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 17653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3278 0.030 - 0.060: 747 0.060 - 0.090: 279 0.090 - 0.119: 120 0.119 - 0.149: 20 Chirality restraints: 4444 Sorted by residual: chirality pdb=" CA ILE B1011 " pdb=" N ILE B1011 " pdb=" C ILE B1011 " pdb=" CB ILE B1011 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA ILE A1011 " pdb=" N ILE A1011 " pdb=" C ILE A1011 " pdb=" CB ILE A1011 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE C1011 " pdb=" N ILE C1011 " pdb=" C ILE C1011 " pdb=" CB ILE C1011 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 4441 not shown) Planarity restraints: 4756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 491 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" CD GLU D 491 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU D 491 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU D 491 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D1011 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO D1012 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D1012 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D1012 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B1011 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO B1012 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B1012 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B1012 " 0.018 5.00e-02 4.00e+02 ... (remaining 4753 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 11387 2.91 - 3.41: 30793 3.41 - 3.91: 44647 3.91 - 4.40: 49959 4.40 - 4.90: 82438 Nonbonded interactions: 219224 Sorted by model distance: nonbonded pdb=" O GLU A 435 " pdb=" OE1 GLU A 435 " model vdw 2.416 3.040 nonbonded pdb=" O GLU D 435 " pdb=" OE1 GLU D 435 " model vdw 2.424 3.040 nonbonded pdb=" O GLU C 435 " pdb=" OE1 GLU C 435 " model vdw 2.424 3.040 nonbonded pdb=" O GLU B 435 " pdb=" OE1 GLU B 435 " model vdw 2.424 3.040 nonbonded pdb=" O ASP B 469 " pdb=" OD1 ASP B 469 " model vdw 2.437 3.040 ... (remaining 219219 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 26.290 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.003 0.045 28976 Z= 0.123 Angle : 0.491 10.327 39252 Z= 0.260 Chirality : 0.034 0.149 4444 Planarity : 0.003 0.038 4756 Dihedral : 16.591 88.442 11200 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.39 % Allowed : 18.73 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.15), residues: 3284 helix: 2.65 (0.10), residues: 2360 sheet: -0.57 (0.38), residues: 192 loop : -0.72 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 197 TYR 0.009 0.001 TYR B 905 PHE 0.008 0.001 PHE B 738 TRP 0.010 0.001 TRP A 994 HIS 0.003 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (28976) covalent geometry : angle 0.49129 / 0.26 (39252) hydrogen bonds : bond 0.14669 / 9.55 ( 1818) hydrogen bonds : angle 5.36275 / 3.84 ( 5418) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 354 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ILE cc_start: 0.8186 (mt) cc_final: 0.7973 (mt) REVERT: A 198 ASP cc_start: 0.7351 (m-30) cc_final: 0.6946 (m-30) REVERT: A 631 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 894 GLN cc_start: 0.7774 (pm20) cc_final: 0.6938 (mp10) REVERT: A 898 TRP cc_start: 0.7317 (m-10) cc_final: 0.7117 (m-10) REVERT: A 905 TYR cc_start: 0.6729 (p90) cc_final: 0.6523 (p90) REVERT: A 1066 LYS cc_start: 0.8779 (mttt) cc_final: 0.8419 (mtpp) REVERT: D 353 MET cc_start: 0.7875 (mtt) cc_final: 0.7667 (mtm) REVERT: D 485 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7626 (mp10) REVERT: D 631 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8216 (tm-30) REVERT: D 905 TYR cc_start: 0.6775 (p90) cc_final: 0.6559 (p90) REVERT: D 964 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7612 (mmt) REVERT: D 1066 LYS cc_start: 0.8832 (mttt) cc_final: 0.8468 (mtpp) REVERT: C 194 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7113 (mm-30) REVERT: C 198 ASP cc_start: 0.7306 (m-30) cc_final: 0.6881 (m-30) REVERT: C 353 MET cc_start: 0.7874 (mtt) cc_final: 0.7665 (mtm) REVERT: C 485 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7614 (mp10) REVERT: C 631 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8165 (tm-30) REVERT: C 871 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8793 (mt) REVERT: C 905 TYR cc_start: 0.6734 (p90) cc_final: 0.6509 (p90) REVERT: C 1066 LYS cc_start: 0.8820 (mttt) cc_final: 0.8450 (mtpp) REVERT: B 194 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7175 (mm-30) REVERT: B 198 ASP cc_start: 0.7397 (m-30) cc_final: 0.6983 (m-30) REVERT: B 353 MET cc_start: 0.7888 (mtt) cc_final: 0.7676 (mtm) REVERT: B 485 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7624 (mp10) REVERT: B 631 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8213 (tm-30) REVERT: B 863 MET cc_start: 0.8937 (mtt) cc_final: 0.8728 (mtt) REVERT: B 871 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8847 (mt) REVERT: B 905 TYR cc_start: 0.6780 (p90) cc_final: 0.6566 (p90) REVERT: B 1066 LYS cc_start: 0.8781 (mttt) cc_final: 0.8424 (mtpp) outliers start: 42 outliers final: 33 residues processed: 390 average time/residue: 0.1775 time to fit residues: 113.6733 Evaluate side-chains 368 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 332 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 682 TRP Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 651 TRP Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 994 TRP Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 651 TRP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 651 TRP Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 GLN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN C 438 GLN B 438 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.193238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.149372 restraints weight = 35516.901| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.41 r_work: 0.3339 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28976 Z= 0.120 Angle : 0.493 9.760 39252 Z= 0.257 Chirality : 0.037 0.153 4444 Planarity : 0.004 0.035 4756 Dihedral : 8.954 84.832 4714 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.48 % Allowed : 18.82 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.14), residues: 3284 helix: 2.53 (0.10), residues: 2440 sheet: -0.60 (0.38), residues: 192 loop : -0.77 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 197 TYR 0.013 0.001 TYR D 186 PHE 0.023 0.001 PHE A 874 TRP 0.011 0.001 TRP A 994 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (28976) covalent geometry : angle 0.49276 / 0.26 (39252) hydrogen bonds : bond 0.04610 / 3.09 ( 1818) hydrogen bonds : angle 4.06602 / 2.93 ( 5418) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 372 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7120 (mm-30) REVERT: A 198 ASP cc_start: 0.7562 (m-30) cc_final: 0.7070 (m-30) REVERT: A 254 ASP cc_start: 0.6359 (t70) cc_final: 0.5884 (m-30) REVERT: A 521 LEU cc_start: 0.8253 (tp) cc_final: 0.7967 (tt) REVERT: A 863 MET cc_start: 0.8374 (mtt) cc_final: 0.7903 (mtp) REVERT: A 871 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8656 (mt) REVERT: A 894 GLN cc_start: 0.7478 (pm20) cc_final: 0.6977 (mp10) REVERT: A 898 TRP cc_start: 0.7358 (m-10) cc_final: 0.7141 (m-10) REVERT: D 217 TRP cc_start: 0.6637 (t-100) cc_final: 0.6197 (t-100) REVERT: D 254 ASP cc_start: 0.6308 (t70) cc_final: 0.5756 (m-30) REVERT: D 485 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7767 (mp10) REVERT: D 521 LEU cc_start: 0.8236 (tp) cc_final: 0.7952 (tt) REVERT: D 771 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7602 (tt) REVERT: D 804 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8483 (mp) REVERT: D 871 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8641 (mt) REVERT: C 198 ASP cc_start: 0.7419 (m-30) cc_final: 0.7203 (m-30) REVERT: C 217 TRP cc_start: 0.6622 (t-100) cc_final: 0.6190 (t-100) REVERT: C 254 ASP cc_start: 0.6313 (t70) cc_final: 0.5769 (m-30) REVERT: C 485 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7779 (mp10) REVERT: C 521 LEU cc_start: 0.8237 (tp) cc_final: 0.7957 (tt) REVERT: C 771 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7601 (tt) REVERT: C 871 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8711 (mt) REVERT: B 194 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7018 (mm-30) REVERT: B 198 ASP cc_start: 0.7506 (m-30) cc_final: 0.7005 (m-30) REVERT: B 217 TRP cc_start: 0.6630 (t-100) cc_final: 0.6072 (t-100) REVERT: B 254 ASP cc_start: 0.6449 (t70) cc_final: 0.5722 (m-30) REVERT: B 485 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7783 (mp10) REVERT: B 521 LEU cc_start: 0.8240 (tp) cc_final: 0.7958 (tt) REVERT: B 771 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7608 (tt) REVERT: B 804 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8482 (mp) REVERT: B 863 MET cc_start: 0.8387 (mtt) cc_final: 0.8184 (mtt) REVERT: B 871 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8768 (mt) outliers start: 75 outliers final: 32 residues processed: 431 average time/residue: 0.1741 time to fit residues: 123.7924 Evaluate side-chains 366 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 325 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 956 THR Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 0.9980 chunk 281 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 317 optimal weight: 0.8980 chunk 316 optimal weight: 0.6980 chunk 172 optimal weight: 9.9990 chunk 165 optimal weight: 0.6980 chunk 214 optimal weight: 3.9990 chunk 149 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.193155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147616 restraints weight = 35698.190| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.43 r_work: 0.3323 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28976 Z= 0.108 Angle : 0.461 7.925 39252 Z= 0.240 Chirality : 0.036 0.137 4444 Planarity : 0.003 0.033 4756 Dihedral : 8.647 82.560 4690 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.28 % Allowed : 18.53 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.15), residues: 3284 helix: 2.57 (0.10), residues: 2440 sheet: -0.64 (0.37), residues: 192 loop : -0.83 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 197 TYR 0.011 0.001 TYR B 905 PHE 0.012 0.001 PHE D 868 TRP 0.011 0.001 TRP A 994 HIS 0.003 0.000 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (28976) covalent geometry : angle 0.46050 / 0.24 (39252) hydrogen bonds : bond 0.04100 / 2.74 ( 1818) hydrogen bonds : angle 3.90155 / 2.81 ( 5418) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 366 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7044 (mm-30) REVERT: A 198 ASP cc_start: 0.7683 (m-30) cc_final: 0.7179 (m-30) REVERT: A 254 ASP cc_start: 0.6279 (t70) cc_final: 0.5789 (m-30) REVERT: A 485 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7789 (mp10) REVERT: A 521 LEU cc_start: 0.8285 (tp) cc_final: 0.8032 (tt) REVERT: A 871 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8803 (mt) REVERT: A 894 GLN cc_start: 0.7450 (pm20) cc_final: 0.7063 (mp10) REVERT: A 898 TRP cc_start: 0.7283 (m-10) cc_final: 0.6994 (m-10) REVERT: D 254 ASP cc_start: 0.6462 (t70) cc_final: 0.5645 (m-30) REVERT: D 485 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7926 (tm-30) REVERT: D 521 LEU cc_start: 0.8260 (tp) cc_final: 0.8019 (tt) REVERT: D 642 GLN cc_start: 0.8286 (tt0) cc_final: 0.8047 (mt0) REVERT: D 871 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8805 (mt) REVERT: C 198 ASP cc_start: 0.7565 (m-30) cc_final: 0.7046 (m-30) REVERT: C 254 ASP cc_start: 0.6468 (t70) cc_final: 0.5641 (m-30) REVERT: C 485 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7967 (tm-30) REVERT: C 521 LEU cc_start: 0.8260 (tp) cc_final: 0.8018 (tt) REVERT: C 642 GLN cc_start: 0.8320 (tt0) cc_final: 0.8082 (mt0) REVERT: B 194 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7021 (mm-30) REVERT: B 198 ASP cc_start: 0.7623 (m-30) cc_final: 0.7107 (m-30) REVERT: B 254 ASP cc_start: 0.6420 (t70) cc_final: 0.5687 (m-30) REVERT: B 485 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7983 (tm-30) REVERT: B 521 LEU cc_start: 0.8258 (tp) cc_final: 0.8017 (tt) REVERT: B 642 GLN cc_start: 0.8332 (tt0) cc_final: 0.8094 (mt0) outliers start: 69 outliers final: 42 residues processed: 421 average time/residue: 0.1813 time to fit residues: 125.7177 Evaluate side-chains 371 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 327 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 994 TRP Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 956 THR Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1069 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 159 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 332 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 272 optimal weight: 0.9980 chunk 257 optimal weight: 0.9990 chunk 327 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.192252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.148040 restraints weight = 35685.477| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.61 r_work: 0.3326 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28976 Z= 0.113 Angle : 0.470 9.129 39252 Z= 0.242 Chirality : 0.036 0.138 4444 Planarity : 0.003 0.037 4756 Dihedral : 8.577 81.298 4686 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.41 % Allowed : 18.96 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.15), residues: 3284 helix: 2.56 (0.10), residues: 2436 sheet: -0.53 (0.38), residues: 192 loop : -0.94 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 197 TYR 0.013 0.001 TYR B 284 PHE 0.014 0.001 PHE A 979 TRP 0.014 0.001 TRP B 217 HIS 0.002 0.000 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (28976) covalent geometry : angle 0.47049 / 0.24 (39252) hydrogen bonds : bond 0.04032 / 2.69 ( 1818) hydrogen bonds : angle 3.82557 / 2.75 ( 5418) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 361 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7018 (mm-30) REVERT: A 198 ASP cc_start: 0.7633 (m-30) cc_final: 0.7122 (m-30) REVERT: A 217 TRP cc_start: 0.6345 (t-100) cc_final: 0.6043 (t-100) REVERT: A 254 ASP cc_start: 0.6292 (t70) cc_final: 0.5837 (m-30) REVERT: A 521 LEU cc_start: 0.8279 (tp) cc_final: 0.8036 (tt) REVERT: A 871 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8783 (mt) REVERT: A 894 GLN cc_start: 0.7458 (pm20) cc_final: 0.7075 (mp10) REVERT: A 898 TRP cc_start: 0.7392 (m-10) cc_final: 0.7020 (m-10) REVERT: D 178 TRP cc_start: 0.7372 (m-10) cc_final: 0.6626 (m-10) REVERT: D 254 ASP cc_start: 0.6491 (t70) cc_final: 0.5706 (m-30) REVERT: D 485 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7934 (tm-30) REVERT: D 521 LEU cc_start: 0.8261 (tp) cc_final: 0.8033 (tt) REVERT: D 642 GLN cc_start: 0.8339 (tt0) cc_final: 0.8111 (mt0) REVERT: D 871 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8805 (mt) REVERT: C 198 ASP cc_start: 0.7550 (m-30) cc_final: 0.7026 (m-30) REVERT: C 254 ASP cc_start: 0.6492 (t70) cc_final: 0.5694 (m-30) REVERT: C 485 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7958 (tm-30) REVERT: C 521 LEU cc_start: 0.8295 (tp) cc_final: 0.8025 (tt) REVERT: C 642 GLN cc_start: 0.8359 (tt0) cc_final: 0.8130 (mt0) REVERT: B 178 TRP cc_start: 0.7409 (m-10) cc_final: 0.6703 (m-10) REVERT: B 194 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7035 (mm-30) REVERT: B 198 ASP cc_start: 0.7640 (m-30) cc_final: 0.7111 (m-30) REVERT: B 254 ASP cc_start: 0.6470 (t70) cc_final: 0.5729 (m-30) REVERT: B 284 TYR cc_start: 0.7200 (t80) cc_final: 0.6998 (t80) REVERT: B 485 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7966 (tm-30) REVERT: B 521 LEU cc_start: 0.8294 (tp) cc_final: 0.8026 (tt) REVERT: B 642 GLN cc_start: 0.8367 (tt0) cc_final: 0.8133 (mt0) outliers start: 73 outliers final: 50 residues processed: 421 average time/residue: 0.1807 time to fit residues: 124.5669 Evaluate side-chains 381 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 329 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 994 TRP Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 956 THR Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 95 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 331 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 chunk 273 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 219 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 312 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.191521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.145435 restraints weight = 35335.888| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.59 r_work: 0.3310 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28976 Z= 0.126 Angle : 0.485 9.390 39252 Z= 0.247 Chirality : 0.037 0.133 4444 Planarity : 0.003 0.040 4756 Dihedral : 8.568 80.726 4686 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.84 % Allowed : 18.23 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.15), residues: 3284 helix: 2.55 (0.10), residues: 2436 sheet: -0.57 (0.38), residues: 196 loop : -0.94 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 197 TYR 0.009 0.001 TYR B 284 PHE 0.015 0.001 PHE D 776 TRP 0.011 0.001 TRP B 994 HIS 0.005 0.001 HIS B 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (28976) covalent geometry : angle 0.48476 / 0.25 (39252) hydrogen bonds : bond 0.04270 / 2.85 ( 1818) hydrogen bonds : angle 3.80928 / 2.75 ( 5418) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 357 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7008 (mm-30) REVERT: A 198 ASP cc_start: 0.7522 (m-30) cc_final: 0.7008 (m-30) REVERT: A 217 TRP cc_start: 0.6374 (t-100) cc_final: 0.6131 (t-100) REVERT: A 254 ASP cc_start: 0.6453 (t70) cc_final: 0.5976 (m-30) REVERT: A 485 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7743 (mp10) REVERT: A 521 LEU cc_start: 0.8288 (tp) cc_final: 0.8029 (tt) REVERT: A 688 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7989 (mtp180) REVERT: A 871 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8759 (mt) REVERT: A 898 TRP cc_start: 0.7425 (m-10) cc_final: 0.7041 (m-10) REVERT: D 178 TRP cc_start: 0.7313 (m-10) cc_final: 0.6524 (m-10) REVERT: D 254 ASP cc_start: 0.6574 (t70) cc_final: 0.5774 (m-30) REVERT: D 521 LEU cc_start: 0.8285 (tp) cc_final: 0.8029 (tt) REVERT: D 642 GLN cc_start: 0.8381 (tt0) cc_final: 0.8134 (mt0) REVERT: D 688 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7995 (mtp180) REVERT: D 863 MET cc_start: 0.8451 (mtt) cc_final: 0.8157 (mtp) REVERT: D 871 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8791 (mt) REVERT: C 198 ASP cc_start: 0.7490 (m-30) cc_final: 0.6946 (m-30) REVERT: C 254 ASP cc_start: 0.6575 (t70) cc_final: 0.5764 (m-30) REVERT: C 485 GLN cc_start: 0.8259 (tm-30) cc_final: 0.8058 (tm-30) REVERT: C 521 LEU cc_start: 0.8286 (tp) cc_final: 0.8031 (tt) REVERT: C 642 GLN cc_start: 0.8399 (tt0) cc_final: 0.8158 (mt0) REVERT: C 688 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7996 (mtp180) REVERT: C 863 MET cc_start: 0.8485 (mtt) cc_final: 0.8196 (mtp) REVERT: B 194 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6710 (mm-30) REVERT: B 197 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7644 (ttm170) REVERT: B 198 ASP cc_start: 0.7558 (m-30) cc_final: 0.7031 (m-30) REVERT: B 254 ASP cc_start: 0.6557 (t70) cc_final: 0.5825 (m-30) REVERT: B 485 GLN cc_start: 0.8259 (tm-30) cc_final: 0.8057 (tm-30) REVERT: B 521 LEU cc_start: 0.8288 (tp) cc_final: 0.8029 (tt) REVERT: B 642 GLN cc_start: 0.8411 (tt0) cc_final: 0.8171 (mt0) outliers start: 86 outliers final: 51 residues processed: 421 average time/residue: 0.1859 time to fit residues: 128.6792 Evaluate side-chains 397 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 341 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 688 ARG Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 688 ARG Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 956 THR Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1069 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 320 optimal weight: 1.9990 chunk 331 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 271 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 270 optimal weight: 0.8980 chunk 189 optimal weight: 0.5980 chunk 292 optimal weight: 0.6980 chunk 187 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.193208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.148223 restraints weight = 35215.873| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.45 r_work: 0.3335 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28976 Z= 0.103 Angle : 0.466 10.181 39252 Z= 0.238 Chirality : 0.036 0.137 4444 Planarity : 0.003 0.043 4756 Dihedral : 8.373 81.046 4674 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.71 % Allowed : 18.92 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.15), residues: 3284 helix: 2.58 (0.10), residues: 2444 sheet: -0.52 (0.38), residues: 196 loop : -0.86 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 197 TYR 0.011 0.001 TYR A 905 PHE 0.011 0.001 PHE A 868 TRP 0.011 0.001 TRP D 994 HIS 0.004 0.000 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (28976) covalent geometry : angle 0.46627 / 0.24 (39252) hydrogen bonds : bond 0.03746 / 2.50 ( 1818) hydrogen bonds : angle 3.72066 / 2.68 ( 5418) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 369 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TRP cc_start: 0.7459 (m-10) cc_final: 0.6757 (m-10) REVERT: A 194 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6990 (mm-30) REVERT: A 198 ASP cc_start: 0.7628 (m-30) cc_final: 0.7069 (m-30) REVERT: A 254 ASP cc_start: 0.6339 (t70) cc_final: 0.5843 (m-30) REVERT: A 449 ASN cc_start: 0.6263 (OUTLIER) cc_final: 0.6060 (t0) REVERT: A 521 LEU cc_start: 0.8290 (tp) cc_final: 0.8035 (tt) REVERT: A 871 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8816 (mt) REVERT: A 898 TRP cc_start: 0.7408 (m-10) cc_final: 0.7039 (m-10) REVERT: A 1066 LYS cc_start: 0.8626 (mtpp) cc_final: 0.7906 (ttpp) REVERT: D 178 TRP cc_start: 0.7439 (m-10) cc_final: 0.6777 (m-10) REVERT: D 188 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7235 (mp) REVERT: D 254 ASP cc_start: 0.6471 (t70) cc_final: 0.5662 (m-30) REVERT: D 485 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7686 (mp10) REVERT: D 521 LEU cc_start: 0.8285 (tp) cc_final: 0.8053 (tt) REVERT: D 642 GLN cc_start: 0.8346 (tt0) cc_final: 0.8146 (mt0) REVERT: D 863 MET cc_start: 0.8327 (mtt) cc_final: 0.8055 (mtp) REVERT: D 871 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8810 (mt) REVERT: C 178 TRP cc_start: 0.7472 (m-10) cc_final: 0.6763 (m-10) REVERT: C 188 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7257 (mp) REVERT: C 198 ASP cc_start: 0.7598 (m-30) cc_final: 0.7045 (m-30) REVERT: C 254 ASP cc_start: 0.6464 (t70) cc_final: 0.5645 (m-30) REVERT: C 485 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7828 (mp10) REVERT: C 521 LEU cc_start: 0.8285 (tp) cc_final: 0.8051 (tt) REVERT: C 642 GLN cc_start: 0.8370 (tt0) cc_final: 0.8169 (mt0) REVERT: C 863 MET cc_start: 0.8319 (mtt) cc_final: 0.8062 (mtp) REVERT: B 178 TRP cc_start: 0.7450 (m-10) cc_final: 0.6725 (m-10) REVERT: B 198 ASP cc_start: 0.7696 (m-30) cc_final: 0.7127 (m-30) REVERT: B 254 ASP cc_start: 0.6429 (t70) cc_final: 0.5699 (m-30) REVERT: B 485 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7829 (mp10) REVERT: B 521 LEU cc_start: 0.8289 (tp) cc_final: 0.8053 (tt) REVERT: B 642 GLN cc_start: 0.8387 (tt0) cc_final: 0.8177 (mt0) REVERT: B 688 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7961 (mtp180) outliers start: 82 outliers final: 56 residues processed: 431 average time/residue: 0.1748 time to fit residues: 124.3725 Evaluate side-chains 394 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 332 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 994 TRP Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 956 THR Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 688 ARG Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1069 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 166 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 145 optimal weight: 0.5980 chunk 313 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 210 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 GLN ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.191401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.146452 restraints weight = 35480.756| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.77 r_work: 0.3289 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28976 Z= 0.131 Angle : 0.497 10.761 39252 Z= 0.254 Chirality : 0.037 0.165 4444 Planarity : 0.003 0.045 4756 Dihedral : 8.373 79.978 4672 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.58 % Allowed : 19.29 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.15), residues: 3284 helix: 2.53 (0.10), residues: 2444 sheet: -0.55 (0.38), residues: 196 loop : -0.97 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 197 TYR 0.015 0.001 TYR B 284 PHE 0.011 0.001 PHE A 868 TRP 0.014 0.001 TRP A 217 HIS 0.003 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (28976) covalent geometry : angle 0.49748 / 0.25 (39252) hydrogen bonds : bond 0.04285 / 2.87 ( 1818) hydrogen bonds : angle 3.80393 / 2.74 ( 5418) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 351 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TRP cc_start: 0.7464 (m-10) cc_final: 0.6726 (m-10) REVERT: A 194 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7027 (mm-30) REVERT: A 198 ASP cc_start: 0.7632 (m-30) cc_final: 0.7087 (m-30) REVERT: A 254 ASP cc_start: 0.6415 (t70) cc_final: 0.5888 (m-30) REVERT: A 449 ASN cc_start: 0.6289 (OUTLIER) cc_final: 0.6071 (t0) REVERT: A 521 LEU cc_start: 0.8322 (tp) cc_final: 0.8041 (tt) REVERT: A 688 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8052 (mtp180) REVERT: A 871 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8771 (mt) REVERT: A 898 TRP cc_start: 0.7419 (m-10) cc_final: 0.7039 (m-10) REVERT: D 178 TRP cc_start: 0.7419 (m-10) cc_final: 0.6723 (m-10) REVERT: D 188 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7244 (mp) REVERT: D 254 ASP cc_start: 0.6513 (t70) cc_final: 0.5696 (m-30) REVERT: D 485 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7726 (mp10) REVERT: D 521 LEU cc_start: 0.8319 (tp) cc_final: 0.8040 (tt) REVERT: D 642 GLN cc_start: 0.8416 (tt0) cc_final: 0.8190 (mt0) REVERT: D 688 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8044 (mtp180) REVERT: D 871 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8783 (mt) REVERT: C 178 TRP cc_start: 0.7459 (m-10) cc_final: 0.6739 (m-10) REVERT: C 188 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7244 (mp) REVERT: C 194 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7264 (mm-30) REVERT: C 198 ASP cc_start: 0.7596 (m-30) cc_final: 0.7054 (m-30) REVERT: C 254 ASP cc_start: 0.6525 (t70) cc_final: 0.5701 (m-30) REVERT: C 284 TYR cc_start: 0.7193 (t80) cc_final: 0.6992 (t80) REVERT: C 485 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7823 (mp10) REVERT: C 521 LEU cc_start: 0.8314 (tp) cc_final: 0.8035 (tt) REVERT: C 642 GLN cc_start: 0.8434 (tt0) cc_final: 0.8211 (mt0) REVERT: C 688 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8043 (mtp180) REVERT: B 178 TRP cc_start: 0.7456 (m-10) cc_final: 0.6698 (m-10) REVERT: B 198 ASP cc_start: 0.7691 (m-30) cc_final: 0.7140 (m-30) REVERT: B 254 ASP cc_start: 0.6559 (t70) cc_final: 0.5764 (m-30) REVERT: B 485 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7823 (mp10) REVERT: B 521 LEU cc_start: 0.8317 (tp) cc_final: 0.8035 (tt) REVERT: B 642 GLN cc_start: 0.8438 (tt0) cc_final: 0.8216 (mt0) REVERT: B 688 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8047 (mtp180) outliers start: 78 outliers final: 59 residues processed: 408 average time/residue: 0.1803 time to fit residues: 119.7905 Evaluate side-chains 406 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 338 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 688 ARG Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 688 ARG Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 956 THR Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 688 ARG Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1069 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 62 optimal weight: 0.4980 chunk 249 optimal weight: 5.9990 chunk 204 optimal weight: 0.2980 chunk 160 optimal weight: 0.9990 chunk 319 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 266 optimal weight: 0.0770 chunk 235 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 overall best weight: 0.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.194306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149264 restraints weight = 35555.737| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.61 r_work: 0.3333 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 28976 Z= 0.100 Angle : 0.478 12.169 39252 Z= 0.242 Chirality : 0.036 0.153 4444 Planarity : 0.003 0.046 4756 Dihedral : 8.247 81.032 4672 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.68 % Allowed : 19.45 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.15), residues: 3284 helix: 2.61 (0.10), residues: 2444 sheet: -0.57 (0.38), residues: 196 loop : -0.88 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 197 TYR 0.037 0.001 TYR B 284 PHE 0.010 0.001 PHE D 868 TRP 0.019 0.001 TRP A 217 HIS 0.002 0.000 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (28976) covalent geometry : angle 0.47794 / 0.24 (39252) hydrogen bonds : bond 0.03574 / 2.39 ( 1818) hydrogen bonds : angle 3.69625 / 2.66 ( 5418) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 374 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TRP cc_start: 0.7430 (m-10) cc_final: 0.6676 (m-10) REVERT: A 198 ASP cc_start: 0.7553 (m-30) cc_final: 0.6990 (m-30) REVERT: A 212 ILE cc_start: 0.8740 (mt) cc_final: 0.8457 (mm) REVERT: A 217 TRP cc_start: 0.5540 (t-100) cc_final: 0.4962 (t-100) REVERT: A 254 ASP cc_start: 0.6357 (t70) cc_final: 0.5865 (m-30) REVERT: A 521 LEU cc_start: 0.8260 (tp) cc_final: 0.8044 (tt) REVERT: A 688 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7907 (mtp180) REVERT: A 871 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8826 (mt) REVERT: A 898 TRP cc_start: 0.7432 (m-10) cc_final: 0.7046 (m-10) REVERT: A 1066 LYS cc_start: 0.8627 (mtpp) cc_final: 0.7915 (ttpp) REVERT: D 178 TRP cc_start: 0.7415 (m-10) cc_final: 0.6663 (m-10) REVERT: D 188 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7280 (mp) REVERT: D 189 MET cc_start: 0.6061 (mmt) cc_final: 0.5614 (mmt) REVERT: D 212 ILE cc_start: 0.8773 (mt) cc_final: 0.8477 (mm) REVERT: D 217 TRP cc_start: 0.6358 (t-100) cc_final: 0.5617 (t-100) REVERT: D 254 ASP cc_start: 0.6455 (t70) cc_final: 0.5668 (m-30) REVERT: D 284 TYR cc_start: 0.7184 (t80) cc_final: 0.6913 (t80) REVERT: D 485 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7788 (mp10) REVERT: D 521 LEU cc_start: 0.8259 (tp) cc_final: 0.8044 (tt) REVERT: D 642 GLN cc_start: 0.8382 (tt0) cc_final: 0.8168 (mt0) REVERT: D 688 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7906 (mtp180) REVERT: D 871 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8798 (mt) REVERT: C 178 TRP cc_start: 0.7464 (m-10) cc_final: 0.6705 (m-10) REVERT: C 188 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7286 (mp) REVERT: C 198 ASP cc_start: 0.7518 (m-30) cc_final: 0.6957 (m-30) REVERT: C 212 ILE cc_start: 0.8783 (mt) cc_final: 0.8477 (mm) REVERT: C 217 TRP cc_start: 0.6352 (t-100) cc_final: 0.5616 (t-100) REVERT: C 254 ASP cc_start: 0.6446 (t70) cc_final: 0.5655 (m-30) REVERT: C 485 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7862 (mp10) REVERT: C 521 LEU cc_start: 0.8258 (tp) cc_final: 0.8041 (tt) REVERT: C 642 GLN cc_start: 0.8393 (tt0) cc_final: 0.8188 (mt0) REVERT: C 688 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7906 (mtp180) REVERT: C 1066 LYS cc_start: 0.8622 (mtpp) cc_final: 0.7930 (ttpp) REVERT: B 178 TRP cc_start: 0.7414 (m-10) cc_final: 0.6649 (m-10) REVERT: B 212 ILE cc_start: 0.8776 (mt) cc_final: 0.8463 (mm) REVERT: B 217 TRP cc_start: 0.6313 (t-100) cc_final: 0.5699 (t-100) REVERT: B 254 ASP cc_start: 0.6515 (t70) cc_final: 0.5750 (m-30) REVERT: B 485 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7855 (mp10) REVERT: B 521 LEU cc_start: 0.8260 (tp) cc_final: 0.8040 (tt) REVERT: B 642 GLN cc_start: 0.8387 (tt0) cc_final: 0.8178 (mt0) REVERT: B 688 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7905 (mtp180) outliers start: 81 outliers final: 60 residues processed: 432 average time/residue: 0.1747 time to fit residues: 122.7494 Evaluate side-chains 411 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 343 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 688 ARG Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 688 ARG Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 956 THR Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 688 ARG Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1069 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 286 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 3 optimal weight: 10.0000 chunk 258 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 990 ASN D 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.187512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142494 restraints weight = 35356.663| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.22 r_work: 0.3192 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 28976 Z= 0.203 Angle : 0.583 12.183 39252 Z= 0.297 Chirality : 0.040 0.156 4444 Planarity : 0.004 0.059 4756 Dihedral : 8.564 79.485 4672 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.14 % Allowed : 19.42 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.15), residues: 3284 helix: 2.42 (0.10), residues: 2440 sheet: -0.74 (0.37), residues: 196 loop : -1.19 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.034 0.002 TYR C 284 PHE 0.015 0.001 PHE A 868 TRP 0.015 0.002 TRP B 682 HIS 0.003 0.001 HIS A 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.20 (28976) covalent geometry : angle 0.58305 / 0.30 (39252) hydrogen bonds : bond 0.05561 / 3.73 ( 1818) hydrogen bonds : angle 3.98523 / 2.87 ( 5418) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 350 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7284 (mp) REVERT: A 194 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7166 (mm-30) REVERT: A 198 ASP cc_start: 0.7715 (m-30) cc_final: 0.7194 (m-30) REVERT: A 449 ASN cc_start: 0.6338 (OUTLIER) cc_final: 0.6082 (t0) REVERT: A 688 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8179 (mtp180) REVERT: A 898 TRP cc_start: 0.7492 (m-10) cc_final: 0.7090 (m-10) REVERT: A 990 ASN cc_start: 0.6268 (OUTLIER) cc_final: 0.5778 (m110) REVERT: A 1066 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8022 (ttpt) REVERT: D 178 TRP cc_start: 0.7468 (m-10) cc_final: 0.6754 (m-10) REVERT: D 188 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7256 (mp) REVERT: D 198 ASP cc_start: 0.7693 (m-30) cc_final: 0.7447 (m-30) REVERT: D 254 ASP cc_start: 0.6490 (t70) cc_final: 0.5687 (m-30) REVERT: D 284 TYR cc_start: 0.7194 (t80) cc_final: 0.6912 (t80) REVERT: D 485 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7690 (mp10) REVERT: D 601 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8490 (mp) REVERT: D 688 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8189 (mtp180) REVERT: C 178 TRP cc_start: 0.7510 (m-10) cc_final: 0.6760 (m-10) REVERT: C 198 ASP cc_start: 0.7607 (m-30) cc_final: 0.7088 (m-30) REVERT: C 485 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8134 (tm-30) REVERT: C 601 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8429 (mp) REVERT: C 688 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8192 (mtp180) REVERT: C 1066 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8056 (ttpt) REVERT: B 178 TRP cc_start: 0.7463 (m-10) cc_final: 0.6719 (m-10) REVERT: B 198 ASP cc_start: 0.7772 (m-30) cc_final: 0.7237 (m-30) REVERT: B 485 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8129 (tm-30) REVERT: B 601 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8487 (mp) REVERT: B 688 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8180 (mtp180) outliers start: 95 outliers final: 74 residues processed: 416 average time/residue: 0.1787 time to fit residues: 120.9882 Evaluate side-chains 433 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 346 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1066 LYS Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 651 TRP Chi-restraints excluded: chain D residue 688 ARG Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 831 ILE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 651 TRP Chi-restraints excluded: chain C residue 688 ARG Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 956 THR Chi-restraints excluded: chain C residue 978 MET Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1066 LYS Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 651 TRP Chi-restraints excluded: chain B residue 688 ARG Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 831 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 994 TRP Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1069 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 224 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 283 optimal weight: 0.8980 chunk 284 optimal weight: 0.9980 chunk 267 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 291 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 990 ASN D 419 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.191622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.147513 restraints weight = 35130.453| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.55 r_work: 0.3297 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28976 Z= 0.118 Angle : 0.523 13.196 39252 Z= 0.266 Chirality : 0.037 0.140 4444 Planarity : 0.004 0.066 4756 Dihedral : 8.392 82.405 4672 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.21 % Allowed : 20.34 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.15), residues: 3284 helix: 2.55 (0.10), residues: 2440 sheet: -0.73 (0.38), residues: 196 loop : -1.10 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.038 0.001 TYR C 284 PHE 0.017 0.001 PHE D 979 TRP 0.028 0.001 TRP B 898 HIS 0.003 0.000 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (28976) covalent geometry : angle 0.52286 / 0.27 (39252) hydrogen bonds : bond 0.04227 / 2.83 ( 1818) hydrogen bonds : angle 3.80768 / 2.74 ( 5418) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6568 Ramachandran restraints generated. 3284 Oldfield, 0 Emsley, 3284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 358 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.5888 (mmt) cc_final: 0.5522 (mmt) REVERT: A 194 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7164 (mm-30) REVERT: A 198 ASP cc_start: 0.7635 (m-30) cc_final: 0.7074 (m-30) REVERT: A 521 LEU cc_start: 0.8323 (tp) cc_final: 0.8022 (tt) REVERT: A 688 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7940 (mtp180) REVERT: A 871 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8975 (mt) REVERT: A 898 TRP cc_start: 0.7463 (m-10) cc_final: 0.7087 (m-10) REVERT: A 990 ASN cc_start: 0.6111 (OUTLIER) cc_final: 0.5712 (m110) REVERT: A 1066 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7885 (ttpp) REVERT: D 178 TRP cc_start: 0.7397 (m-10) cc_final: 0.6655 (m-10) REVERT: D 188 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7274 (mp) REVERT: D 217 TRP cc_start: 0.6417 (t-100) cc_final: 0.5654 (t-100) REVERT: D 254 ASP cc_start: 0.6554 (t70) cc_final: 0.5733 (m-30) REVERT: D 284 TYR cc_start: 0.7206 (t80) cc_final: 0.6916 (t80) REVERT: D 485 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7726 (mp10) REVERT: D 521 LEU cc_start: 0.8316 (tp) cc_final: 0.8027 (tt) REVERT: D 642 GLN cc_start: 0.8374 (tt0) cc_final: 0.8098 (mt0) REVERT: D 688 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7936 (mtp180) REVERT: D 871 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8956 (mt) REVERT: D 1066 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8030 (ttpt) REVERT: C 178 TRP cc_start: 0.7458 (m-10) cc_final: 0.6725 (m-10) REVERT: C 198 ASP cc_start: 0.7532 (m-30) cc_final: 0.6963 (m-30) REVERT: C 217 TRP cc_start: 0.6391 (t-100) cc_final: 0.5639 (t-100) REVERT: C 254 ASP cc_start: 0.6145 (t70) cc_final: 0.5345 (m-30) REVERT: C 485 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7819 (mp10) REVERT: C 521 LEU cc_start: 0.8316 (tp) cc_final: 0.8027 (tt) REVERT: C 642 GLN cc_start: 0.8394 (tt0) cc_final: 0.8122 (mt0) REVERT: C 688 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7939 (mtp180) REVERT: C 1066 LYS cc_start: 0.8638 (mtpp) cc_final: 0.7993 (ttpp) REVERT: B 178 TRP cc_start: 0.7450 (m-10) cc_final: 0.6729 (m-10) REVERT: B 198 ASP cc_start: 0.7629 (m-30) cc_final: 0.7069 (m-30) REVERT: B 485 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7818 (mp10) REVERT: B 521 LEU cc_start: 0.8320 (tp) cc_final: 0.8027 (tt) REVERT: B 642 GLN cc_start: 0.8397 (tt0) cc_final: 0.8121 (mt0) REVERT: B 688 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7942 (mtp180) REVERT: B 1066 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8040 (ttpt) outliers start: 67 outliers final: 57 residues processed: 407 average time/residue: 0.1877 time to fit residues: 124.4064 Evaluate side-chains 411 residues out of total 3028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 345 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 688 ARG Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1066 LYS Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 651 TRP Chi-restraints excluded: chain D residue 688 ARG Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 1052 THR Chi-restraints excluded: chain D residue 1069 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 688 ARG Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 956 THR Chi-restraints excluded: chain C residue 994 TRP Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 651 TRP Chi-restraints excluded: chain B residue 688 ARG Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain B residue 1069 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 196 optimal weight: 8.9990 chunk 232 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 331 optimal weight: 0.0000 chunk 213 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 overall best weight: 2.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 990 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.187880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144288 restraints weight = 35509.861| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.15 r_work: 0.3197 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 28976 Z= 0.202 Angle : 0.594 12.827 39252 Z= 0.302 Chirality : 0.040 0.143 4444 Planarity : 0.004 0.090 4756 Dihedral : 8.585 79.900 4672 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.71 % Allowed : 19.95 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.15), residues: 3284 helix: 2.35 (0.10), residues: 2444 sheet: -0.80 (0.37), residues: 196 loop : -1.19 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.038 0.002 TYR C 284 PHE 0.016 0.001 PHE D 868 TRP 0.020 0.002 TRP B 898 HIS 0.004 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.20 (28976) covalent geometry : angle 0.59406 / 0.30 (39252) hydrogen bonds : bond 0.05435 / 3.64 ( 1818) hydrogen bonds : angle 3.98971 / 2.88 ( 5418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5965.63 seconds wall clock time: 103 minutes 25.50 seconds (6205.50 seconds total)