Starting phenix.real_space_refine on Sun Jul 5 03:02:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7eb5_31052/07_2026/7eb5_31052.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eb5_31052/07_2026/7eb5_31052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eb5_31052/07_2026/7eb5_31052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eb5_31052/07_2026/7eb5_31052.map" model { file = "/net/cci-nas-00/data/ceres_data/7eb5_31052/07_2026/7eb5_31052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eb5_31052/07_2026/7eb5_31052.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7eb5_31052/07_2026/7eb5_31052.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7eb5_31052/07_2026/7eb5_31052.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 15839 2.51 5 N 4041 2.21 5 O 4917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24902 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7985 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 51, 'TRANS': 971} Chain breaks: 6 Chain: "A" Number of atoms: 7887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7887 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 50, 'TRANS': 960} Chain breaks: 7 Chain: "B" Number of atoms: 7994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7994 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.96, per 1000 atoms: 0.28 Number of scatterers: 24902 At special positions: 0 Unit cell: (139.7, 143, 200.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4917 8.00 N 4041 7.00 C 15839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 234 " " NAG A2005 " - " ASN A 343 " " NAG A2006 " - " ASN A 603 " " NAG A2007 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 165 " " NAG B2004 " - " ASN B 331 " " NAG B2005 " - " ASN B 343 " " NAG B2006 " - " ASN B 603 " " NAG B2007 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 331 " " NAG C2005 " - " ASN C 603 " " NAG C2006 " - " ASN C 657 " " NAG D 1 " - " ASN C 234 " " NAG E 1 " - " ASN C 282 " " NAG F 1 " - " ASN C 616 " " NAG G 1 " - " ASN C 709 " " NAG H 1 " - " ASN C 717 " " NAG I 1 " - " ASN C 801 " " NAG J 1 " - " ASN C1074 " " NAG K 1 " - " ASN C1098 " " NAG L 1 " - " ASN C1134 " " NAG M 1 " - " ASN A 282 " " NAG N 1 " - " ASN A 331 " " NAG O 1 " - " ASN A 616 " " NAG P 1 " - " ASN A 709 " " NAG Q 1 " - " ASN A 717 " " NAG R 1 " - " ASN A 801 " " NAG S 1 " - " ASN A1074 " " NAG T 1 " - " ASN A1098 " " NAG U 1 " - " ASN A1134 " " NAG V 1 " - " ASN B 234 " " NAG W 1 " - " ASN B 282 " " NAG X 1 " - " ASN B 616 " " NAG Y 1 " - " ASN B 709 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B 801 " " NAG b 1 " - " ASN B1074 " " NAG c 1 " - " ASN B1098 " " NAG d 1 " - " ASN B1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.2 seconds 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5726 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 46 sheets defined 25.4% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.516A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.828A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.632A pdb=" N ILE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.542A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.752A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.762A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.645A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.741A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.574A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1035 removed outlier: 4.274A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.821A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.208A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.042A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.682A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 783 removed outlier: 4.349A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.703A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.592A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.556A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.588A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.823A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.348A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.638A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.522A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.161A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.743A pdb=" N ARG B 634 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL B 635 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.901A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 764 removed outlier: 3.811A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 783 removed outlier: 3.968A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.705A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 919' Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.565A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.712A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 6.320A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.555A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.223A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.698A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.505A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.287A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.519A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.963A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.554A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 573 through 576 removed outlier: 3.998A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.782A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.574A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.642A pdb=" N VAL C1065 " --> pdb=" O MET C1050 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'C' and resid 787 through 789 removed outlier: 5.816A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.881A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AB9, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.778A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.691A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.218A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 192 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.744A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AC5, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.398A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.000A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 587 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.051A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 717 through 719 Processing sheet with id=AD2, first strand: chain 'A' and resid 717 through 719 removed outlier: 3.718A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.668A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.569A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.536A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.640A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 191 through 197 removed outlier: 6.414A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 310 through 313 Processing sheet with id=AE2, first strand: chain 'B' and resid 310 through 313 removed outlier: 4.855A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 323 through 328 removed outlier: 6.457A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.367A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.643A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.643A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.779A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) 851 hydrogen bonds defined for protein. 2301 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: 5.82 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7861 1.35 - 1.47: 6530 1.47 - 1.59: 10929 1.59 - 1.72: 0 1.72 - 1.84: 129 Bond restraints: 25449 Sorted by residual: bond pdb=" N VAL C 642 " pdb=" CA VAL C 642 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.86e+00 bond pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.98e+00 bond pdb=" CA SER C 640 " pdb=" CB SER C 640 " ideal model delta sigma weight residual 1.530 1.497 0.034 1.69e-02 3.50e+03 3.94e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C1 NAG B2004 " pdb=" O5 NAG B2004 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.87e+00 ... (remaining 25444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 34043 2.17 - 4.34: 554 4.34 - 6.51: 40 6.51 - 8.68: 5 8.68 - 10.85: 2 Bond angle restraints: 34644 Sorted by residual: angle pdb=" N VAL A1128 " pdb=" CA VAL A1128 " pdb=" C VAL A1128 " ideal model delta sigma weight residual 113.42 108.83 4.59 1.17e+00 7.31e-01 1.54e+01 angle pdb=" CA GLY C 639 " pdb=" C GLY C 639 " pdb=" O GLY C 639 " ideal model delta sigma weight residual 121.44 117.02 4.42 1.26e+00 6.30e-01 1.23e+01 angle pdb=" CA THR C 638 " pdb=" C THR C 638 " pdb=" O THR C 638 " ideal model delta sigma weight residual 121.40 117.58 3.82 1.11e+00 8.12e-01 1.19e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.90 -4.20 1.22e+00 6.72e-01 1.18e+01 angle pdb=" N SER C 605 " pdb=" CA SER C 605 " pdb=" C SER C 605 " ideal model delta sigma weight residual 108.34 112.28 -3.94 1.31e+00 5.83e-01 9.03e+00 ... (remaining 34639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 13119 17.81 - 35.63: 1126 35.63 - 53.44: 218 53.44 - 71.25: 35 71.25 - 89.06: 30 Dihedral angle restraints: 14528 sinusoidal: 5631 harmonic: 8897 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -172.10 86.10 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 165.00 -72.00 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 153.33 -60.33 1 1.00e+01 1.00e-02 4.85e+01 ... (remaining 14525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 4136 0.159 - 0.318: 18 0.318 - 0.476: 2 0.476 - 0.635: 5 0.635 - 0.794: 1 Chirality restraints: 4162 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.01e+00 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.51e+00 ... (remaining 4159 not shown) Planarity restraints: 4432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 229 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO B 230 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 230 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 230 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.037 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 479 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " -0.020 2.00e-02 2.50e+03 1.92e-02 4.62e+00 pdb=" CG ASN B 234 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.020 2.00e-02 2.50e+03 ... (remaining 4429 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 866 2.71 - 3.26: 24408 3.26 - 3.80: 37499 3.80 - 4.35: 44144 4.35 - 4.90: 75523 Nonbonded interactions: 182440 Sorted by model distance: nonbonded pdb=" O PRO B 85 " pdb=" OH TYR B 269 " model vdw 2.162 3.040 nonbonded pdb=" ND1 HIS B 625 " pdb=" OD1 ASP B 627 " model vdw 2.171 3.120 nonbonded pdb=" O THR A 998 " pdb=" NE2 GLN A1002 " model vdw 2.178 3.120 nonbonded pdb=" O PRO A 85 " pdb=" OH TYR A 269 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OG1 THR B 114 " model vdw 2.206 3.040 ... (remaining 182435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 827 or resid 855 through 2006)) selection = (chain 'B' and (resid 27 through 622 or resid 636 through 827 or resid 855 throu \ gh 2006)) selection = (chain 'C' and (resid 27 through 622 or resid 636 through 2006)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = 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: 6.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 27.830 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.080 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 0.004 0.059 25559 Z= 0.194 Angle : 0.700 17.838 34936 Z= 0.338 Chirality : 0.052 0.794 4162 Planarity : 0.004 0.076 4385 Dihedral : 13.895 89.063 8697 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 0.11 % Allowed : 0.34 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 3014 helix: 1.03 (0.22), residues: 666 sheet: -0.46 (0.20), residues: 639 loop : -1.57 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 273 TYR 0.011 0.001 TYR C 91 PHE 0.021 0.001 PHE C 906 TRP 0.006 0.001 TRP C 436 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (25449) covalent geometry : angle 0.63684 / 0.32 (34644) SS BOND : bond 0.00425 / 0.29 ( 35) SS BOND : angle 1.26172 / 0.85 ( 70) hydrogen bonds : bond 0.15673 / 9.99 ( 831) hydrogen bonds : angle 6.21373 / 4.24 ( 2301) Misc. bond : bond 0.00164 / 0.09 ( 1) link_BETA1-4 : bond 0.00652 / 0.39 ( 27) link_BETA1-4 : angle 3.67938 / 2.44 ( 81) link_NAG-ASN : bond 0.00664 / 0.48 ( 47) link_NAG-ASN : angle 3.61766 / 2.13 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.944 Fit side-chains REVERT: C 641 ASN cc_start: 0.6181 (OUTLIER) cc_final: 0.5882 (m-40) REVERT: C 957 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 869 MET cc_start: 0.8633 (mpp) cc_final: 0.8002 (mpp) REVERT: A 1029 MET cc_start: 0.9015 (tmm) cc_final: 0.8286 (tmm) REVERT: B 342 PHE cc_start: 0.8927 (m-80) cc_final: 0.8671 (m-80) REVERT: B 957 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8330 (tm-30) REVERT: B 1029 MET cc_start: 0.8592 (ttp) cc_final: 0.7947 (tmm) outliers start: 3 outliers final: 0 residues processed: 136 average time/residue: 0.1512 time to fit residues: 35.3711 Evaluate side-chains 102 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 641 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 360 ASN C 487 ASN C1002 GLN C1048 HIS C1106 GLN A1054 GLN B 49 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.139101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.089580 restraints weight = 58442.006| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 5.23 r_work: 0.3084 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25559 Z= 0.187 Angle : 0.665 12.779 34936 Z= 0.322 Chirality : 0.049 0.475 4162 Planarity : 0.004 0.061 4385 Dihedral : 4.298 54.594 3271 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.26 % Rotamer: Outliers : 0.41 % Allowed : 7.72 % Favored : 91.87 % 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: -1.09 (0.15), residues: 3014 helix: 1.02 (0.21), residues: 673 sheet: -0.56 (0.20), residues: 662 loop : -1.57 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 466 TYR 0.022 0.001 TYR C1067 PHE 0.024 0.002 PHE B 201 TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (25449) covalent geometry : angle 0.61762 / 0.31 (34644) SS BOND : bond 0.00447 / 0.30 ( 35) SS BOND : angle 1.32880 / 0.88 ( 70) hydrogen bonds : bond 0.05412 / 3.52 ( 831) hydrogen bonds : angle 5.20569 / 3.54 ( 2301) Misc. bond : bond 0.00103 / 0.05 ( 1) link_BETA1-4 : bond 0.00571 / 0.32 ( 27) link_BETA1-4 : angle 2.61848 / 1.69 ( 81) link_NAG-ASN : bond 0.00586 / 0.42 ( 47) link_NAG-ASN : angle 3.34022 / 2.01 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: C 329 PHE cc_start: 0.7720 (m-10) cc_final: 0.7373 (m-10) REVERT: C 619 GLU cc_start: 0.8659 (mp0) cc_final: 0.8435 (mp0) REVERT: A 133 PHE cc_start: 0.7404 (m-10) cc_final: 0.7163 (m-10) REVERT: A 239 GLN cc_start: 0.7489 (tp40) cc_final: 0.6970 (mm110) REVERT: A 773 GLU cc_start: 0.8872 (tp30) cc_final: 0.8648 (tp30) REVERT: A 869 MET cc_start: 0.9119 (mpp) cc_final: 0.8383 (mpp) REVERT: A 1029 MET cc_start: 0.9068 (tmm) cc_final: 0.8419 (tmm) REVERT: B 338 PHE cc_start: 0.8252 (m-80) cc_final: 0.8005 (m-10) REVERT: B 342 PHE cc_start: 0.9010 (m-10) cc_final: 0.8695 (m-80) REVERT: B 957 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8545 (tm-30) REVERT: B 1029 MET cc_start: 0.8631 (ttp) cc_final: 0.8364 (ttm) outliers start: 11 outliers final: 9 residues processed: 120 average time/residue: 0.1458 time to fit residues: 30.0743 Evaluate side-chains 100 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 50.0000 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 chunk 217 optimal weight: 0.5980 chunk 34 optimal weight: 20.0000 chunk 301 optimal weight: 0.3980 chunk 192 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 128 optimal weight: 30.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 641 ASN A 544 ASN A 564 GLN A1142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.141430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.091735 restraints weight = 58547.355| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 4.50 r_work: 0.3127 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25559 Z= 0.122 Angle : 0.606 12.545 34936 Z= 0.291 Chirality : 0.048 0.479 4162 Planarity : 0.004 0.063 4385 Dihedral : 4.013 20.159 3269 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.84 % Favored : 95.06 % Rotamer: Outliers : 0.71 % Allowed : 10.37 % Favored : 88.91 % 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: -0.96 (0.15), residues: 3014 helix: 1.19 (0.22), residues: 668 sheet: -0.43 (0.20), residues: 651 loop : -1.52 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 273 TYR 0.018 0.001 TYR B1067 PHE 0.018 0.001 PHE B 201 TRP 0.006 0.001 TRP C 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (25449) covalent geometry : angle 0.55742 / 0.28 (34644) SS BOND : bond 0.00370 / 0.24 ( 35) SS BOND : angle 1.12293 / 0.73 ( 70) hydrogen bonds : bond 0.04755 / 3.09 ( 831) hydrogen bonds : angle 4.94326 / 3.36 ( 2301) Misc. bond : bond 0.00079 / 0.04 ( 1) link_BETA1-4 : bond 0.00583 / 0.33 ( 27) link_BETA1-4 : angle 2.58506 / 1.66 ( 81) link_NAG-ASN : bond 0.00611 / 0.44 ( 47) link_NAG-ASN : angle 3.21285 / 1.94 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.964 Fit side-chains REVERT: C 327 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8145 (p) REVERT: C 619 GLU cc_start: 0.8666 (mp0) cc_final: 0.8380 (mp0) REVERT: C 641 ASN cc_start: 0.6568 (OUTLIER) cc_final: 0.6166 (m110) REVERT: A 133 PHE cc_start: 0.7407 (m-10) cc_final: 0.7090 (m-10) REVERT: A 239 GLN cc_start: 0.7564 (tp40) cc_final: 0.6993 (mm110) REVERT: A 773 GLU cc_start: 0.8833 (tp30) cc_final: 0.8578 (tp30) REVERT: A 869 MET cc_start: 0.9093 (mpp) cc_final: 0.8355 (mpp) REVERT: A 1029 MET cc_start: 0.9014 (tmm) cc_final: 0.8311 (tmm) REVERT: B 338 PHE cc_start: 0.8225 (m-80) cc_final: 0.7941 (m-10) REVERT: B 342 PHE cc_start: 0.9004 (m-10) cc_final: 0.8673 (m-80) REVERT: B 957 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8550 (tm-30) REVERT: B 1029 MET cc_start: 0.8558 (ttp) cc_final: 0.7919 (tmm) outliers start: 19 outliers final: 10 residues processed: 120 average time/residue: 0.1553 time to fit residues: 32.0039 Evaluate side-chains 105 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 150 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 273 optimal weight: 1.9990 chunk 225 optimal weight: 0.0670 chunk 241 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 563 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.139165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.089385 restraints weight = 57690.265| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 5.33 r_work: 0.3066 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25559 Z= 0.147 Angle : 0.614 12.112 34936 Z= 0.296 Chirality : 0.048 0.474 4162 Planarity : 0.004 0.061 4385 Dihedral : 4.003 20.424 3269 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.24 % Favored : 94.66 % Rotamer: Outliers : 1.16 % Allowed : 12.21 % Favored : 86.63 % 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: -1.00 (0.15), residues: 3014 helix: 1.11 (0.22), residues: 673 sheet: -0.45 (0.20), residues: 659 loop : -1.55 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1019 TYR 0.018 0.001 TYR C1067 PHE 0.019 0.001 PHE C 201 TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (25449) covalent geometry : angle 0.56758 / 0.29 (34644) SS BOND : bond 0.00397 / 0.27 ( 35) SS BOND : angle 1.19020 / 0.78 ( 70) hydrogen bonds : bond 0.04891 / 3.19 ( 831) hydrogen bonds : angle 4.89446 / 3.33 ( 2301) Misc. bond : bond 0.00073 / 0.04 ( 1) link_BETA1-4 : bond 0.00588 / 0.32 ( 27) link_BETA1-4 : angle 2.52777 / 1.62 ( 81) link_NAG-ASN : bond 0.00562 / 0.41 ( 47) link_NAG-ASN : angle 3.15549 / 1.91 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 619 GLU cc_start: 0.8719 (mp0) cc_final: 0.8429 (mp0) REVERT: A 133 PHE cc_start: 0.7402 (m-80) cc_final: 0.7049 (m-10) REVERT: A 773 GLU cc_start: 0.8939 (tp30) cc_final: 0.8695 (tp30) REVERT: A 869 MET cc_start: 0.9154 (mpp) cc_final: 0.8437 (mpp) REVERT: A 1029 MET cc_start: 0.9070 (tmm) cc_final: 0.8406 (tmm) REVERT: B 338 PHE cc_start: 0.8189 (m-80) cc_final: 0.7856 (m-10) REVERT: B 342 PHE cc_start: 0.9026 (m-10) cc_final: 0.8662 (m-80) REVERT: B 957 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8632 (tm-30) REVERT: B 1029 MET cc_start: 0.8586 (ttp) cc_final: 0.8306 (ttm) outliers start: 31 outliers final: 18 residues processed: 123 average time/residue: 0.1495 time to fit residues: 32.0914 Evaluate side-chains 114 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 26 optimal weight: 30.0000 chunk 41 optimal weight: 30.0000 chunk 244 optimal weight: 30.0000 chunk 273 optimal weight: 0.0970 chunk 92 optimal weight: 0.1980 chunk 54 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 chunk 93 optimal weight: 0.0980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 271 GLN A 321 GLN A1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.141792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.092492 restraints weight = 59351.134| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 4.44 r_work: 0.3120 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25559 Z= 0.125 Angle : 0.599 11.587 34936 Z= 0.286 Chirality : 0.047 0.476 4162 Planarity : 0.004 0.060 4385 Dihedral : 3.927 20.058 3269 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.11 % Favored : 94.79 % Rotamer: Outliers : 1.46 % Allowed : 13.45 % Favored : 85.09 % 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: -0.90 (0.15), residues: 3014 helix: 1.23 (0.22), residues: 659 sheet: -0.38 (0.21), residues: 649 loop : -1.48 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.017 0.001 TYR B1067 PHE 0.016 0.001 PHE B 201 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (25449) covalent geometry : angle 0.55313 / 0.28 (34644) SS BOND : bond 0.00336 / 0.22 ( 35) SS BOND : angle 1.10298 / 0.72 ( 70) hydrogen bonds : bond 0.04626 / 3.01 ( 831) hydrogen bonds : angle 4.79492 / 3.26 ( 2301) Misc. bond : bond 0.00073 / 0.04 ( 1) link_BETA1-4 : bond 0.00615 / 0.34 ( 27) link_BETA1-4 : angle 2.46048 / 1.56 ( 81) link_NAG-ASN : bond 0.00567 / 0.41 ( 47) link_NAG-ASN : angle 3.08681 / 1.88 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: C 619 GLU cc_start: 0.8715 (mp0) cc_final: 0.8427 (mp0) REVERT: A 133 PHE cc_start: 0.7338 (m-80) cc_final: 0.7002 (m-10) REVERT: A 239 GLN cc_start: 0.7096 (tp40) cc_final: 0.6729 (mm110) REVERT: A 773 GLU cc_start: 0.8932 (tp30) cc_final: 0.8657 (tp30) REVERT: A 869 MET cc_start: 0.9168 (mpp) cc_final: 0.8398 (mpp) REVERT: A 1029 MET cc_start: 0.9052 (tmm) cc_final: 0.8386 (tmm) REVERT: B 338 PHE cc_start: 0.8170 (m-80) cc_final: 0.7880 (m-80) REVERT: B 342 PHE cc_start: 0.9102 (m-10) cc_final: 0.8762 (m-80) REVERT: B 981 LEU cc_start: 0.8942 (mt) cc_final: 0.8702 (pp) REVERT: B 1029 MET cc_start: 0.8588 (ttp) cc_final: 0.8317 (ttm) outliers start: 39 outliers final: 26 residues processed: 133 average time/residue: 0.1482 time to fit residues: 34.2261 Evaluate side-chains 122 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1083 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 222 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 256 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 30 optimal weight: 0.0070 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 764 ASN A1142 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.139144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.089481 restraints weight = 57693.118| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 5.28 r_work: 0.3085 rms_B_bonded: 5.12 restraints_weight: 2.0000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25559 Z= 0.129 Angle : 0.602 11.224 34936 Z= 0.288 Chirality : 0.047 0.470 4162 Planarity : 0.004 0.058 4385 Dihedral : 3.918 20.173 3269 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.01 % Favored : 94.89 % Rotamer: Outliers : 1.99 % Allowed : 13.82 % Favored : 84.19 % 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: -0.91 (0.15), residues: 3014 helix: 1.19 (0.22), residues: 664 sheet: -0.37 (0.21), residues: 649 loop : -1.48 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.024 0.001 TYR C 200 PHE 0.025 0.001 PHE B 133 TRP 0.006 0.001 TRP A 436 HIS 0.003 0.000 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (25449) covalent geometry : angle 0.55860 / 0.28 (34644) SS BOND : bond 0.00349 / 0.23 ( 35) SS BOND : angle 1.10791 / 0.72 ( 70) hydrogen bonds : bond 0.04650 / 3.03 ( 831) hydrogen bonds : angle 4.74658 / 3.23 ( 2301) Misc. bond : bond 0.00068 / 0.04 ( 1) link_BETA1-4 : bond 0.00592 / 0.32 ( 27) link_BETA1-4 : angle 2.40104 / 1.51 ( 81) link_NAG-ASN : bond 0.00550 / 0.40 ( 47) link_NAG-ASN : angle 3.03689 / 1.85 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 98 time to evaluate : 0.970 Fit side-chains REVERT: C 619 GLU cc_start: 0.8745 (mp0) cc_final: 0.8517 (mp0) REVERT: C 622 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8173 (p) REVERT: A 133 PHE cc_start: 0.7448 (m-80) cc_final: 0.7078 (m-10) REVERT: A 239 GLN cc_start: 0.7138 (tp40) cc_final: 0.6784 (mm110) REVERT: A 773 GLU cc_start: 0.8989 (tp30) cc_final: 0.8732 (tp30) REVERT: A 869 MET cc_start: 0.9196 (mpp) cc_final: 0.8433 (mpp) REVERT: A 1029 MET cc_start: 0.9080 (tmm) cc_final: 0.8367 (tmm) REVERT: B 342 PHE cc_start: 0.9091 (m-10) cc_final: 0.8732 (m-80) REVERT: B 981 LEU cc_start: 0.8974 (mt) cc_final: 0.8734 (pp) REVERT: B 1029 MET cc_start: 0.8609 (ttp) cc_final: 0.8348 (ttm) outliers start: 53 outliers final: 32 residues processed: 143 average time/residue: 0.1435 time to fit residues: 36.0295 Evaluate side-chains 127 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 294 optimal weight: 0.0060 chunk 262 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1142 GLN B 675 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.141833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092791 restraints weight = 58655.327| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 4.39 r_work: 0.3138 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25559 Z= 0.122 Angle : 0.595 10.879 34936 Z= 0.285 Chirality : 0.047 0.469 4162 Planarity : 0.004 0.055 4385 Dihedral : 3.892 19.880 3269 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.84 % Favored : 95.06 % Rotamer: Outliers : 1.65 % Allowed : 14.68 % Favored : 83.67 % 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: -0.87 (0.15), residues: 3014 helix: 1.25 (0.22), residues: 656 sheet: -0.40 (0.21), residues: 651 loop : -1.42 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.017 0.001 TYR B1067 PHE 0.015 0.001 PHE A1121 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (25449) covalent geometry : angle 0.55161 / 0.27 (34644) SS BOND : bond 0.00393 / 0.24 ( 35) SS BOND : angle 1.34620 / 0.89 ( 70) hydrogen bonds : bond 0.04534 / 2.95 ( 831) hydrogen bonds : angle 4.67739 / 3.19 ( 2301) Misc. bond : bond 0.00069 / 0.04 ( 1) link_BETA1-4 : bond 0.00594 / 0.33 ( 27) link_BETA1-4 : angle 2.32007 / 1.44 ( 81) link_NAG-ASN : bond 0.00550 / 0.40 ( 47) link_NAG-ASN : angle 2.97864 / 1.81 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 103 time to evaluate : 0.967 Fit side-chains REVERT: C 619 GLU cc_start: 0.8721 (mp0) cc_final: 0.8433 (mp0) REVERT: A 133 PHE cc_start: 0.7441 (m-80) cc_final: 0.6714 (m-10) REVERT: A 239 GLN cc_start: 0.7199 (tp40) cc_final: 0.6850 (mm110) REVERT: A 773 GLU cc_start: 0.8929 (tp30) cc_final: 0.8690 (tp30) REVERT: A 869 MET cc_start: 0.9164 (mpp) cc_final: 0.8425 (mpp) REVERT: A 1029 MET cc_start: 0.9060 (tmm) cc_final: 0.8358 (tmm) REVERT: B 338 PHE cc_start: 0.8160 (m-10) cc_final: 0.7761 (m-80) REVERT: B 342 PHE cc_start: 0.9061 (m-10) cc_final: 0.8705 (m-80) REVERT: B 1029 MET cc_start: 0.8613 (ttp) cc_final: 0.8348 (ttm) outliers start: 44 outliers final: 31 residues processed: 140 average time/residue: 0.1323 time to fit residues: 32.0931 Evaluate side-chains 129 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 48 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 259 optimal weight: 0.9990 chunk 280 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 641 ASN A1002 GLN A1142 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.141168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.091513 restraints weight = 58694.139| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 4.46 r_work: 0.3109 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25559 Z= 0.143 Angle : 0.612 10.619 34936 Z= 0.293 Chirality : 0.047 0.465 4162 Planarity : 0.004 0.054 4385 Dihedral : 3.935 20.276 3269 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.51 % Favored : 94.39 % Rotamer: Outliers : 1.84 % Allowed : 15.28 % Favored : 82.88 % 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: -0.92 (0.15), residues: 3014 helix: 1.19 (0.22), residues: 663 sheet: -0.43 (0.21), residues: 661 loop : -1.47 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.017 0.001 TYR C1067 PHE 0.019 0.001 PHE C 201 TRP 0.006 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (25449) covalent geometry : angle 0.57167 / 0.28 (34644) SS BOND : bond 0.00521 / 0.36 ( 35) SS BOND : angle 1.34261 / 0.89 ( 70) hydrogen bonds : bond 0.04769 / 3.10 ( 831) hydrogen bonds : angle 4.70321 / 3.21 ( 2301) Misc. bond : bond 0.00066 / 0.03 ( 1) link_BETA1-4 : bond 0.00573 / 0.31 ( 27) link_BETA1-4 : angle 2.21947 / 1.36 ( 81) link_NAG-ASN : bond 0.00524 / 0.38 ( 47) link_NAG-ASN : angle 2.95848 / 1.80 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 95 time to evaluate : 0.958 Fit side-chains REVERT: C 120 VAL cc_start: 0.7192 (t) cc_final: 0.6989 (m) REVERT: C 619 GLU cc_start: 0.8703 (mp0) cc_final: 0.8492 (mp0) REVERT: C 622 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8151 (p) REVERT: C 641 ASN cc_start: 0.6562 (OUTLIER) cc_final: 0.6230 (m110) REVERT: A 133 PHE cc_start: 0.7618 (m-80) cc_final: 0.6896 (m-10) REVERT: A 239 GLN cc_start: 0.7154 (tp40) cc_final: 0.6789 (mm110) REVERT: A 773 GLU cc_start: 0.8949 (tp30) cc_final: 0.8713 (tp30) REVERT: A 869 MET cc_start: 0.9186 (mpp) cc_final: 0.8435 (mpp) REVERT: A 1029 MET cc_start: 0.9082 (tmm) cc_final: 0.8402 (tmm) REVERT: B 338 PHE cc_start: 0.8226 (m-10) cc_final: 0.7885 (m-80) REVERT: B 342 PHE cc_start: 0.9053 (m-10) cc_final: 0.8656 (m-80) REVERT: B 1029 MET cc_start: 0.8634 (ttp) cc_final: 0.8390 (ttm) outliers start: 49 outliers final: 38 residues processed: 136 average time/residue: 0.1364 time to fit residues: 32.5057 Evaluate side-chains 131 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 224 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 40 optimal weight: 0.0170 chunk 27 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 641 ASN ** B 957 GLN ** 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 = 0.4167 r_free = 0.4167 target = 0.138196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088726 restraints weight = 57891.945| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 5.24 r_work: 0.3088 rms_B_bonded: 5.06 restraints_weight: 2.0000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25559 Z= 0.147 Angle : 0.621 17.433 34936 Z= 0.297 Chirality : 0.048 0.469 4162 Planarity : 0.004 0.054 4385 Dihedral : 3.955 20.483 3269 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.14 % Favored : 94.76 % Rotamer: Outliers : 1.84 % Allowed : 15.62 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.94 (0.15), residues: 3014 helix: 1.20 (0.22), residues: 663 sheet: -0.48 (0.21), residues: 665 loop : -1.48 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.018 0.001 TYR B1067 PHE 0.025 0.001 PHE B 133 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (25449) covalent geometry : angle 0.58239 / 0.29 (34644) SS BOND : bond 0.00421 / 0.27 ( 35) SS BOND : angle 1.30637 / 0.87 ( 70) hydrogen bonds : bond 0.04792 / 3.12 ( 831) hydrogen bonds : angle 4.70498 / 3.21 ( 2301) Misc. bond : bond 0.00066 / 0.03 ( 1) link_BETA1-4 : bond 0.00589 / 0.33 ( 27) link_BETA1-4 : angle 2.12592 / 1.29 ( 81) link_NAG-ASN : bond 0.00526 / 0.39 ( 47) link_NAG-ASN : angle 2.96578 / 1.81 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 96 time to evaluate : 0.683 Fit side-chains REVERT: C 120 VAL cc_start: 0.7010 (t) cc_final: 0.6799 (m) REVERT: C 622 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8249 (p) REVERT: A 133 PHE cc_start: 0.7642 (m-80) cc_final: 0.7234 (m-10) REVERT: A 239 GLN cc_start: 0.7246 (tp40) cc_final: 0.6869 (mm110) REVERT: A 581 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8884 (p) REVERT: A 773 GLU cc_start: 0.8967 (tp30) cc_final: 0.8726 (tp30) REVERT: A 869 MET cc_start: 0.9203 (mpp) cc_final: 0.8442 (mpp) REVERT: A 1029 MET cc_start: 0.9068 (tmm) cc_final: 0.8379 (tmm) REVERT: B 338 PHE cc_start: 0.8183 (m-10) cc_final: 0.7833 (m-80) REVERT: B 342 PHE cc_start: 0.9044 (m-10) cc_final: 0.8656 (m-80) REVERT: B 1029 MET cc_start: 0.8633 (ttp) cc_final: 0.8393 (ttm) outliers start: 49 outliers final: 40 residues processed: 137 average time/residue: 0.1397 time to fit residues: 32.6782 Evaluate side-chains 134 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 200 optimal weight: 0.6980 chunk 127 optimal weight: 0.0170 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 GLN A1142 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.142000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092845 restraints weight = 59412.965| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 4.42 r_work: 0.3132 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25559 Z= 0.109 Angle : 0.600 14.301 34936 Z= 0.287 Chirality : 0.047 0.467 4162 Planarity : 0.004 0.054 4385 Dihedral : 3.852 19.156 3269 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.01 % Favored : 94.89 % Rotamer: Outliers : 1.50 % Allowed : 16.25 % Favored : 82.25 % 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: -0.84 (0.15), residues: 3014 helix: 1.26 (0.22), residues: 658 sheet: -0.36 (0.21), residues: 654 loop : -1.42 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.016 0.001 TYR B1067 PHE 0.021 0.001 PHE C 201 TRP 0.007 0.001 TRP A 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (25449) covalent geometry : angle 0.56374 / 0.28 (34644) SS BOND : bond 0.00373 / 0.24 ( 35) SS BOND : angle 1.15718 / 0.77 ( 70) hydrogen bonds : bond 0.04387 / 2.85 ( 831) hydrogen bonds : angle 4.59820 / 3.14 ( 2301) Misc. bond : bond 0.00075 / 0.04 ( 1) link_BETA1-4 : bond 0.00622 / 0.35 ( 27) link_BETA1-4 : angle 2.01806 / 1.21 ( 81) link_NAG-ASN : bond 0.00559 / 0.41 ( 47) link_NAG-ASN : angle 2.87357 / 1.76 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.962 Fit side-chains REVERT: C 622 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8239 (p) REVERT: A 133 PHE cc_start: 0.7632 (m-80) cc_final: 0.7232 (m-10) REVERT: A 239 GLN cc_start: 0.7300 (tp40) cc_final: 0.6960 (mm110) REVERT: A 581 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8880 (p) REVERT: A 773 GLU cc_start: 0.8913 (tp30) cc_final: 0.8639 (tp30) REVERT: A 869 MET cc_start: 0.9195 (mpp) cc_final: 0.8425 (mpp) REVERT: A 1029 MET cc_start: 0.9022 (tmm) cc_final: 0.8337 (tmm) REVERT: B 338 PHE cc_start: 0.8196 (m-10) cc_final: 0.7842 (m-10) REVERT: B 342 PHE cc_start: 0.9098 (m-10) cc_final: 0.8708 (m-80) REVERT: B 1029 MET cc_start: 0.8679 (ttp) cc_final: 0.8030 (tmm) outliers start: 40 outliers final: 34 residues processed: 136 average time/residue: 0.1450 time to fit residues: 34.4920 Evaluate side-chains 132 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 272 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 303 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 294 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.138458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.088652 restraints weight = 57898.340| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 5.27 r_work: 0.3076 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25559 Z= 0.142 Angle : 0.610 13.479 34936 Z= 0.294 Chirality : 0.047 0.464 4162 Planarity : 0.004 0.054 4385 Dihedral : 3.892 19.824 3269 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.04 % Favored : 94.86 % Rotamer: Outliers : 1.57 % Allowed : 16.33 % Favored : 82.10 % 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: -0.87 (0.15), residues: 3014 helix: 1.27 (0.22), residues: 650 sheet: -0.40 (0.21), residues: 651 loop : -1.43 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.017 0.001 TYR C1067 PHE 0.023 0.001 PHE B 133 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (25449) covalent geometry : angle 0.57422 / 0.29 (34644) SS BOND : bond 0.00397 / 0.26 ( 35) SS BOND : angle 1.18978 / 0.78 ( 70) hydrogen bonds : bond 0.04596 / 2.99 ( 831) hydrogen bonds : angle 4.63598 / 3.16 ( 2301) Misc. bond : bond 0.00065 / 0.03 ( 1) link_BETA1-4 : bond 0.00597 / 0.34 ( 27) link_BETA1-4 : angle 1.98797 / 1.19 ( 81) link_NAG-ASN : bond 0.00522 / 0.38 ( 47) link_NAG-ASN : angle 2.88227 / 1.76 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7233.18 seconds wall clock time: 124 minutes 32.77 seconds (7472.77 seconds total)