Starting phenix.real_space_refine on Sun Jul 5 20:43:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ej4_30669/07_2026/7ej4_30669.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej4_30669/07_2026/7ej4_30669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ej4_30669/07_2026/7ej4_30669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej4_30669/07_2026/7ej4_30669.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ej4_30669/07_2026/7ej4_30669.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ej4_30669/07_2026/7ej4_30669.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ej4_30669/07_2026/7ej4_30669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej4_30669/07_2026/7ej4_30669.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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 135 5.16 5 C 19057 2.51 5 N 4886 2.21 5 O 5962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 30040 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7872 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 50, 'TRANS': 957} Chain breaks: 8 Chain: "B" Number of atoms: 7986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7986 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 51, 'TRANS': 970} Chain breaks: 7 Chain: "C" Number of atoms: 7906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7906 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 50, 'TRANS': 960} Chain breaks: 8 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "I" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "M" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "J" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} 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: "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: "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: "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: "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 Chain: "C" 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: 5.48, per 1000 atoms: 0.18 Number of scatterers: 30040 At special positions: 0 Unit cell: (139.7, 170.5, 225.5, 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 135 16.00 O 5962 8.00 N 4886 7.00 C 19057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 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 480 " - pdb=" SG CYS A 488 " 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=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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 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=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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=2.02 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 H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 89 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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 K 1 " - " NAG K 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 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-ASN " 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 234 " " NAG C2005 " - " ASN C 343 " " NAG C2006 " - " ASN C 603 " " NAG C2007 " - " ASN C 657 " " NAG D 1 " - " ASN A 282 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 709 " " NAG K 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1074 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " " NAG S 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 282 " " NAG U 1 " - " ASN B 616 " " NAG V 1 " - " ASN B 709 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B1074 " " NAG Z 1 " - " ASN B1098 " " NAG a 1 " - " ASN B1134 " " NAG b 1 " - " ASN C 282 " " NAG c 1 " - " ASN C 331 " " NAG d 1 " - " ASN C 616 " " NAG e 1 " - " ASN C 709 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6946 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 57 sheets defined 21.6% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.039A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.937A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.843A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.556A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.706A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.524A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.734A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.557A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.968A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.594A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.984A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.579A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.549A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.239A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.870A 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 337 through 343 removed outlier: 4.163A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.960A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.247A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 5.697A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 624 removed outlier: 4.430A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.890A 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 754 removed outlier: 3.822A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 4.667A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.602A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.638A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.584A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.602A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 910 " --> pdb=" O PHE B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.427A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 912 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.509A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) 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 983 removed outlier: 3.907A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.569A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.664A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.224A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 4.074A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.360A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.716A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.820A pdb=" N THR C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 634 through 638' Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.981A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.781A 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 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.861A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 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: 3.556A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.207A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.924A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.094A pdb=" N ALA H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.173A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.953A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.163A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 removed outlier: 3.540A pdb=" N ASP M 83 " --> pdb=" O GLU M 80 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA M 84 " --> pdb=" O ALA M 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 80 through 84' Processing helix chain 'N' and resid 80 through 84 removed outlier: 4.108A pdb=" N ALA N 84 " --> pdb=" O ALA N 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.778A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.496A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.726A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.649A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.183A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.857A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.561A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.565A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.791A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.647A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.700A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.781A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.599A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.575A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.507A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.803A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.583A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.246A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 715 through 719 removed outlier: 5.959A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 719 removed outlier: 5.959A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.615A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.842A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.769A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.921A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.943A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.699A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.663A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.153A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.711A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.677A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AE7, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AE8, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.966A pdb=" N ASN H 59 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.146A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER L 68 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.088A pdb=" N GLU L 106 " --> pdb=" O VAL L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'L' and resid 49 through 50 Processing sheet with id=AF3, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.674A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 19 through 21 Processing sheet with id=AF5, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.545A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'M' and resid 12 through 14 removed outlier: 6.684A pdb=" N VAL M 13 " --> pdb=" O LYS M 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'M' and resid 54 through 55 removed outlier: 4.303A pdb=" N ILE M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 19 through 21 Processing sheet with id=AG1, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.822A pdb=" N ASN J 59 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU J 50 " --> pdb=" O ASN J 59 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA J 92 " --> pdb=" O VAL J 114 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL J 114 " --> pdb=" O ALA J 92 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.898A pdb=" N SER N 71 " --> pdb=" O SER N 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER N 68 " --> pdb=" O SER N 71 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 10 through 14 removed outlier: 6.073A pdb=" N MET N 11 " --> pdb=" O GLU N 106 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS N 108 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL N 13 " --> pdb=" O LYS N 108 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLN N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU N 47 " --> pdb=" O GLN N 38 " (cutoff:3.500A) 1037 hydrogen bonds defined for protein. 2766 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: 6.89 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9479 1.34 - 1.46: 7680 1.46 - 1.58: 13368 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 30704 Sorted by residual: bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C1 NAG h 1 " pdb=" O5 NAG h 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.12e+00 ... (remaining 30699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 40360 1.54 - 3.08: 1211 3.08 - 4.61: 147 4.61 - 6.15: 33 6.15 - 7.69: 11 Bond angle restraints: 41762 Sorted by residual: angle pdb=" C PHE C 486 " pdb=" N ASN C 487 " pdb=" CA ASN C 487 " ideal model delta sigma weight residual 122.61 128.22 -5.61 1.56e+00 4.11e-01 1.29e+01 angle pdb=" C PHE B 486 " pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C ASN C 234 " pdb=" N ILE C 235 " pdb=" CA ILE C 235 " ideal model delta sigma weight residual 121.97 128.18 -6.21 1.80e+00 3.09e-01 1.19e+01 angle pdb=" N GLY A 593 " pdb=" CA GLY A 593 " pdb=" C GLY A 593 " ideal model delta sigma weight residual 110.63 115.32 -4.69 1.45e+00 4.76e-01 1.05e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.64 -3.94 1.22e+00 6.72e-01 1.05e+01 ... (remaining 41757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 15877 17.50 - 35.00: 1428 35.00 - 52.51: 247 52.51 - 70.01: 45 70.01 - 87.51: 24 Dihedral angle restraints: 17621 sinusoidal: 6799 harmonic: 10822 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 14.84 78.16 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -164.06 78.06 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 17.74 75.26 1 1.00e+01 1.00e-02 7.16e+01 ... (remaining 17618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 4900 0.140 - 0.280: 33 0.280 - 0.419: 0 0.419 - 0.559: 2 0.559 - 0.699: 1 Chirality restraints: 4936 Sorted by residual: chirality pdb=" C1 NAG j 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG j 1 " pdb=" O5 NAG j 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" C1 NAG A2007 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A2007 " pdb=" O5 NAG A2007 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 4933 not shown) Planarity restraints: 5326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.024 2.00e-02 2.50e+03 2.24e-02 6.30e+00 pdb=" CG ASN B 234 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.022 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO A 521 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO C 986 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.026 5.00e-02 4.00e+02 ... (remaining 5323 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 773 2.69 - 3.24: 29027 3.24 - 3.79: 45150 3.79 - 4.35: 56687 4.35 - 4.90: 94410 Nonbonded interactions: 226047 Sorted by model distance: nonbonded pdb=" OG1 THR H 33 " pdb=" O PHE H 99 " model vdw 2.132 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.150 3.040 nonbonded pdb=" OH TYR C 453 " pdb=" OG SER N 31 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR B 716 " pdb=" O GLN B1071 " model vdw 2.171 3.040 nonbonded pdb=" O PHE I 29 " pdb=" OG SER I 53 " model vdw 2.174 3.040 ... (remaining 226042 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' selection = (chain 'B' and (resid 27 through 622 or resid 636 through 827 or resid 855 throu \ gh 2007)) selection = (chain 'C' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 2007)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' 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' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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 group one per residue 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.930 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30821 Z= 0.171 Angle : 0.651 16.735 42070 Z= 0.320 Chirality : 0.048 0.699 4936 Planarity : 0.004 0.048 5279 Dihedral : 13.431 87.509 10546 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -1.14 (0.14), residues: 3661 helix: 1.71 (0.22), residues: 649 sheet: -0.51 (0.17), residues: 914 loop : -1.75 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 815 TYR 0.018 0.001 TYR I 95 PHE 0.019 0.001 PHE B 906 TRP 0.022 0.001 TRP M 48 HIS 0.002 0.000 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (30704) covalent geometry : angle 0.61720 / 0.31 (41762) SS BOND : bond 0.00410 / 0.28 ( 43) SS BOND : angle 1.23502 / 0.81 ( 86) hydrogen bonds : bond 0.14749 / 9.21 ( 1033) hydrogen bonds : angle 6.40924 / 4.29 ( 2766) link_BETA1-4 : bond 0.00526 / 0.34 ( 27) link_BETA1-4 : angle 3.17071 / 2.02 ( 81) link_NAG-ASN : bond 0.00353 / 0.24 ( 47) link_NAG-ASN : angle 2.59933 / 1.51 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8717 (t80) cc_final: 0.7999 (t80) REVERT: A 902 MET cc_start: 0.8566 (mmm) cc_final: 0.8307 (mmt) REVERT: B 759 PHE cc_start: 0.7058 (p90) cc_final: 0.6806 (p90) REVERT: B 869 MET cc_start: 0.8448 (mpp) cc_final: 0.8024 (mpp) REVERT: B 1031 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8234 (tm-30) REVERT: C 452 LEU cc_start: 0.8476 (mm) cc_final: 0.8243 (tp) REVERT: C 740 MET cc_start: 0.8097 (tpt) cc_final: 0.7857 (mmm) REVERT: H 80 TYR cc_start: 0.9103 (m-80) cc_final: 0.8668 (m-80) REVERT: N 21 MET cc_start: 0.7488 (tmm) cc_final: 0.7256 (tmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1633 time to fit residues: 45.1493 Evaluate side-chains 120 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A1106 GLN C 196 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** N 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.098424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.063387 restraints weight = 133481.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.065794 restraints weight = 73161.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.065917 restraints weight = 50076.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.066660 restraints weight = 38062.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.066683 restraints weight = 31879.586| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30821 Z= 0.158 Angle : 0.620 11.263 42070 Z= 0.311 Chirality : 0.046 0.426 4936 Planarity : 0.004 0.052 5279 Dihedral : 4.207 31.210 4001 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.94 % Rotamer: Outliers : 0.40 % Allowed : 6.69 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.11 (0.14), residues: 3661 helix: 1.57 (0.22), residues: 666 sheet: -0.45 (0.17), residues: 928 loop : -1.73 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 67 TYR 0.017 0.001 TYR C 91 PHE 0.015 0.001 PHE A 456 TRP 0.017 0.001 TRP M 48 HIS 0.004 0.001 HIS M 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (30704) covalent geometry : angle 0.59816 / 0.31 (41762) SS BOND : bond 0.00348 / 0.24 ( 43) SS BOND : angle 1.05861 / 0.69 ( 86) hydrogen bonds : bond 0.05525 / 3.55 ( 1033) hydrogen bonds : angle 5.44996 / 3.66 ( 2766) link_BETA1-4 : bond 0.00461 / 0.27 ( 27) link_BETA1-4 : angle 2.25539 / 1.46 ( 81) link_NAG-ASN : bond 0.00239 / 0.17 ( 47) link_NAG-ASN : angle 2.27036 / 1.37 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 869 MET cc_start: 0.8469 (mpp) cc_final: 0.7981 (mpp) REVERT: C 740 MET cc_start: 0.8136 (tpt) cc_final: 0.7887 (mmm) REVERT: H 80 TYR cc_start: 0.9336 (m-80) cc_final: 0.9107 (m-80) REVERT: L 21 MET cc_start: 0.5010 (ttp) cc_final: 0.4633 (mpp) outliers start: 13 outliers final: 10 residues processed: 141 average time/residue: 0.1693 time to fit residues: 40.5720 Evaluate side-chains 128 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain M residue 35 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 179 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 256 optimal weight: 4.9990 chunk 169 optimal weight: 0.2980 chunk 349 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 317 optimal weight: 10.0000 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 437 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN L 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.098744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.062262 restraints weight = 119743.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.064380 restraints weight = 61822.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.065751 restraints weight = 42663.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.066570 restraints weight = 34147.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.067030 restraints weight = 29845.104| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30821 Z= 0.159 Angle : 0.600 11.310 42070 Z= 0.299 Chirality : 0.045 0.414 4936 Planarity : 0.004 0.049 5279 Dihedral : 4.197 31.232 4001 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 0.71 % Allowed : 10.58 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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 (0.14), residues: 3661 helix: 1.54 (0.21), residues: 677 sheet: -0.38 (0.17), residues: 918 loop : -1.74 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 67 TYR 0.026 0.001 TYR N 37 PHE 0.016 0.001 PHE B 759 TRP 0.014 0.001 TRP N 48 HIS 0.005 0.001 HIS N 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (30704) covalent geometry : angle 0.57742 / 0.29 (41762) SS BOND : bond 0.00292 / 0.21 ( 43) SS BOND : angle 1.04361 / 0.68 ( 86) hydrogen bonds : bond 0.05543 / 3.56 ( 1033) hydrogen bonds : angle 5.25429 / 3.55 ( 2766) link_BETA1-4 : bond 0.00423 / 0.26 ( 27) link_BETA1-4 : angle 2.22486 / 1.44 ( 81) link_NAG-ASN : bond 0.00254 / 0.18 ( 47) link_NAG-ASN : angle 2.23642 / 1.35 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 869 MET cc_start: 0.8524 (mpp) cc_final: 0.8058 (mpp) REVERT: C 740 MET cc_start: 0.8153 (tpt) cc_final: 0.7902 (mmm) REVERT: H 67 ARG cc_start: 0.6898 (ptm-80) cc_final: 0.6687 (ttp80) REVERT: H 80 TYR cc_start: 0.9107 (m-80) cc_final: 0.8697 (m-80) REVERT: M 29 VAL cc_start: 0.5549 (OUTLIER) cc_final: 0.5125 (m) outliers start: 23 outliers final: 15 residues processed: 140 average time/residue: 0.1653 time to fit residues: 39.4007 Evaluate side-chains 128 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 265 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 299 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 236 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN N 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.096358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.059724 restraints weight = 133232.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.061455 restraints weight = 70085.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.062483 restraints weight = 48259.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.063048 restraints weight = 38882.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.063433 restraints weight = 34304.915| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 30821 Z= 0.249 Angle : 0.682 11.714 42070 Z= 0.341 Chirality : 0.047 0.412 4936 Planarity : 0.004 0.049 5279 Dihedral : 4.532 32.331 4001 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.32 % Favored : 92.60 % Rotamer: Outliers : 1.67 % Allowed : 13.43 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.32 (0.13), residues: 3661 helix: 1.20 (0.21), residues: 674 sheet: -0.50 (0.17), residues: 916 loop : -1.84 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1107 TYR 0.027 0.002 TYR C 91 PHE 0.021 0.002 PHE C 275 TRP 0.014 0.001 TRP M 48 HIS 0.008 0.001 HIS N 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.25 (30704) covalent geometry : angle 0.65968 / 0.34 (41762) SS BOND : bond 0.00342 / 0.23 ( 43) SS BOND : angle 1.27472 / 0.85 ( 86) hydrogen bonds : bond 0.06594 / 4.23 ( 1033) hydrogen bonds : angle 5.53120 / 3.75 ( 2766) link_BETA1-4 : bond 0.00372 / 0.24 ( 27) link_BETA1-4 : angle 2.23692 / 1.45 ( 81) link_NAG-ASN : bond 0.00406 / 0.26 ( 47) link_NAG-ASN : angle 2.43154 / 1.48 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 123 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 869 MET cc_start: 0.8543 (mpp) cc_final: 0.8200 (mpp) REVERT: C 740 MET cc_start: 0.8096 (tpt) cc_final: 0.7882 (mmm) REVERT: H 80 TYR cc_start: 0.9398 (m-80) cc_final: 0.9160 (m-80) REVERT: L 21 MET cc_start: 0.7099 (mpp) cc_final: 0.5566 (ttp) REVERT: L 33 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: L 48 TRP cc_start: 0.6002 (OUTLIER) cc_final: 0.5366 (m-10) REVERT: M 11 MET cc_start: 0.6781 (mmp) cc_final: 0.6345 (mtm) REVERT: J 34 MET cc_start: 0.5585 (tpt) cc_final: 0.5370 (tpt) outliers start: 54 outliers final: 28 residues processed: 167 average time/residue: 0.1600 time to fit residues: 45.2211 Evaluate side-chains 138 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 188 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 125 optimal weight: 0.0370 chunk 278 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 362 optimal weight: 50.0000 chunk 37 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** 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 = 0.4139 r_free = 0.4139 target = 0.098091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.062125 restraints weight = 121900.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.064332 restraints weight = 61132.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.065703 restraints weight = 41348.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.066556 restraints weight = 32799.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.067044 restraints weight = 28457.375| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 30821 Z= 0.107 Angle : 0.579 11.246 42070 Z= 0.286 Chirality : 0.045 0.427 4936 Planarity : 0.004 0.048 5279 Dihedral : 4.105 30.849 4001 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 1.02 % Allowed : 15.29 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.03 (0.14), residues: 3661 helix: 1.70 (0.21), residues: 661 sheet: -0.32 (0.17), residues: 895 loop : -1.72 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 67 TYR 0.015 0.001 TYR H 95 PHE 0.011 0.001 PHE C 201 TRP 0.015 0.001 TRP N 48 HIS 0.003 0.001 HIS N 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (30704) covalent geometry : angle 0.55733 / 0.28 (41762) SS BOND : bond 0.00284 / 0.20 ( 43) SS BOND : angle 1.03190 / 0.71 ( 86) hydrogen bonds : bond 0.05023 / 3.24 ( 1033) hydrogen bonds : angle 5.01119 / 3.38 ( 2766) link_BETA1-4 : bond 0.00490 / 0.29 ( 27) link_BETA1-4 : angle 2.17202 / 1.40 ( 81) link_NAG-ASN : bond 0.00320 / 0.22 ( 47) link_NAG-ASN : angle 2.18676 / 1.32 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.8843 (tmm) cc_final: 0.8635 (tmm) REVERT: B 869 MET cc_start: 0.8478 (mpp) cc_final: 0.7992 (mpp) REVERT: C 740 MET cc_start: 0.7980 (tpt) cc_final: 0.7746 (mmm) REVERT: L 11 MET cc_start: 0.6916 (mpp) cc_final: 0.6514 (pmm) REVERT: L 21 MET cc_start: 0.6636 (mpp) cc_final: 0.4741 (ttp) REVERT: L 33 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6785 (m-10) REVERT: L 48 TRP cc_start: 0.4862 (OUTLIER) cc_final: 0.4384 (m-10) REVERT: M 29 VAL cc_start: 0.5719 (OUTLIER) cc_final: 0.5351 (m) REVERT: J 1 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7250 (pp20) REVERT: J 34 MET cc_start: 0.7113 (tpt) cc_final: 0.6311 (tpt) REVERT: N 63 PHE cc_start: 0.4642 (t80) cc_final: 0.3794 (m-80) outliers start: 33 outliers final: 18 residues processed: 153 average time/residue: 0.1564 time to fit residues: 41.6664 Evaluate side-chains 141 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 35 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 108 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 309 optimal weight: 0.0010 chunk 71 optimal weight: 3.9990 chunk 364 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.097183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.060943 restraints weight = 121839.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.063067 restraints weight = 62593.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.064391 restraints weight = 43004.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.065224 restraints weight = 34392.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.065672 restraints weight = 29958.613| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30821 Z= 0.168 Angle : 0.604 11.630 42070 Z= 0.299 Chirality : 0.045 0.404 4936 Planarity : 0.004 0.049 5279 Dihedral : 4.164 31.138 4001 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.26 % Favored : 93.66 % Rotamer: Outliers : 1.45 % Allowed : 16.03 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.03 (0.14), residues: 3661 helix: 1.65 (0.21), residues: 666 sheet: -0.26 (0.17), residues: 894 loop : -1.73 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.019 0.001 TYR C 91 PHE 0.013 0.001 PHE A 92 TRP 0.016 0.001 TRP N 48 HIS 0.005 0.001 HIS N 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (30704) covalent geometry : angle 0.58175 / 0.29 (41762) SS BOND : bond 0.00326 / 0.21 ( 43) SS BOND : angle 1.05843 / 0.71 ( 86) hydrogen bonds : bond 0.05551 / 3.56 ( 1033) hydrogen bonds : angle 5.12289 / 3.47 ( 2766) link_BETA1-4 : bond 0.00426 / 0.27 ( 27) link_BETA1-4 : angle 2.15948 / 1.39 ( 81) link_NAG-ASN : bond 0.00274 / 0.18 ( 47) link_NAG-ASN : angle 2.28192 / 1.38 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 869 MET cc_start: 0.8558 (mpp) cc_final: 0.8083 (mpp) REVERT: C 740 MET cc_start: 0.8092 (tpt) cc_final: 0.7864 (mmm) REVERT: L 11 MET cc_start: 0.6964 (mpp) cc_final: 0.6521 (pmm) REVERT: L 33 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.6783 (m-80) REVERT: L 48 TRP cc_start: 0.5017 (OUTLIER) cc_final: 0.4493 (m-10) REVERT: I 1 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6458 (pp20) REVERT: I 50 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7904 (tp30) REVERT: J 1 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7268 (pp20) REVERT: J 34 MET cc_start: 0.7106 (tpt) cc_final: 0.6786 (tpt) REVERT: N 63 PHE cc_start: 0.4578 (t80) cc_final: 0.3824 (m-80) outliers start: 47 outliers final: 28 residues processed: 164 average time/residue: 0.1538 time to fit residues: 43.2483 Evaluate side-chains 148 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain N residue 35 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 355 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 225 optimal weight: 0.8980 chunk 133 optimal weight: 20.0000 chunk 306 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.097803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.061715 restraints weight = 121482.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.063869 restraints weight = 61769.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.065221 restraints weight = 42220.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.066076 restraints weight = 33630.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.066514 restraints weight = 29206.524| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30821 Z= 0.122 Angle : 0.582 11.370 42070 Z= 0.286 Chirality : 0.044 0.413 4936 Planarity : 0.004 0.049 5279 Dihedral : 4.077 30.716 4001 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 1.39 % Allowed : 16.40 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -0.97 (0.14), residues: 3661 helix: 1.76 (0.21), residues: 660 sheet: -0.18 (0.17), residues: 885 loop : -1.73 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 67 TYR 0.017 0.001 TYR C 91 PHE 0.010 0.001 PHE C 201 TRP 0.017 0.001 TRP N 48 HIS 0.003 0.001 HIS N 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (30704) covalent geometry : angle 0.56035 / 0.28 (41762) SS BOND : bond 0.00362 / 0.22 ( 43) SS BOND : angle 0.97769 / 0.65 ( 86) hydrogen bonds : bond 0.05115 / 3.29 ( 1033) hydrogen bonds : angle 4.96379 / 3.35 ( 2766) link_BETA1-4 : bond 0.00465 / 0.29 ( 27) link_BETA1-4 : angle 2.13443 / 1.38 ( 81) link_NAG-ASN : bond 0.00255 / 0.18 ( 47) link_NAG-ASN : angle 2.20026 / 1.33 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8159 (t0) REVERT: B 581 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9133 (p) REVERT: B 869 MET cc_start: 0.8504 (mpp) cc_final: 0.8033 (mpp) REVERT: C 740 MET cc_start: 0.8059 (tpt) cc_final: 0.7805 (mmm) REVERT: L 11 MET cc_start: 0.7145 (mpp) cc_final: 0.6701 (pmm) REVERT: L 48 TRP cc_start: 0.5223 (OUTLIER) cc_final: 0.4572 (m-10) REVERT: I 1 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6409 (pp20) REVERT: I 50 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7903 (tp30) REVERT: J 1 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7311 (pp20) REVERT: J 34 MET cc_start: 0.7126 (tpt) cc_final: 0.6792 (tpt) REVERT: N 63 PHE cc_start: 0.4565 (OUTLIER) cc_final: 0.3975 (m-80) outliers start: 45 outliers final: 29 residues processed: 157 average time/residue: 0.1535 time to fit residues: 42.4204 Evaluate side-chains 153 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 35 HIS Chi-restraints excluded: chain N residue 63 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 32 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 83 optimal weight: 0.0000 chunk 24 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 323 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.097277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.060962 restraints weight = 122006.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.063087 restraints weight = 62355.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.064412 restraints weight = 42829.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.065180 restraints weight = 34219.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.065737 restraints weight = 29901.448| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30821 Z= 0.178 Angle : 0.613 12.417 42070 Z= 0.302 Chirality : 0.045 0.403 4936 Planarity : 0.004 0.050 5279 Dihedral : 4.170 30.881 4001 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.50 % Rotamer: Outliers : 1.73 % Allowed : 16.50 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.07 (0.14), residues: 3661 helix: 1.67 (0.21), residues: 659 sheet: -0.28 (0.17), residues: 903 loop : -1.78 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 67 TYR 0.021 0.001 TYR C 91 PHE 0.013 0.001 PHE C 43 TRP 0.015 0.001 TRP N 48 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (30704) covalent geometry : angle 0.59083 / 0.30 (41762) SS BOND : bond 0.00302 / 0.20 ( 43) SS BOND : angle 1.12000 / 0.74 ( 86) hydrogen bonds : bond 0.05537 / 3.55 ( 1033) hydrogen bonds : angle 5.08099 / 3.43 ( 2766) link_BETA1-4 : bond 0.00418 / 0.26 ( 27) link_BETA1-4 : angle 2.14822 / 1.39 ( 81) link_NAG-ASN : bond 0.00265 / 0.18 ( 47) link_NAG-ASN : angle 2.26965 / 1.37 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 119 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8214 (t0) REVERT: B 468 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.6996 (mm) REVERT: B 581 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.9124 (p) REVERT: B 869 MET cc_start: 0.8574 (mpp) cc_final: 0.8088 (mpp) REVERT: C 740 MET cc_start: 0.8134 (tpt) cc_final: 0.7884 (mmm) REVERT: L 11 MET cc_start: 0.7134 (mpp) cc_final: 0.6709 (pmm) REVERT: L 48 TRP cc_start: 0.5327 (OUTLIER) cc_final: 0.4769 (m100) REVERT: I 1 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6284 (pp20) REVERT: I 50 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7961 (tp30) REVERT: M 11 MET cc_start: 0.7043 (mmp) cc_final: 0.6577 (mpp) REVERT: J 1 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7414 (pp20) REVERT: J 34 MET cc_start: 0.7230 (tpt) cc_final: 0.6869 (tpt) REVERT: N 63 PHE cc_start: 0.4482 (OUTLIER) cc_final: 0.3831 (m-80) outliers start: 56 outliers final: 39 residues processed: 165 average time/residue: 0.1637 time to fit residues: 46.6546 Evaluate side-chains 161 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 115 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 35 HIS Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 63 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 chunk 237 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 46 optimal weight: 0.0030 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 356 optimal weight: 9.9990 chunk 344 optimal weight: 40.0000 overall best weight: 3.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 437 ASN ** 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 = 0.4105 r_free = 0.4105 target = 0.096030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.060751 restraints weight = 133193.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.064378 restraints weight = 75389.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.063600 restraints weight = 43381.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.063800 restraints weight = 37974.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.064026 restraints weight = 38367.231| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30821 Z= 0.264 Angle : 0.691 11.984 42070 Z= 0.343 Chirality : 0.046 0.399 4936 Planarity : 0.004 0.050 5279 Dihedral : 4.499 31.707 4001 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.43 % Favored : 92.49 % Rotamer: Outliers : 1.80 % Allowed : 16.99 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.35 (0.13), residues: 3661 helix: 1.27 (0.21), residues: 670 sheet: -0.56 (0.17), residues: 919 loop : -1.87 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 34 TYR 0.031 0.002 TYR C 91 PHE 0.019 0.002 PHE B 238 TRP 0.017 0.001 TRP M 48 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.26 (30704) covalent geometry : angle 0.66928 / 0.34 (41762) SS BOND : bond 0.00337 / 0.21 ( 43) SS BOND : angle 1.34955 / 0.90 ( 86) hydrogen bonds : bond 0.06530 / 4.17 ( 1033) hydrogen bonds : angle 5.42910 / 3.68 ( 2766) link_BETA1-4 : bond 0.00388 / 0.25 ( 27) link_BETA1-4 : angle 2.22599 / 1.44 ( 81) link_NAG-ASN : bond 0.00410 / 0.26 ( 47) link_NAG-ASN : angle 2.43977 / 1.49 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 118 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8246 (t0) REVERT: B 468 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.6973 (mm) REVERT: B 581 THR cc_start: 0.9341 (OUTLIER) cc_final: 0.9120 (p) REVERT: B 869 MET cc_start: 0.8586 (mpp) cc_final: 0.8063 (mpp) REVERT: C 740 MET cc_start: 0.8130 (tpt) cc_final: 0.7927 (mmm) REVERT: L 11 MET cc_start: 0.7652 (mpp) cc_final: 0.7082 (pmm) REVERT: L 48 TRP cc_start: 0.6135 (OUTLIER) cc_final: 0.5626 (m100) REVERT: I 1 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6655 (pp20) REVERT: I 50 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7869 (tp30) REVERT: M 11 MET cc_start: 0.7528 (mmp) cc_final: 0.7041 (mtm) REVERT: N 21 MET cc_start: 0.7702 (tmm) cc_final: 0.7453 (tmm) REVERT: N 63 PHE cc_start: 0.4521 (OUTLIER) cc_final: 0.3870 (m-80) outliers start: 58 outliers final: 45 residues processed: 169 average time/residue: 0.1580 time to fit residues: 46.0931 Evaluate side-chains 165 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 35 HIS Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 63 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 181 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 chunk 317 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 318 optimal weight: 0.9980 chunk 278 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 306 optimal weight: 20.0000 chunk 136 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.099471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.063143 restraints weight = 117307.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.065216 restraints weight = 61066.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.066531 restraints weight = 42424.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.067356 restraints weight = 34150.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.067839 restraints weight = 29887.125| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30821 Z= 0.120 Angle : 0.597 11.456 42070 Z= 0.294 Chirality : 0.045 0.417 4936 Planarity : 0.004 0.050 5279 Dihedral : 4.164 30.761 4001 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.21 % Rotamer: Outliers : 1.61 % Allowed : 17.30 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.10 (0.14), residues: 3661 helix: 1.67 (0.21), residues: 666 sheet: -0.36 (0.17), residues: 904 loop : -1.79 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 67 TYR 0.015 0.001 TYR C 91 PHE 0.011 0.001 PHE A 456 TRP 0.017 0.001 TRP C 104 HIS 0.004 0.001 HIS N 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (30704) covalent geometry : angle 0.57460 / 0.29 (41762) SS BOND : bond 0.00277 / 0.19 ( 43) SS BOND : angle 1.16175 / 0.76 ( 86) hydrogen bonds : bond 0.05305 / 3.40 ( 1033) hydrogen bonds : angle 5.01160 / 3.38 ( 2766) link_BETA1-4 : bond 0.00497 / 0.31 ( 27) link_BETA1-4 : angle 2.14914 / 1.38 ( 81) link_NAG-ASN : bond 0.00258 / 0.18 ( 47) link_NAG-ASN : angle 2.24625 / 1.36 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7322 Ramachandran restraints generated. 3661 Oldfield, 0 Emsley, 3661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 123 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8195 (t0) REVERT: B 468 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7128 (mm) REVERT: B 581 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9119 (p) REVERT: B 869 MET cc_start: 0.8535 (mpp) cc_final: 0.8036 (mpp) REVERT: C 740 MET cc_start: 0.8024 (tpt) cc_final: 0.7763 (mmm) REVERT: H 13 LYS cc_start: 0.8201 (pttm) cc_final: 0.7880 (ttmm) REVERT: L 11 MET cc_start: 0.7096 (mpp) cc_final: 0.6793 (pmm) REVERT: L 48 TRP cc_start: 0.5461 (OUTLIER) cc_final: 0.4752 (m-10) REVERT: I 1 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.6221 (pp20) REVERT: I 4 LEU cc_start: 0.7125 (mt) cc_final: 0.6809 (mp) REVERT: I 50 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7987 (tp30) REVERT: M 11 MET cc_start: 0.7144 (mmp) cc_final: 0.6707 (mtm) REVERT: J 34 MET cc_start: 0.6990 (tpt) cc_final: 0.6737 (tpt) REVERT: N 63 PHE cc_start: 0.4067 (OUTLIER) cc_final: 0.3405 (m-80) outliers start: 52 outliers final: 38 residues processed: 165 average time/residue: 0.1565 time to fit residues: 44.3662 Evaluate side-chains 166 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 48 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain N residue 35 HIS Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 63 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 39 optimal weight: 0.1980 chunk 100 optimal weight: 10.0000 chunk 303 optimal weight: 30.0000 chunk 306 optimal weight: 20.0000 chunk 171 optimal weight: 0.0040 chunk 338 optimal weight: 30.0000 chunk 189 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 334 optimal weight: 10.0000 overall best weight: 2.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.097247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.062119 restraints weight = 133811.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.064809 restraints weight = 73869.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.065075 restraints weight = 48477.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.065598 restraints weight = 35090.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.065684 restraints weight = 31194.685| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30821 Z= 0.159 Angle : 0.611 11.524 42070 Z= 0.300 Chirality : 0.045 0.408 4936 Planarity : 0.004 0.050 5279 Dihedral : 4.179 30.872 4001 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.61 % Favored : 93.31 % Rotamer: Outliers : 1.58 % Allowed : 17.27 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.11 (0.14), residues: 3661 helix: 1.65 (0.21), residues: 668 sheet: -0.41 (0.17), residues: 928 loop : -1.78 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 408 TYR 0.020 0.001 TYR C 91 PHE 0.011 0.001 PHE C 43 TRP 0.015 0.001 TRP N 48 HIS 0.013 0.001 HIS N 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (30704) covalent geometry : angle 0.58874 / 0.30 (41762) SS BOND : bond 0.00298 / 0.20 ( 43) SS BOND : angle 1.15416 / 0.76 ( 86) hydrogen bonds : bond 0.05490 / 3.51 ( 1033) hydrogen bonds : angle 5.03053 / 3.40 ( 2766) link_BETA1-4 : bond 0.00431 / 0.28 ( 27) link_BETA1-4 : angle 2.14338 / 1.38 ( 81) link_NAG-ASN : bond 0.00262 / 0.18 ( 47) link_NAG-ASN : angle 2.27133 / 1.38 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5845.79 seconds wall clock time: 101 minutes 33.81 seconds (6093.81 seconds total)