Starting phenix.real_space_refine on Thu Mar 5 20:27:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eb5_31052/03_2026/7eb5_31052.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eb5_31052/03_2026/7eb5_31052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7eb5_31052/03_2026/7eb5_31052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eb5_31052/03_2026/7eb5_31052.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eb5_31052/03_2026/7eb5_31052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eb5_31052/03_2026/7eb5_31052.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 15839 2.51 5 N 4041 2.21 5 O 4917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24902 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7985 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 51, 'TRANS': 971} Chain breaks: 6 Chain: "A" Number of atoms: 7887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7887 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 50, 'TRANS': 960} Chain breaks: 7 Chain: "B" Number of atoms: 7994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7994 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.68, per 1000 atoms: 0.23 Number of scatterers: 24902 At special positions: 0 Unit cell: (139.7, 143, 200.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4917 8.00 N 4041 7.00 C 15839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 234 " " NAG A2005 " - " ASN A 343 " " NAG A2006 " - " ASN A 603 " " NAG A2007 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 165 " " NAG B2004 " - " ASN B 331 " " NAG B2005 " - " ASN B 343 " " NAG B2006 " - " ASN B 603 " " NAG B2007 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 331 " " NAG C2005 " - " ASN C 603 " " NAG C2006 " - " ASN C 657 " " NAG D 1 " - " ASN C 234 " " NAG E 1 " - " ASN C 282 " " NAG F 1 " - " ASN C 616 " " NAG G 1 " - " ASN C 709 " " NAG H 1 " - " ASN C 717 " " NAG I 1 " - " ASN C 801 " " NAG J 1 " - " ASN C1074 " " NAG K 1 " - " ASN C1098 " " NAG L 1 " - " ASN C1134 " " NAG M 1 " - " ASN A 282 " " NAG N 1 " - " ASN A 331 " " NAG O 1 " - " ASN A 616 " " NAG P 1 " - " ASN A 709 " " NAG Q 1 " - " ASN A 717 " " NAG R 1 " - " ASN A 801 " " NAG S 1 " - " ASN A1074 " " NAG T 1 " - " ASN A1098 " " NAG U 1 " - " ASN A1134 " " NAG V 1 " - " ASN B 234 " " NAG W 1 " - " ASN B 282 " " NAG X 1 " - " ASN B 616 " " NAG Y 1 " - " ASN B 709 " " NAG Z 1 " - " ASN B 717 " " NAG a 1 " - " ASN B 801 " " NAG b 1 " - " ASN B1074 " " NAG c 1 " - " ASN B1098 " " NAG d 1 " - " ASN B1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.0 seconds 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5726 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 46 sheets defined 25.4% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.516A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.828A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.632A pdb=" N ILE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.542A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.752A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.762A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.645A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.741A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.574A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1035 removed outlier: 4.274A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.821A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.208A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.042A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.682A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 783 removed outlier: 4.349A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.703A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.592A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.556A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.588A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.823A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.348A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.638A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.522A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.161A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.743A pdb=" N ARG B 634 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL B 635 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.901A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 764 removed outlier: 3.811A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 783 removed outlier: 3.968A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.705A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 919' Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.565A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.712A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 6.320A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.555A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.223A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.698A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.505A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.287A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.519A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.963A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.554A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 573 through 576 removed outlier: 3.998A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.782A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.574A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.642A pdb=" N VAL C1065 " --> pdb=" O MET C1050 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'C' and resid 787 through 789 removed outlier: 5.816A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.881A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AB9, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.778A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.691A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.218A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 192 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.744A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AC5, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.398A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.000A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 587 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.051A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 717 through 719 Processing sheet with id=AD2, first strand: chain 'A' and resid 717 through 719 removed outlier: 3.718A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.668A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.569A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.536A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.640A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 191 through 197 removed outlier: 6.414A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 310 through 313 Processing sheet with id=AE2, first strand: chain 'B' and resid 310 through 313 removed outlier: 4.855A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 323 through 328 removed outlier: 6.457A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.367A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.643A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.643A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.779A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) 851 hydrogen bonds defined for protein. 2301 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.63 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7861 1.35 - 1.47: 6530 1.47 - 1.59: 10929 1.59 - 1.72: 0 1.72 - 1.84: 129 Bond restraints: 25449 Sorted by residual: bond pdb=" N VAL C 642 " pdb=" CA VAL C 642 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.86e+00 bond pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.98e+00 bond pdb=" CA SER C 640 " pdb=" CB SER C 640 " ideal model delta sigma weight residual 1.530 1.497 0.034 1.69e-02 3.50e+03 3.94e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C1 NAG B2004 " pdb=" O5 NAG B2004 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.87e+00 ... (remaining 25444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 34043 2.17 - 4.34: 554 4.34 - 6.51: 40 6.51 - 8.68: 5 8.68 - 10.85: 2 Bond angle restraints: 34644 Sorted by residual: angle pdb=" N VAL A1128 " pdb=" CA VAL A1128 " pdb=" C VAL A1128 " ideal model delta sigma weight residual 113.42 108.83 4.59 1.17e+00 7.31e-01 1.54e+01 angle pdb=" CA GLY C 639 " pdb=" C GLY C 639 " pdb=" O GLY C 639 " ideal model delta sigma weight residual 121.44 117.02 4.42 1.26e+00 6.30e-01 1.23e+01 angle pdb=" CA THR C 638 " pdb=" C THR C 638 " pdb=" O THR C 638 " ideal model delta sigma weight residual 121.40 117.58 3.82 1.11e+00 8.12e-01 1.19e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.90 -4.20 1.22e+00 6.72e-01 1.18e+01 angle pdb=" N SER C 605 " pdb=" CA SER C 605 " pdb=" C SER C 605 " ideal model delta sigma weight residual 108.34 112.28 -3.94 1.31e+00 5.83e-01 9.03e+00 ... (remaining 34639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.28: 15034 23.28 - 46.55: 843 46.55 - 69.83: 138 69.83 - 93.11: 42 93.11 - 116.39: 25 Dihedral angle restraints: 16082 sinusoidal: 7185 harmonic: 8897 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -172.10 86.10 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 165.00 -72.00 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 153.33 -60.33 1 1.00e+01 1.00e-02 4.85e+01 ... (remaining 16079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 4136 0.159 - 0.318: 18 0.318 - 0.476: 2 0.476 - 0.635: 5 0.635 - 0.794: 1 Chirality restraints: 4162 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.01e+00 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.51e+00 ... (remaining 4159 not shown) Planarity restraints: 4432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 229 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO B 230 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 230 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 230 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.037 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 479 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " -0.020 2.00e-02 2.50e+03 1.92e-02 4.62e+00 pdb=" CG ASN B 234 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.020 2.00e-02 2.50e+03 ... (remaining 4429 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 866 2.71 - 3.26: 24408 3.26 - 3.80: 37499 3.80 - 4.35: 44144 4.35 - 4.90: 75523 Nonbonded interactions: 182440 Sorted by model distance: nonbonded pdb=" O PRO B 85 " pdb=" OH TYR B 269 " model vdw 2.162 3.040 nonbonded pdb=" ND1 HIS B 625 " pdb=" OD1 ASP B 627 " model vdw 2.171 3.120 nonbonded pdb=" O THR A 998 " pdb=" NE2 GLN A1002 " model vdw 2.178 3.120 nonbonded pdb=" O PRO A 85 " pdb=" OH TYR A 269 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OG1 THR B 114 " model vdw 2.206 3.040 ... (remaining 182435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 827 or resid 855 through 2006)) selection = (chain 'B' and (resid 27 through 622 or resid 636 through 827 or resid 855 throu \ gh 2006)) selection = (chain 'C' and (resid 27 through 622 or resid 636 through 2006)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 22.720 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25559 Z= 0.194 Angle : 0.700 17.838 34936 Z= 0.338 Chirality : 0.052 0.794 4162 Planarity : 0.004 0.076 4385 Dihedral : 15.011 116.387 10251 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 0.11 % Allowed : 0.34 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 3014 helix: 1.03 (0.22), residues: 666 sheet: -0.46 (0.20), residues: 639 loop : -1.57 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 273 TYR 0.011 0.001 TYR C 91 PHE 0.021 0.001 PHE C 906 TRP 0.006 0.001 TRP C 436 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00402 (25449) covalent geometry : angle 0.63684 (34644) SS BOND : bond 0.00425 ( 35) SS BOND : angle 1.26172 ( 70) hydrogen bonds : bond 0.15673 ( 831) hydrogen bonds : angle 6.21373 ( 2301) Misc. bond : bond 0.00164 ( 1) link_BETA1-4 : bond 0.00652 ( 27) link_BETA1-4 : angle 3.67938 ( 81) link_NAG-ASN : bond 0.00664 ( 47) link_NAG-ASN : angle 3.61766 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.941 Fit side-chains REVERT: C 641 ASN cc_start: 0.6181 (OUTLIER) cc_final: 0.5882 (m-40) REVERT: C 957 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 869 MET cc_start: 0.8633 (mpp) cc_final: 0.8002 (mpp) REVERT: A 1029 MET cc_start: 0.9015 (tmm) cc_final: 0.8286 (tmm) REVERT: B 342 PHE cc_start: 0.8927 (m-80) cc_final: 0.8671 (m-80) REVERT: B 957 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8330 (tm-30) REVERT: B 1029 MET cc_start: 0.8592 (ttp) cc_final: 0.7947 (tmm) outliers start: 3 outliers final: 0 residues processed: 136 average time/residue: 0.1412 time to fit residues: 33.3544 Evaluate side-chains 102 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 641 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN C 487 ASN C1048 HIS C1106 GLN A1054 GLN B 49 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.139331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.089786 restraints weight = 58273.458| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 5.26 r_work: 0.3085 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25559 Z= 0.188 Angle : 0.679 13.037 34936 Z= 0.326 Chirality : 0.050 0.480 4162 Planarity : 0.004 0.061 4385 Dihedral : 9.874 107.965 4825 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.26 % Rotamer: Outliers : 0.45 % Allowed : 7.34 % Favored : 92.21 % 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: -1.08 (0.15), residues: 3014 helix: 1.04 (0.21), residues: 673 sheet: -0.56 (0.20), residues: 662 loop : -1.57 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 273 TYR 0.022 0.001 TYR C1067 PHE 0.025 0.002 PHE B 201 TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00442 (25449) covalent geometry : angle 0.62786 (34644) SS BOND : bond 0.00446 ( 35) SS BOND : angle 1.31183 ( 70) hydrogen bonds : bond 0.05379 ( 831) hydrogen bonds : angle 5.20255 ( 2301) Misc. bond : bond 0.00095 ( 1) link_BETA1-4 : bond 0.00572 ( 27) link_BETA1-4 : angle 2.94229 ( 81) link_NAG-ASN : bond 0.00572 ( 47) link_NAG-ASN : angle 3.41671 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: C 329 PHE cc_start: 0.7720 (m-10) cc_final: 0.7394 (m-10) REVERT: C 619 GLU cc_start: 0.8663 (mp0) cc_final: 0.8408 (mp0) REVERT: C 641 ASN cc_start: 0.6622 (OUTLIER) cc_final: 0.6215 (m110) REVERT: C 957 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8236 (tm-30) REVERT: A 133 PHE cc_start: 0.7296 (m-10) cc_final: 0.7057 (m-10) REVERT: A 239 GLN cc_start: 0.7479 (tp40) cc_final: 0.6960 (mm110) REVERT: A 773 GLU cc_start: 0.8872 (tp30) cc_final: 0.8660 (tp30) REVERT: A 869 MET cc_start: 0.9113 (mpp) cc_final: 0.8357 (mpp) REVERT: A 1029 MET cc_start: 0.9076 (tmm) cc_final: 0.8448 (tmm) REVERT: B 338 PHE cc_start: 0.8252 (m-80) cc_final: 0.8014 (m-10) REVERT: B 342 PHE cc_start: 0.9024 (m-10) cc_final: 0.8719 (m-80) REVERT: B 957 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8538 (tm-30) REVERT: B 1029 MET cc_start: 0.8610 (ttp) cc_final: 0.8345 (ttm) outliers start: 12 outliers final: 9 residues processed: 119 average time/residue: 0.1371 time to fit residues: 28.4313 Evaluate side-chains 102 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 50.0000 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 chunk 301 optimal weight: 0.1980 chunk 192 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 128 optimal weight: 8.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 GLN C 641 ASN A 544 ASN A 564 GLN A1142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.142463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092887 restraints weight = 58663.779| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 4.50 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25559 Z= 0.108 Angle : 0.608 12.796 34936 Z= 0.287 Chirality : 0.048 0.492 4162 Planarity : 0.004 0.060 4385 Dihedral : 8.709 100.176 4825 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 0.67 % Allowed : 10.11 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 3014 helix: 1.27 (0.22), residues: 667 sheet: -0.38 (0.20), residues: 653 loop : -1.51 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 466 TYR 0.018 0.001 TYR B1067 PHE 0.018 0.001 PHE B 201 TRP 0.006 0.001 TRP C 436 HIS 0.003 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00239 (25449) covalent geometry : angle 0.55438 (34644) SS BOND : bond 0.00354 ( 35) SS BOND : angle 1.06802 ( 70) hydrogen bonds : bond 0.04494 ( 831) hydrogen bonds : angle 4.86495 ( 2301) Misc. bond : bond 0.00086 ( 1) link_BETA1-4 : bond 0.00627 ( 27) link_BETA1-4 : angle 2.92398 ( 81) link_NAG-ASN : bond 0.00607 ( 47) link_NAG-ASN : angle 3.27623 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.875 Fit side-chains REVERT: C 327 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8066 (p) REVERT: C 619 GLU cc_start: 0.8661 (mp0) cc_final: 0.8383 (mp0) REVERT: C 641 ASN cc_start: 0.6669 (OUTLIER) cc_final: 0.6454 (m-40) REVERT: C 957 GLN cc_start: 0.8348 (tm-30) cc_final: 0.8042 (tm-30) REVERT: A 133 PHE cc_start: 0.7509 (m-10) cc_final: 0.7182 (m-10) REVERT: A 239 GLN cc_start: 0.7570 (tp40) cc_final: 0.6984 (mm110) REVERT: A 773 GLU cc_start: 0.8505 (tp30) cc_final: 0.8253 (tp30) REVERT: A 869 MET cc_start: 0.8916 (mpp) cc_final: 0.8139 (mpp) REVERT: A 1029 MET cc_start: 0.8933 (tmm) cc_final: 0.8176 (tmm) REVERT: B 338 PHE cc_start: 0.8216 (m-80) cc_final: 0.7893 (m-10) REVERT: B 342 PHE cc_start: 0.8948 (m-10) cc_final: 0.8632 (m-80) REVERT: B 957 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8412 (tm-30) REVERT: B 1029 MET cc_start: 0.8440 (ttp) cc_final: 0.8104 (ttm) outliers start: 18 outliers final: 9 residues processed: 128 average time/residue: 0.1368 time to fit residues: 30.3567 Evaluate side-chains 108 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 150 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 273 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 241 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 173 optimal weight: 0.2980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 563 GLN C1002 GLN A1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.139124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.089698 restraints weight = 57897.895| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 5.19 r_work: 0.3085 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25559 Z= 0.161 Angle : 0.639 12.228 34936 Z= 0.304 Chirality : 0.048 0.498 4162 Planarity : 0.004 0.055 4385 Dihedral : 8.317 93.156 4825 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.67 % Favored : 94.23 % Rotamer: Outliers : 1.20 % Allowed : 12.28 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 3014 helix: 1.14 (0.22), residues: 672 sheet: -0.41 (0.21), residues: 653 loop : -1.55 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.019 0.001 TYR C1067 PHE 0.021 0.001 PHE A1121 TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00378 (25449) covalent geometry : angle 0.58758 (34644) SS BOND : bond 0.00406 ( 35) SS BOND : angle 1.22115 ( 70) hydrogen bonds : bond 0.05013 ( 831) hydrogen bonds : angle 4.90838 ( 2301) Misc. bond : bond 0.00086 ( 1) link_BETA1-4 : bond 0.00590 ( 27) link_BETA1-4 : angle 2.89956 ( 81) link_NAG-ASN : bond 0.00532 ( 47) link_NAG-ASN : angle 3.27154 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 619 GLU cc_start: 0.8715 (mp0) cc_final: 0.8424 (mp0) REVERT: C 641 ASN cc_start: 0.6532 (OUTLIER) cc_final: 0.6205 (m110) REVERT: A 133 PHE cc_start: 0.7407 (m-80) cc_final: 0.7047 (m-10) REVERT: A 773 GLU cc_start: 0.8933 (tp30) cc_final: 0.8702 (tp30) REVERT: A 869 MET cc_start: 0.9154 (mpp) cc_final: 0.8436 (mpp) REVERT: A 1029 MET cc_start: 0.9082 (tmm) cc_final: 0.8417 (tmm) REVERT: B 342 PHE cc_start: 0.9054 (m-10) cc_final: 0.8695 (m-80) REVERT: B 957 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8589 (tm-30) REVERT: B 1029 MET cc_start: 0.8597 (ttp) cc_final: 0.8336 (ttm) outliers start: 32 outliers final: 18 residues processed: 128 average time/residue: 0.1340 time to fit residues: 29.9968 Evaluate side-chains 116 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 26 optimal weight: 30.0000 chunk 41 optimal weight: 0.0980 chunk 244 optimal weight: 8.9990 chunk 273 optimal weight: 0.0970 chunk 92 optimal weight: 0.0270 chunk 54 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.0370 chunk 298 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.0712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 777 ASN A 919 ASN A1142 GLN B 675 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.144062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.094630 restraints weight = 58941.104| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 4.52 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25559 Z= 0.102 Angle : 0.598 12.248 34936 Z= 0.281 Chirality : 0.048 0.497 4162 Planarity : 0.004 0.058 4385 Dihedral : 7.921 90.008 4825 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.35 % Favored : 95.55 % Rotamer: Outliers : 1.24 % Allowed : 13.41 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 3014 helix: 1.36 (0.22), residues: 655 sheet: -0.23 (0.21), residues: 649 loop : -1.40 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.017 0.001 TYR B1067 PHE 0.016 0.001 PHE B 201 TRP 0.007 0.001 TRP A 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00211 (25449) covalent geometry : angle 0.54739 (34644) SS BOND : bond 0.00430 ( 35) SS BOND : angle 0.92629 ( 70) hydrogen bonds : bond 0.03986 ( 831) hydrogen bonds : angle 4.64003 ( 2301) Misc. bond : bond 0.00086 ( 1) link_BETA1-4 : bond 0.00684 ( 27) link_BETA1-4 : angle 2.85243 ( 81) link_NAG-ASN : bond 0.00617 ( 47) link_NAG-ASN : angle 3.14977 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: C 619 GLU cc_start: 0.8722 (mp0) cc_final: 0.8431 (mp0) REVERT: C 641 ASN cc_start: 0.6481 (OUTLIER) cc_final: 0.6033 (m110) REVERT: A 133 PHE cc_start: 0.7486 (m-80) cc_final: 0.7068 (m-10) REVERT: A 239 GLN cc_start: 0.7307 (tp40) cc_final: 0.6921 (mm110) REVERT: A 773 GLU cc_start: 0.8594 (tp30) cc_final: 0.8285 (tp30) REVERT: A 869 MET cc_start: 0.8970 (mpp) cc_final: 0.8080 (mpp) REVERT: A 1029 MET cc_start: 0.8863 (tmm) cc_final: 0.8214 (tmm) REVERT: B 338 PHE cc_start: 0.8134 (m-80) cc_final: 0.7733 (m-10) REVERT: B 342 PHE cc_start: 0.9007 (m-10) cc_final: 0.8665 (m-80) REVERT: B 365 TYR cc_start: 0.8365 (m-80) cc_final: 0.8139 (m-80) REVERT: B 981 LEU cc_start: 0.8954 (mt) cc_final: 0.8726 (pp) REVERT: B 1029 MET cc_start: 0.8487 (ttp) cc_final: 0.8127 (ttm) outliers start: 33 outliers final: 19 residues processed: 143 average time/residue: 0.1309 time to fit residues: 32.6721 Evaluate side-chains 120 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 222 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1142 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.142267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092684 restraints weight = 58768.061| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 4.48 r_work: 0.3128 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25559 Z= 0.129 Angle : 0.609 11.859 34936 Z= 0.286 Chirality : 0.048 0.497 4162 Planarity : 0.004 0.054 4385 Dihedral : 7.739 87.878 4825 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 1.69 % Allowed : 14.12 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 3014 helix: 1.36 (0.22), residues: 655 sheet: -0.25 (0.21), residues: 648 loop : -1.37 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.020 0.001 TYR C 200 PHE 0.022 0.001 PHE C 201 TRP 0.006 0.001 TRP A 436 HIS 0.004 0.000 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00299 (25449) covalent geometry : angle 0.55935 (34644) SS BOND : bond 0.00332 ( 35) SS BOND : angle 1.09053 ( 70) hydrogen bonds : bond 0.04373 ( 831) hydrogen bonds : angle 4.64368 ( 2301) Misc. bond : bond 0.00074 ( 1) link_BETA1-4 : bond 0.00603 ( 27) link_BETA1-4 : angle 2.82119 ( 81) link_NAG-ASN : bond 0.00522 ( 47) link_NAG-ASN : angle 3.13388 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 101 time to evaluate : 0.791 Fit side-chains REVERT: C 619 GLU cc_start: 0.8727 (mp0) cc_final: 0.8483 (mp0) REVERT: C 622 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8138 (p) REVERT: C 641 ASN cc_start: 0.6351 (OUTLIER) cc_final: 0.6018 (m110) REVERT: A 133 PHE cc_start: 0.7485 (m-80) cc_final: 0.7090 (m-10) REVERT: A 239 GLN cc_start: 0.7138 (tp40) cc_final: 0.6798 (mm110) REVERT: A 773 GLU cc_start: 0.8941 (tp30) cc_final: 0.8671 (tp30) REVERT: A 869 MET cc_start: 0.9163 (mpp) cc_final: 0.8400 (mpp) REVERT: A 1029 MET cc_start: 0.9033 (tmm) cc_final: 0.8385 (tmm) REVERT: B 342 PHE cc_start: 0.9066 (m-10) cc_final: 0.8720 (m-80) REVERT: B 365 TYR cc_start: 0.8307 (m-80) cc_final: 0.8065 (m-80) REVERT: B 981 LEU cc_start: 0.8862 (mt) cc_final: 0.8636 (pp) REVERT: B 1029 MET cc_start: 0.8614 (ttp) cc_final: 0.8327 (ttm) outliers start: 45 outliers final: 25 residues processed: 136 average time/residue: 0.1282 time to fit residues: 30.6080 Evaluate side-chains 123 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1083 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 294 optimal weight: 0.0370 chunk 262 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 288 optimal weight: 0.0050 chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 overall best weight: 0.5274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN A1142 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.143349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.093763 restraints weight = 58961.773| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 4.51 r_work: 0.3155 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25559 Z= 0.100 Angle : 0.593 11.810 34936 Z= 0.277 Chirality : 0.047 0.508 4162 Planarity : 0.004 0.055 4385 Dihedral : 7.558 85.672 4825 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 1.50 % Allowed : 14.79 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.16), residues: 3014 helix: 1.40 (0.22), residues: 653 sheet: -0.25 (0.21), residues: 659 loop : -1.31 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.018 0.001 TYR C 200 PHE 0.019 0.001 PHE B 133 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00222 (25449) covalent geometry : angle 0.54366 (34644) SS BOND : bond 0.00312 ( 35) SS BOND : angle 1.00828 ( 70) hydrogen bonds : bond 0.04031 ( 831) hydrogen bonds : angle 4.53318 ( 2301) Misc. bond : bond 0.00079 ( 1) link_BETA1-4 : bond 0.00613 ( 27) link_BETA1-4 : angle 2.80004 ( 81) link_NAG-ASN : bond 0.00561 ( 47) link_NAG-ASN : angle 3.09136 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.881 Fit side-chains REVERT: C 619 GLU cc_start: 0.8719 (mp0) cc_final: 0.8403 (mp0) REVERT: A 133 PHE cc_start: 0.7331 (m-80) cc_final: 0.6681 (m-10) REVERT: A 239 GLN cc_start: 0.7126 (tp40) cc_final: 0.6745 (mm110) REVERT: A 773 GLU cc_start: 0.8923 (tp30) cc_final: 0.8609 (tp30) REVERT: A 869 MET cc_start: 0.9140 (mpp) cc_final: 0.8365 (mpp) REVERT: A 1029 MET cc_start: 0.9018 (tmm) cc_final: 0.8377 (tmm) REVERT: B 338 PHE cc_start: 0.8143 (m-80) cc_final: 0.7854 (m-10) REVERT: B 342 PHE cc_start: 0.9070 (m-10) cc_final: 0.8716 (m-80) REVERT: B 365 TYR cc_start: 0.8291 (m-80) cc_final: 0.8067 (m-80) REVERT: B 981 LEU cc_start: 0.8897 (mt) cc_final: 0.8666 (pp) REVERT: B 1029 MET cc_start: 0.8580 (ttp) cc_final: 0.8298 (ttm) outliers start: 40 outliers final: 24 residues processed: 140 average time/residue: 0.1252 time to fit residues: 30.5335 Evaluate side-chains 124 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1083 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 48 optimal weight: 5.9990 chunk 108 optimal weight: 0.0170 chunk 120 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 211 optimal weight: 0.8980 chunk 41 optimal weight: 0.0970 chunk 177 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.143327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.093734 restraints weight = 58401.003| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 4.49 r_work: 0.3160 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25559 Z= 0.099 Angle : 0.591 11.691 34936 Z= 0.276 Chirality : 0.047 0.498 4162 Planarity : 0.003 0.055 4385 Dihedral : 7.391 84.200 4823 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 1.39 % Allowed : 15.09 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.16), residues: 3014 helix: 1.41 (0.22), residues: 649 sheet: -0.19 (0.21), residues: 657 loop : -1.28 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.016 0.001 TYR B1067 PHE 0.024 0.001 PHE C 201 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00220 (25449) covalent geometry : angle 0.54143 (34644) SS BOND : bond 0.00360 ( 35) SS BOND : angle 1.17487 ( 70) hydrogen bonds : bond 0.03916 ( 831) hydrogen bonds : angle 4.48906 ( 2301) Misc. bond : bond 0.00081 ( 1) link_BETA1-4 : bond 0.00616 ( 27) link_BETA1-4 : angle 2.77659 ( 81) link_NAG-ASN : bond 0.00553 ( 47) link_NAG-ASN : angle 3.04239 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.851 Fit side-chains REVERT: C 546 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7357 (pp) REVERT: C 619 GLU cc_start: 0.8705 (mp0) cc_final: 0.8437 (mp0) REVERT: C 622 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8142 (p) REVERT: C 1029 MET cc_start: 0.9268 (tmm) cc_final: 0.8958 (tmm) REVERT: A 133 PHE cc_start: 0.7496 (m-80) cc_final: 0.6843 (m-10) REVERT: A 239 GLN cc_start: 0.7012 (tp40) cc_final: 0.6696 (mm110) REVERT: A 869 MET cc_start: 0.9139 (mpp) cc_final: 0.8370 (mpp) REVERT: A 1029 MET cc_start: 0.9011 (tmm) cc_final: 0.8350 (tmm) REVERT: B 338 PHE cc_start: 0.8086 (m-80) cc_final: 0.7845 (m-10) REVERT: B 342 PHE cc_start: 0.9107 (m-10) cc_final: 0.8762 (m-80) REVERT: B 365 TYR cc_start: 0.8232 (m-80) cc_final: 0.8008 (m-80) REVERT: B 1029 MET cc_start: 0.8593 (ttp) cc_final: 0.8311 (ttm) outliers start: 37 outliers final: 27 residues processed: 136 average time/residue: 0.1384 time to fit residues: 32.8743 Evaluate side-chains 129 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1083 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 224 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.140642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090910 restraints weight = 59135.275| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 4.45 r_work: 0.3092 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25559 Z= 0.193 Angle : 0.656 11.336 34936 Z= 0.313 Chirality : 0.049 0.530 4162 Planarity : 0.004 0.053 4385 Dihedral : 7.467 81.006 4823 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.67 % Favored : 94.23 % Rotamer: Outliers : 1.31 % Allowed : 15.36 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.16), residues: 3014 helix: 1.14 (0.22), residues: 666 sheet: -0.43 (0.21), residues: 665 loop : -1.38 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.019 0.001 TYR B1067 PHE 0.025 0.001 PHE A1121 TRP 0.009 0.001 TRP A1102 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00453 (25449) covalent geometry : angle 0.60879 (34644) SS BOND : bond 0.00450 ( 35) SS BOND : angle 1.44266 ( 70) hydrogen bonds : bond 0.05009 ( 831) hydrogen bonds : angle 4.74536 ( 2301) Misc. bond : bond 0.00064 ( 1) link_BETA1-4 : bond 0.00559 ( 27) link_BETA1-4 : angle 2.77461 ( 81) link_NAG-ASN : bond 0.00488 ( 47) link_NAG-ASN : angle 3.16893 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.934 Fit side-chains REVERT: C 619 GLU cc_start: 0.8717 (mp0) cc_final: 0.8466 (mp0) REVERT: C 622 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8167 (p) REVERT: A 133 PHE cc_start: 0.7620 (m-80) cc_final: 0.6886 (m-10) REVERT: A 239 GLN cc_start: 0.7122 (tp40) cc_final: 0.6815 (mm110) REVERT: A 581 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8818 (p) REVERT: A 869 MET cc_start: 0.9207 (mpp) cc_final: 0.8459 (mpp) REVERT: A 1029 MET cc_start: 0.9118 (tmm) cc_final: 0.8464 (tmm) REVERT: B 342 PHE cc_start: 0.9087 (m-10) cc_final: 0.8697 (m-80) REVERT: B 365 TYR cc_start: 0.8282 (m-80) cc_final: 0.8053 (m-80) REVERT: B 1029 MET cc_start: 0.8686 (ttp) cc_final: 0.8439 (ttm) outliers start: 35 outliers final: 31 residues processed: 128 average time/residue: 0.1318 time to fit residues: 29.7103 Evaluate side-chains 127 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 200 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 266 optimal weight: 0.8980 chunk 76 optimal weight: 0.0970 chunk 123 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1142 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.139378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.088758 restraints weight = 57978.449| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 4.67 r_work: 0.3124 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25559 Z= 0.112 Angle : 0.624 16.611 34936 Z= 0.293 Chirality : 0.048 0.532 4162 Planarity : 0.004 0.054 4385 Dihedral : 7.379 79.785 4823 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.74 % Favored : 95.16 % Rotamer: Outliers : 1.24 % Allowed : 15.77 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.16), residues: 3014 helix: 1.25 (0.22), residues: 664 sheet: -0.35 (0.21), residues: 657 loop : -1.36 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1000 TYR 0.017 0.001 TYR B1067 PHE 0.014 0.001 PHE B 201 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.000 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00254 (25449) covalent geometry : angle 0.57686 (34644) SS BOND : bond 0.00390 ( 35) SS BOND : angle 1.26017 ( 70) hydrogen bonds : bond 0.04431 ( 831) hydrogen bonds : angle 4.59118 ( 2301) Misc. bond : bond 0.00084 ( 1) link_BETA1-4 : bond 0.00605 ( 27) link_BETA1-4 : angle 2.77296 ( 81) link_NAG-ASN : bond 0.00543 ( 47) link_NAG-ASN : angle 3.10707 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.890 Fit side-chains REVERT: C 619 GLU cc_start: 0.8711 (mp0) cc_final: 0.8450 (mp0) REVERT: C 622 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8235 (p) REVERT: A 581 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8869 (p) REVERT: A 869 MET cc_start: 0.9179 (mpp) cc_final: 0.8387 (mpp) REVERT: A 1029 MET cc_start: 0.8990 (tmm) cc_final: 0.8277 (tmm) REVERT: B 338 PHE cc_start: 0.8164 (m-10) cc_final: 0.7824 (m-80) REVERT: B 342 PHE cc_start: 0.9082 (m-10) cc_final: 0.8690 (m-80) REVERT: B 365 TYR cc_start: 0.8277 (m-80) cc_final: 0.8048 (m-80) REVERT: B 1029 MET cc_start: 0.8641 (ttp) cc_final: 0.7954 (tmm) outliers start: 33 outliers final: 28 residues processed: 129 average time/residue: 0.1299 time to fit residues: 29.2428 Evaluate side-chains 129 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 272 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 303 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 294 optimal weight: 0.4980 chunk 108 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.139004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.089230 restraints weight = 57839.880| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 5.15 r_work: 0.3101 rms_B_bonded: 5.06 restraints_weight: 2.0000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25559 Z= 0.139 Angle : 0.632 14.642 34936 Z= 0.298 Chirality : 0.048 0.528 4162 Planarity : 0.004 0.053 4385 Dihedral : 7.349 78.307 4823 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.21 % Favored : 94.69 % Rotamer: Outliers : 1.27 % Allowed : 15.96 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 3014 helix: 1.24 (0.22), residues: 658 sheet: -0.39 (0.21), residues: 657 loop : -1.36 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.017 0.001 TYR B1067 PHE 0.017 0.001 PHE A1121 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00324 (25449) covalent geometry : angle 0.58536 (34644) SS BOND : bond 0.00393 ( 35) SS BOND : angle 1.27987 ( 70) hydrogen bonds : bond 0.04563 ( 831) hydrogen bonds : angle 4.61764 ( 2301) Misc. bond : bond 0.00078 ( 1) link_BETA1-4 : bond 0.00581 ( 27) link_BETA1-4 : angle 2.76226 ( 81) link_NAG-ASN : bond 0.00515 ( 47) link_NAG-ASN : angle 3.10421 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6719.41 seconds wall clock time: 115 minutes 22.68 seconds (6922.68 seconds total)