Starting phenix.real_space_refine on Tue Apr 7 04:52:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eb4_31051/04_2026/7eb4_31051.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eb4_31051/04_2026/7eb4_31051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7eb4_31051/04_2026/7eb4_31051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eb4_31051/04_2026/7eb4_31051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eb4_31051/04_2026/7eb4_31051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eb4_31051/04_2026/7eb4_31051.map" } resolution = 3.5 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 15794 2.51 5 N 4027 2.21 5 O 4906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24832 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 7879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7879 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 50, 'TRANS': 959} Chain breaks: 7 Chain: "B" Number of atoms: 7993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7993 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 6 Chain: "C" Number of atoms: 7913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7913 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 50, 'TRANS': 962} Chain breaks: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" 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: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.43, per 1000 atoms: 0.22 Number of scatterers: 24832 At special positions: 0 Unit cell: (140.8, 141.9, 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 4906 8.00 N 4027 7.00 C 15794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " 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 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=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 603 " " NAG A2005 " - " 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 603 " " NAG B2006 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 331 " " NAG C2004 " - " ASN C 603 " " NAG C2005 " - " ASN C 657 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 282 " " NAG Q 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 709 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1074 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 282 " " NAG Y 1 " - " ASN C 343 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 709 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 730.0 milliseconds 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5704 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 46 sheets defined 25.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.596A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.242A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.808A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 removed outlier: 3.905A pdb=" N GLY A 757 " --> pdb=" O LEU A 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.665A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.859A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.504A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 4.029A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.576A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.557A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.594A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.540A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.756A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.617A 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 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.354A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.790A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 630 through 632 No H-bonds generated for 'chain 'B' and resid 630 through 632' Processing helix chain 'B' and resid 633 through 638 removed outlier: 4.018A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.821A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.788A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.527A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.529A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.706A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.529A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.781A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.524A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.749A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.511A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.626A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.167A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.302A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.278A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.616A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 removed outlier: 3.682A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.672A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.914A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.617A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.625A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.837A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.530A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.421A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.823A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 230 removed outlier: 6.642A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.233A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.280A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 573 through 576 removed outlier: 4.012A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.686A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 717 through 722 removed outlier: 6.711A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1078 removed outlier: 3.728A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.538A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.127A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.698A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.839A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.413A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.999A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.197A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.998A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 719 Processing sheet with id=AD3, first strand: chain 'B' and resid 717 through 719 removed outlier: 3.652A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.727A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.972A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.521A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 191 through 197 removed outlier: 3.567A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.743A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 323 through 328 removed outlier: 4.399A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.779A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.075A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.645A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.645A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.593A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.505A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2415 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: 4.99 Time building geometry restraints manager: 2.84 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: 7832 1.35 - 1.47: 6516 1.47 - 1.59: 10899 1.59 - 1.72: 0 1.72 - 1.84: 129 Bond restraints: 25376 Sorted by residual: bond pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.26e+00 bond pdb=" N SER B 640 " pdb=" CA SER B 640 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.32e-02 5.74e+03 8.93e+00 bond pdb=" N GLY B 639 " pdb=" CA GLY B 639 " ideal model delta sigma weight residual 1.449 1.484 -0.035 1.45e-02 4.76e+03 5.84e+00 bond pdb=" C1 NAG C2001 " pdb=" O5 NAG C2001 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.81e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.32e+00 ... (remaining 25371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 34054 2.35 - 4.70: 451 4.70 - 7.04: 32 7.04 - 9.39: 1 9.39 - 11.74: 2 Bond angle restraints: 34540 Sorted by residual: angle pdb=" C LEU C 984 " pdb=" N ASP C 985 " pdb=" CA ASP C 985 " ideal model delta sigma weight residual 120.94 130.32 -9.38 1.90e+00 2.77e-01 2.44e+01 angle pdb=" N VAL C 130 " pdb=" CA VAL C 130 " pdb=" C VAL C 130 " ideal model delta sigma weight residual 112.29 108.29 4.00 9.40e-01 1.13e+00 1.81e+01 angle pdb=" C SER B 640 " pdb=" N ASN B 641 " pdb=" CA ASN B 641 " ideal model delta sigma weight residual 120.82 115.07 5.75 1.41e+00 5.03e-01 1.66e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.58 -4.88 1.22e+00 6.72e-01 1.60e+01 angle pdb=" CA SER B 640 " pdb=" C SER B 640 " pdb=" O SER B 640 " ideal model delta sigma weight residual 121.07 117.03 4.04 1.08e+00 8.57e-01 1.40e+01 ... (remaining 34535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 14911 21.98 - 43.97: 958 43.97 - 65.95: 128 65.95 - 87.94: 35 87.94 - 109.92: 15 Dihedral angle restraints: 16047 sinusoidal: 7184 harmonic: 8863 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 175.60 -82.60 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 169.56 -76.56 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -157.77 71.77 1 1.00e+01 1.00e-02 6.60e+01 ... (remaining 16044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 4135 0.150 - 0.300: 14 0.300 - 0.451: 1 0.451 - 0.601: 0 0.601 - 0.751: 1 Chirality restraints: 4151 Sorted by residual: chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" C1 NAG B2004 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B2004 " pdb=" O5 NAG B2004 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 4148 not shown) Planarity restraints: 4414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 61 " 0.023 2.00e-02 2.50e+03 2.16e-02 5.84e+00 pdb=" CG ASN C 61 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN C 61 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 61 " -0.020 2.00e-02 2.50e+03 pdb=" C1 NAG C2001 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 640 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C SER C 640 " 0.033 2.00e-02 2.50e+03 pdb=" O SER C 640 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN C 641 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 330 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.026 5.00e-02 4.00e+02 ... (remaining 4411 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 759 2.70 - 3.25: 23847 3.25 - 3.80: 36647 3.80 - 4.35: 44021 4.35 - 4.90: 75911 Nonbonded interactions: 181185 Sorted by model distance: nonbonded pdb=" OH TYR C 756 " pdb=" OD2 ASP C 994 " model vdw 2.156 3.040 nonbonded pdb=" OG1 THR B 716 " pdb=" O GLN B1071 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR C 716 " pdb=" O GLN C1071 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 2.238 3.040 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.239 3.120 ... (remaining 181180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 622 or resid 636 through 827 or resid 855 throu \ gh 2005)) selection = (chain 'C' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 2005)) } ncs_group { reference = 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' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.910 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 0.049 25485 Z= 0.184 Angle : 0.669 15.519 34833 Z= 0.321 Chirality : 0.047 0.751 4151 Planarity : 0.004 0.046 4369 Dihedral : 14.117 109.923 10241 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 0.04 % Allowed : 0.45 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 3001 helix: 1.66 (0.22), residues: 644 sheet: -0.12 (0.21), residues: 659 loop : -1.72 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 357 TYR 0.016 0.001 TYR C 369 PHE 0.015 0.001 PHE C 823 TRP 0.007 0.001 TRP C 104 HIS 0.002 0.000 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00366 (25376) covalent geometry : angle 0.62125 (34540) SS BOND : bond 0.00403 ( 34) SS BOND : angle 1.24661 ( 68) hydrogen bonds : bond 0.14361 ( 876) hydrogen bonds : angle 5.96611 ( 2415) link_BETA1-4 : bond 0.00590 ( 30) link_BETA1-4 : angle 3.24586 ( 90) link_NAG-ASN : bond 0.00398 ( 45) link_NAG-ASN : angle 2.97727 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.6908 (t80) cc_final: 0.6509 (t80) REVERT: A 697 MET cc_start: 0.8587 (ttm) cc_final: 0.8115 (ttp) REVERT: B 775 ASP cc_start: 0.7585 (t0) cc_final: 0.7362 (t0) REVERT: C 87 ASN cc_start: 0.7471 (m110) cc_final: 0.7229 (m110) REVERT: C 191 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7063 (tm-30) REVERT: C 238 PHE cc_start: 0.7267 (p90) cc_final: 0.6504 (p90) REVERT: C 574 ASP cc_start: 0.8099 (t70) cc_final: 0.7716 (t0) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1504 time to fit residues: 33.4224 Evaluate side-chains 90 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.2980 chunk 298 optimal weight: 0.9980 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 360 ASN A 487 ASN A 506 GLN A 774 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 487 ASN B 919 ASN B 955 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.133370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.088154 restraints weight = 57459.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090819 restraints weight = 32182.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.093012 restraints weight = 22693.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092615 restraints weight = 21874.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092674 restraints weight = 17117.248| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25485 Z= 0.140 Angle : 0.631 13.034 34833 Z= 0.306 Chirality : 0.045 0.535 4151 Planarity : 0.004 0.131 4369 Dihedral : 8.489 95.324 4830 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 0.38 % Allowed : 5.56 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 3001 helix: 1.39 (0.21), residues: 678 sheet: -0.17 (0.21), residues: 653 loop : -1.73 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 357 TYR 0.019 0.001 TYR C1067 PHE 0.020 0.001 PHE C 201 TRP 0.019 0.001 TRP A 436 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00320 (25376) covalent geometry : angle 0.59216 (34540) SS BOND : bond 0.00394 ( 34) SS BOND : angle 1.77412 ( 68) hydrogen bonds : bond 0.05259 ( 876) hydrogen bonds : angle 4.95362 ( 2415) link_BETA1-4 : bond 0.00571 ( 30) link_BETA1-4 : angle 2.53401 ( 90) link_NAG-ASN : bond 0.00321 ( 45) link_NAG-ASN : angle 2.69494 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8296 (m-80) cc_final: 0.7718 (m-80) REVERT: C 191 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6749 (tm-30) REVERT: C 441 LEU cc_start: 0.9015 (mm) cc_final: 0.8561 (tt) REVERT: C 574 ASP cc_start: 0.7682 (t70) cc_final: 0.7252 (t0) REVERT: C 985 ASP cc_start: 0.7225 (t0) cc_final: 0.6985 (t0) REVERT: C 1031 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7471 (tm-30) outliers start: 10 outliers final: 7 residues processed: 112 average time/residue: 0.1469 time to fit residues: 27.7141 Evaluate side-chains 100 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 163 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 237 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 260 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.132534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.086240 restraints weight = 57356.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.089340 restraints weight = 32538.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.090565 restraints weight = 22342.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090652 restraints weight = 22918.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090871 restraints weight = 17886.350| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25485 Z= 0.146 Angle : 0.606 12.331 34833 Z= 0.294 Chirality : 0.045 0.518 4151 Planarity : 0.004 0.053 4369 Dihedral : 7.746 89.084 4830 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.00 % Favored : 94.97 % Rotamer: Outliers : 0.79 % Allowed : 9.02 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 3001 helix: 1.42 (0.21), residues: 678 sheet: -0.24 (0.20), residues: 664 loop : -1.70 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 357 TYR 0.018 0.001 TYR C1067 PHE 0.028 0.001 PHE C 86 TRP 0.013 0.001 TRP A 436 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00336 (25376) covalent geometry : angle 0.56928 (34540) SS BOND : bond 0.00465 ( 34) SS BOND : angle 1.28268 ( 68) hydrogen bonds : bond 0.05333 ( 876) hydrogen bonds : angle 4.76400 ( 2415) link_BETA1-4 : bond 0.00632 ( 30) link_BETA1-4 : angle 2.52696 ( 90) link_NAG-ASN : bond 0.00319 ( 45) link_NAG-ASN : angle 2.62591 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8460 (m-80) cc_final: 0.7866 (m-80) REVERT: A 400 PHE cc_start: 0.8554 (p90) cc_final: 0.8329 (p90) REVERT: A 441 LEU cc_start: 0.8613 (mt) cc_final: 0.8378 (tp) REVERT: B 858 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8705 (pp) REVERT: C 191 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6796 (tm-30) REVERT: C 441 LEU cc_start: 0.9057 (mm) cc_final: 0.8594 (tt) REVERT: C 574 ASP cc_start: 0.7651 (t70) cc_final: 0.7235 (t0) REVERT: C 985 ASP cc_start: 0.7471 (t0) cc_final: 0.7213 (t0) REVERT: C 1029 MET cc_start: 0.8489 (tmm) cc_final: 0.8177 (tmm) outliers start: 21 outliers final: 15 residues processed: 114 average time/residue: 0.1432 time to fit residues: 27.8853 Evaluate side-chains 109 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 300 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 213 optimal weight: 0.4980 chunk 277 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 37 optimal weight: 20.0000 chunk 167 optimal weight: 0.9990 chunk 38 optimal weight: 30.0000 chunk 33 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.132834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.086253 restraints weight = 57165.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090879 restraints weight = 31593.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.093013 restraints weight = 19583.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.092891 restraints weight = 17971.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092919 restraints weight = 14584.893| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25485 Z= 0.125 Angle : 0.589 11.797 34833 Z= 0.283 Chirality : 0.044 0.505 4151 Planarity : 0.004 0.052 4369 Dihedral : 7.332 84.186 4830 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 0.98 % Allowed : 11.65 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.15), residues: 3001 helix: 1.53 (0.21), residues: 672 sheet: -0.20 (0.20), residues: 656 loop : -1.67 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.018 0.001 TYR C1067 PHE 0.025 0.001 PHE C 238 TRP 0.011 0.001 TRP A 436 HIS 0.006 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00284 (25376) covalent geometry : angle 0.55173 (34540) SS BOND : bond 0.00398 ( 34) SS BOND : angle 1.30241 ( 68) hydrogen bonds : bond 0.05065 ( 876) hydrogen bonds : angle 4.62520 ( 2415) link_BETA1-4 : bond 0.00596 ( 30) link_BETA1-4 : angle 2.50714 ( 90) link_NAG-ASN : bond 0.00318 ( 45) link_NAG-ASN : angle 2.53917 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8514 (p90) cc_final: 0.8199 (p90) REVERT: A 441 LEU cc_start: 0.8613 (mt) cc_final: 0.8379 (tp) REVERT: A 976 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8288 (p) REVERT: B 976 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8256 (p) REVERT: C 191 GLU cc_start: 0.6851 (tm-30) cc_final: 0.6557 (tm-30) REVERT: C 441 LEU cc_start: 0.9071 (mm) cc_final: 0.8592 (tt) REVERT: C 574 ASP cc_start: 0.7682 (t70) cc_final: 0.7264 (t0) REVERT: C 985 ASP cc_start: 0.7462 (t0) cc_final: 0.7150 (t0) REVERT: C 1029 MET cc_start: 0.8426 (tmm) cc_final: 0.8109 (tmm) outliers start: 26 outliers final: 17 residues processed: 118 average time/residue: 0.1442 time to fit residues: 29.3541 Evaluate side-chains 109 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 260 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 272 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 chunk 293 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.133256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086364 restraints weight = 56970.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.093278 restraints weight = 32178.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.092802 restraints weight = 17423.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.093060 restraints weight = 15084.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.093600 restraints weight = 15160.972| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25485 Z= 0.125 Angle : 0.582 11.466 34833 Z= 0.281 Chirality : 0.044 0.498 4151 Planarity : 0.004 0.050 4369 Dihedral : 7.011 78.855 4830 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.87 % Rotamer: Outliers : 1.32 % Allowed : 12.63 % Favored : 86.06 % 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 (0.15), residues: 3001 helix: 1.58 (0.21), residues: 670 sheet: -0.14 (0.20), residues: 654 loop : -1.62 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.018 0.001 TYR C1067 PHE 0.029 0.001 PHE C 238 TRP 0.011 0.001 TRP A 436 HIS 0.006 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00286 (25376) covalent geometry : angle 0.54547 (34540) SS BOND : bond 0.00422 ( 34) SS BOND : angle 1.36838 ( 68) hydrogen bonds : bond 0.05017 ( 876) hydrogen bonds : angle 4.55510 ( 2415) link_BETA1-4 : bond 0.00589 ( 30) link_BETA1-4 : angle 2.47904 ( 90) link_NAG-ASN : bond 0.00306 ( 45) link_NAG-ASN : angle 2.49818 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8579 (p90) cc_final: 0.8263 (p90) REVERT: A 441 LEU cc_start: 0.8625 (mt) cc_final: 0.8383 (tp) REVERT: A 786 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8444 (pttm) REVERT: B 725 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6671 (mt-10) REVERT: B 858 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8689 (pp) REVERT: B 976 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8305 (p) REVERT: C 104 TRP cc_start: 0.6785 (m-90) cc_final: 0.6272 (m-10) REVERT: C 191 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6598 (tm-30) REVERT: C 441 LEU cc_start: 0.9090 (mm) cc_final: 0.8612 (tt) REVERT: C 985 ASP cc_start: 0.7476 (t0) cc_final: 0.7095 (t0) REVERT: C 1029 MET cc_start: 0.8435 (tmm) cc_final: 0.8091 (tmm) outliers start: 35 outliers final: 19 residues processed: 131 average time/residue: 0.1406 time to fit residues: 31.7409 Evaluate side-chains 112 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 157 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 129 optimal weight: 0.1980 chunk 134 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 137 optimal weight: 30.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.132258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.085050 restraints weight = 57213.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.091806 restraints weight = 32671.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090606 restraints weight = 18340.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.090871 restraints weight = 17557.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.091219 restraints weight = 16269.293| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25485 Z= 0.132 Angle : 0.587 11.419 34833 Z= 0.282 Chirality : 0.045 0.499 4151 Planarity : 0.004 0.049 4369 Dihedral : 6.867 73.888 4830 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 1.35 % Allowed : 13.75 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.15), residues: 3001 helix: 1.53 (0.21), residues: 677 sheet: -0.08 (0.21), residues: 651 loop : -1.63 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 509 TYR 0.018 0.001 TYR C1067 PHE 0.026 0.001 PHE C 238 TRP 0.012 0.001 TRP B 633 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00304 (25376) covalent geometry : angle 0.55126 (34540) SS BOND : bond 0.00478 ( 34) SS BOND : angle 1.38468 ( 68) hydrogen bonds : bond 0.05092 ( 876) hydrogen bonds : angle 4.52906 ( 2415) link_BETA1-4 : bond 0.00588 ( 30) link_BETA1-4 : angle 2.47333 ( 90) link_NAG-ASN : bond 0.00297 ( 45) link_NAG-ASN : angle 2.47199 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8660 (p90) cc_final: 0.8372 (p90) REVERT: A 441 LEU cc_start: 0.8630 (mt) cc_final: 0.8385 (tp) REVERT: A 786 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8454 (pttm) REVERT: A 948 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7323 (mt) REVERT: B 858 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8699 (pp) REVERT: B 976 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8271 (p) REVERT: C 191 GLU cc_start: 0.6889 (tm-30) cc_final: 0.6626 (tm-30) REVERT: C 441 LEU cc_start: 0.9052 (mm) cc_final: 0.8597 (tt) REVERT: C 985 ASP cc_start: 0.7614 (t0) cc_final: 0.7235 (t0) REVERT: C 1029 MET cc_start: 0.8507 (tmm) cc_final: 0.8086 (tmm) outliers start: 36 outliers final: 23 residues processed: 124 average time/residue: 0.1420 time to fit residues: 30.2606 Evaluate side-chains 115 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 288 optimal weight: 3.9990 chunk 289 optimal weight: 0.6980 chunk 218 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 128 optimal weight: 40.0000 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 0.0020 chunk 107 optimal weight: 2.9990 chunk 195 optimal weight: 0.0060 chunk 271 optimal weight: 0.0370 chunk 43 optimal weight: 7.9990 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.133885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.087558 restraints weight = 57170.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.092113 restraints weight = 31577.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.094832 restraints weight = 19336.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.094568 restraints weight = 17401.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.094555 restraints weight = 14352.578| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25485 Z= 0.099 Angle : 0.568 10.903 34833 Z= 0.271 Chirality : 0.044 0.466 4151 Planarity : 0.004 0.048 4369 Dihedral : 6.577 67.686 4830 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 1.05 % Allowed : 14.32 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 3001 helix: 1.82 (0.22), residues: 652 sheet: 0.02 (0.21), residues: 648 loop : -1.53 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 905 TYR 0.017 0.001 TYR C1067 PHE 0.024 0.001 PHE C 238 TRP 0.012 0.001 TRP A 436 HIS 0.004 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00215 (25376) covalent geometry : angle 0.53452 (34540) SS BOND : bond 0.00358 ( 34) SS BOND : angle 1.09467 ( 68) hydrogen bonds : bond 0.04409 ( 876) hydrogen bonds : angle 4.34811 ( 2415) link_BETA1-4 : bond 0.00639 ( 30) link_BETA1-4 : angle 2.48869 ( 90) link_NAG-ASN : bond 0.00357 ( 45) link_NAG-ASN : angle 2.33517 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8590 (p90) cc_final: 0.8259 (p90) REVERT: A 441 LEU cc_start: 0.8630 (mt) cc_final: 0.8397 (tp) REVERT: A 740 MET cc_start: 0.8525 (tpp) cc_final: 0.7974 (tmm) REVERT: B 725 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6653 (mt-10) REVERT: B 858 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8749 (pp) REVERT: B 976 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8298 (p) REVERT: C 191 GLU cc_start: 0.6842 (tm-30) cc_final: 0.6545 (tm-30) REVERT: C 441 LEU cc_start: 0.9085 (mm) cc_final: 0.8605 (tt) REVERT: C 740 MET cc_start: 0.8285 (tpp) cc_final: 0.8079 (tpp) REVERT: C 985 ASP cc_start: 0.7634 (t0) cc_final: 0.7233 (t0) REVERT: C 1029 MET cc_start: 0.8394 (tmm) cc_final: 0.8036 (tmm) outliers start: 28 outliers final: 20 residues processed: 128 average time/residue: 0.1356 time to fit residues: 30.2919 Evaluate side-chains 115 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 178 optimal weight: 0.8980 chunk 127 optimal weight: 20.0000 chunk 275 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.130882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.083140 restraints weight = 56823.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.089983 restraints weight = 32680.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088847 restraints weight = 17633.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.089022 restraints weight = 17650.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089260 restraints weight = 16811.655| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 25485 Z= 0.198 Angle : 0.640 11.726 34833 Z= 0.310 Chirality : 0.046 0.518 4151 Planarity : 0.004 0.051 4369 Dihedral : 6.656 60.584 4830 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.40 % Favored : 93.57 % Rotamer: Outliers : 1.28 % Allowed : 14.58 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 3001 helix: 1.51 (0.21), residues: 667 sheet: -0.09 (0.20), residues: 667 loop : -1.62 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.021 0.001 TYR C1067 PHE 0.023 0.002 PHE B1121 TRP 0.009 0.001 TRP B 633 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00467 (25376) covalent geometry : angle 0.60557 (34540) SS BOND : bond 0.00489 ( 34) SS BOND : angle 1.69265 ( 68) hydrogen bonds : bond 0.05680 ( 876) hydrogen bonds : angle 4.63777 ( 2415) link_BETA1-4 : bond 0.00544 ( 30) link_BETA1-4 : angle 2.43401 ( 90) link_NAG-ASN : bond 0.00291 ( 45) link_NAG-ASN : angle 2.52639 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8588 (p90) cc_final: 0.8351 (p90) REVERT: A 441 LEU cc_start: 0.8652 (mt) cc_final: 0.8407 (tp) REVERT: A 773 GLU cc_start: 0.8307 (tp30) cc_final: 0.8020 (tp30) REVERT: A 948 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7353 (mt) REVERT: B 858 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8700 (pp) REVERT: C 191 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6897 (tm-30) REVERT: C 238 PHE cc_start: 0.7394 (p90) cc_final: 0.6482 (p90) REVERT: C 441 LEU cc_start: 0.9070 (mm) cc_final: 0.8602 (tt) REVERT: C 985 ASP cc_start: 0.7632 (t0) cc_final: 0.7199 (t0) REVERT: C 1029 MET cc_start: 0.8577 (tmm) cc_final: 0.8073 (tmm) outliers start: 34 outliers final: 22 residues processed: 118 average time/residue: 0.1348 time to fit residues: 27.6601 Evaluate side-chains 109 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 204 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 199 optimal weight: 0.3980 chunk 157 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 196 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 197 optimal weight: 0.0170 chunk 231 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.132646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085970 restraints weight = 56891.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090593 restraints weight = 31988.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.092559 restraints weight = 19768.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092612 restraints weight = 18161.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092635 restraints weight = 14706.553| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25485 Z= 0.111 Angle : 0.590 11.120 34833 Z= 0.282 Chirality : 0.044 0.483 4151 Planarity : 0.004 0.050 4369 Dihedral : 6.470 59.840 4830 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.43 % Rotamer: Outliers : 1.09 % Allowed : 15.30 % Favored : 83.62 % 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 (0.15), residues: 3001 helix: 1.74 (0.21), residues: 654 sheet: 0.01 (0.21), residues: 651 loop : -1.55 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.018 0.001 TYR C1067 PHE 0.023 0.001 PHE C 238 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00250 (25376) covalent geometry : angle 0.55659 (34540) SS BOND : bond 0.00393 ( 34) SS BOND : angle 1.37425 ( 68) hydrogen bonds : bond 0.04893 ( 876) hydrogen bonds : angle 4.43500 ( 2415) link_BETA1-4 : bond 0.00613 ( 30) link_BETA1-4 : angle 2.46225 ( 90) link_NAG-ASN : bond 0.00324 ( 45) link_NAG-ASN : angle 2.34545 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8537 (p90) cc_final: 0.8334 (p90) REVERT: A 441 LEU cc_start: 0.8645 (mt) cc_final: 0.8404 (tp) REVERT: A 740 MET cc_start: 0.8579 (tpp) cc_final: 0.7998 (tmm) REVERT: A 948 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7286 (mt) REVERT: B 725 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6896 (mt-10) REVERT: B 858 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8762 (pp) REVERT: C 191 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6567 (tm-30) REVERT: C 441 LEU cc_start: 0.9098 (mm) cc_final: 0.8618 (tt) REVERT: C 740 MET cc_start: 0.8479 (tpp) cc_final: 0.8195 (tpp) REVERT: C 985 ASP cc_start: 0.7586 (t0) cc_final: 0.7152 (t0) REVERT: C 1029 MET cc_start: 0.8479 (tmm) cc_final: 0.8092 (tmm) outliers start: 29 outliers final: 24 residues processed: 114 average time/residue: 0.1399 time to fit residues: 27.7131 Evaluate side-chains 113 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 101 optimal weight: 10.0000 chunk 136 optimal weight: 50.0000 chunk 221 optimal weight: 8.9990 chunk 210 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 199 optimal weight: 0.4980 chunk 167 optimal weight: 0.0050 chunk 119 optimal weight: 2.9990 chunk 147 optimal weight: 0.0370 overall best weight: 0.8874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.136056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.086624 restraints weight = 55492.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.090322 restraints weight = 28943.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.092586 restraints weight = 20078.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.094151 restraints weight = 16203.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094941 restraints weight = 14045.345| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25485 Z= 0.119 Angle : 0.591 11.075 34833 Z= 0.283 Chirality : 0.044 0.482 4151 Planarity : 0.004 0.050 4369 Dihedral : 6.358 59.851 4830 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 1.09 % Allowed : 15.41 % Favored : 83.50 % 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: -0.63 (0.15), residues: 3001 helix: 1.66 (0.21), residues: 662 sheet: 0.04 (0.21), residues: 646 loop : -1.53 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.017 0.001 TYR C1067 PHE 0.022 0.001 PHE C 238 TRP 0.010 0.001 TRP A 436 HIS 0.005 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00274 (25376) covalent geometry : angle 0.55799 (34540) SS BOND : bond 0.00393 ( 34) SS BOND : angle 1.37974 ( 68) hydrogen bonds : bond 0.04874 ( 876) hydrogen bonds : angle 4.42175 ( 2415) link_BETA1-4 : bond 0.00599 ( 30) link_BETA1-4 : angle 2.44325 ( 90) link_NAG-ASN : bond 0.00287 ( 45) link_NAG-ASN : angle 2.35763 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8649 (mt) cc_final: 0.8398 (tp) REVERT: A 740 MET cc_start: 0.8572 (tpp) cc_final: 0.7945 (tmm) REVERT: A 948 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7174 (mt) REVERT: B 725 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6938 (mt-10) REVERT: B 858 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8751 (pp) REVERT: C 191 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6642 (tm-30) REVERT: C 441 LEU cc_start: 0.9138 (mm) cc_final: 0.8643 (tt) REVERT: C 740 MET cc_start: 0.8492 (tpp) cc_final: 0.8227 (tpp) REVERT: C 985 ASP cc_start: 0.7582 (t0) cc_final: 0.7152 (t0) REVERT: C 1029 MET cc_start: 0.8472 (tmm) cc_final: 0.8061 (tmm) outliers start: 29 outliers final: 25 residues processed: 114 average time/residue: 0.1302 time to fit residues: 26.2392 Evaluate side-chains 114 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 18 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 214 optimal weight: 20.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN C 544 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.129882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.082996 restraints weight = 56882.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088130 restraints weight = 31875.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089017 restraints weight = 18580.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089074 restraints weight = 17044.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.089877 restraints weight = 15386.406| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 25485 Z= 0.243 Angle : 0.688 12.351 34833 Z= 0.338 Chirality : 0.047 0.548 4151 Planarity : 0.004 0.050 4369 Dihedral : 6.597 58.757 4830 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.23 % Favored : 92.74 % Rotamer: Outliers : 1.20 % Allowed : 15.52 % Favored : 83.28 % 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: -0.97 (0.15), residues: 3001 helix: 1.33 (0.21), residues: 662 sheet: -0.23 (0.20), residues: 677 loop : -1.73 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 237 TYR 0.025 0.001 TYR C1067 PHE 0.027 0.002 PHE A 377 TRP 0.011 0.002 TRP C1102 HIS 0.011 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00576 (25376) covalent geometry : angle 0.65368 (34540) SS BOND : bond 0.00531 ( 34) SS BOND : angle 1.96638 ( 68) hydrogen bonds : bond 0.06369 ( 876) hydrogen bonds : angle 4.83309 ( 2415) link_BETA1-4 : bond 0.00545 ( 30) link_BETA1-4 : angle 2.41415 ( 90) link_NAG-ASN : bond 0.00331 ( 45) link_NAG-ASN : angle 2.62639 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4152.33 seconds wall clock time: 72 minutes 48.02 seconds (4368.02 seconds total)