Starting phenix.real_space_refine on Sun Jul 5 02:54:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7eb4_31051/07_2026/7eb4_31051.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eb4_31051/07_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_31051/07_2026/7eb4_31051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eb4_31051/07_2026/7eb4_31051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eb4_31051/07_2026/7eb4_31051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eb4_31051/07_2026/7eb4_31051.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7eb4_31051/07_2026/7eb4_31051.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7eb4_31051/07_2026/7eb4_31051.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 5 Time building chain proxies: 4.99, per 1000 atoms: 0.20 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: 1.97 Conformation dependent library (CDL) restraints added in 845.5 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: 0.91 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: 4.97 Time building geometry restraints manager: 2.53 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 - 17.95: 13079 17.95 - 35.91: 1136 35.91 - 53.86: 203 53.86 - 71.82: 32 71.82 - 89.77: 24 Dihedral angle restraints: 14474 sinusoidal: 5611 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 14471 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.070 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 13.572 89.771 8668 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/Z covalent geometry : bond 0.00366 / 0.18 (25376) covalent geometry : angle 0.62125 / 0.31 (34540) SS BOND : bond 0.00403 / 0.25 ( 34) SS BOND : angle 1.24661 / 0.77 ( 68) hydrogen bonds : bond 0.14361 / 9.51 ( 876) hydrogen bonds : angle 5.96611 / 4.14 ( 2415) link_BETA1-4 : bond 0.00590 / 0.33 ( 30) link_BETA1-4 : angle 3.24586 / 2.21 ( 90) link_NAG-ASN : bond 0.00398 / 0.27 ( 45) link_NAG-ASN : angle 2.97727 / 2.05 ( 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 : 0.585 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: 0.1388 time to fit residues: 30.4125 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 : 0.748 ------------------------------------------------------------------------------- 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... A 164 ASN A 360 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.133416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.087728 restraints weight = 57465.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090892 restraints weight = 31666.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.091172 restraints weight = 21127.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.092049 restraints weight = 20987.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.092026 restraints weight = 18467.274| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25485 Z= 0.139 Angle : 0.624 12.873 34833 Z= 0.304 Chirality : 0.045 0.453 4151 Planarity : 0.004 0.132 4369 Dihedral : 3.974 23.585 3257 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 0.41 % Allowed : 5.37 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.15), residues: 3001 helix: 1.40 (0.21), residues: 678 sheet: -0.16 (0.21), residues: 650 loop : -1.75 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 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 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (25376) covalent geometry : angle 0.58761 / 0.29 (34540) SS BOND : bond 0.00414 / 0.25 ( 34) SS BOND : angle 1.73639 / 1.11 ( 68) hydrogen bonds : bond 0.05305 / 3.57 ( 876) hydrogen bonds : angle 4.97521 / 3.44 ( 2415) link_BETA1-4 : bond 0.00555 / 0.31 ( 30) link_BETA1-4 : angle 2.40030 / 1.65 ( 90) link_NAG-ASN : bond 0.00335 / 0.22 ( 45) link_NAG-ASN : angle 2.61702 / 1.80 ( 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 116 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8276 (m-80) cc_final: 0.7499 (m-80) REVERT: A 400 PHE cc_start: 0.8448 (p90) cc_final: 0.8234 (p90) REVERT: C 191 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6870 (tm-30) REVERT: C 441 LEU cc_start: 0.9020 (mm) cc_final: 0.8611 (tt) REVERT: C 574 ASP cc_start: 0.7651 (t70) cc_final: 0.7221 (t0) REVERT: C 985 ASP cc_start: 0.7184 (t0) cc_final: 0.6947 (t0) REVERT: C 1031 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7472 (tm-30) outliers start: 11 outliers final: 8 residues processed: 113 average time/residue: 0.1333 time to fit residues: 25.3441 Evaluate side-chains 100 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 B residue 780 GLU 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: 8.9990 chunk 303 optimal weight: 3.9990 chunk 171 optimal weight: 0.0770 chunk 237 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 260 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 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 = 0.4077 r_free = 0.4077 target = 0.132446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.086160 restraints weight = 57386.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089460 restraints weight = 32262.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092882 restraints weight = 21953.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092645 restraints weight = 19589.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.092437 restraints weight = 15235.146| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25485 Z= 0.150 Angle : 0.605 12.332 34833 Z= 0.295 Chirality : 0.045 0.448 4151 Planarity : 0.004 0.053 4369 Dihedral : 4.005 23.194 3257 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 0.79 % Allowed : 8.83 % Favored : 90.38 % 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: 679 sheet: -0.22 (0.20), residues: 655 loop : -1.70 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.019 0.001 TYR C1067 PHE 0.033 0.001 PHE C 86 TRP 0.013 0.001 TRP A 436 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (25376) covalent geometry : angle 0.57071 / 0.29 (34540) SS BOND : bond 0.00435 / 0.26 ( 34) SS BOND : angle 1.33199 / 0.87 ( 68) hydrogen bonds : bond 0.05370 / 3.61 ( 876) hydrogen bonds : angle 4.79306 / 3.31 ( 2415) link_BETA1-4 : bond 0.00568 / 0.31 ( 30) link_BETA1-4 : angle 2.33906 / 1.62 ( 90) link_NAG-ASN : bond 0.00311 / 0.21 ( 45) link_NAG-ASN : angle 2.54906 / 1.75 ( 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 117 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8642 (p90) cc_final: 0.8354 (p90) REVERT: C 191 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6745 (tm-30) REVERT: C 441 LEU cc_start: 0.9063 (mm) cc_final: 0.8575 (tt) REVERT: C 574 ASP cc_start: 0.7684 (t70) cc_final: 0.7264 (t0) REVERT: C 985 ASP cc_start: 0.7486 (t0) cc_final: 0.7229 (t0) REVERT: C 1029 MET cc_start: 0.8478 (tmm) cc_final: 0.8158 (tmm) outliers start: 21 outliers final: 16 residues processed: 112 average time/residue: 0.1312 time to fit residues: 24.8681 Evaluate side-chains 108 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 C residue 118 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: 0.4980 chunk 145 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 213 optimal weight: 0.5980 chunk 277 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 167 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.133859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.088776 restraints weight = 56986.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.091681 restraints weight = 31412.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.095123 restraints weight = 21355.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.094711 restraints weight = 18574.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.094759 restraints weight = 14926.524| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25485 Z= 0.112 Angle : 0.575 11.553 34833 Z= 0.278 Chirality : 0.044 0.420 4151 Planarity : 0.004 0.052 4369 Dihedral : 3.874 25.895 3257 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 0.83 % Allowed : 11.12 % Favored : 88.05 % 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: -0.83 (0.15), residues: 3001 helix: 1.56 (0.21), residues: 673 sheet: -0.19 (0.20), residues: 659 loop : -1.68 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 237 TYR 0.023 0.001 TYR A 396 PHE 0.028 0.001 PHE C 238 TRP 0.012 0.001 TRP A 436 HIS 0.005 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (25376) covalent geometry : angle 0.54185 / 0.27 (34540) SS BOND : bond 0.00348 / 0.22 ( 34) SS BOND : angle 1.32425 / 0.86 ( 68) hydrogen bonds : bond 0.04873 / 3.28 ( 876) hydrogen bonds : angle 4.60094 / 3.18 ( 2415) link_BETA1-4 : bond 0.00601 / 0.34 ( 30) link_BETA1-4 : angle 2.31028 / 1.60 ( 90) link_NAG-ASN : bond 0.00333 / 0.22 ( 45) link_NAG-ASN : angle 2.39594 / 1.65 ( 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 124 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8618 (p90) cc_final: 0.8301 (p90) REVERT: A 441 LEU cc_start: 0.8609 (mt) cc_final: 0.8376 (tp) REVERT: B 858 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8677 (pp) REVERT: B 976 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8222 (p) REVERT: C 191 GLU cc_start: 0.6848 (tm-30) cc_final: 0.6579 (tm-30) REVERT: C 441 LEU cc_start: 0.9062 (mm) cc_final: 0.8587 (tt) REVERT: C 574 ASP cc_start: 0.7659 (t70) cc_final: 0.7244 (t0) REVERT: C 985 ASP cc_start: 0.7571 (t0) cc_final: 0.7267 (t0) REVERT: C 1029 MET cc_start: 0.8396 (tmm) cc_final: 0.8084 (tmm) outliers start: 22 outliers final: 14 residues processed: 120 average time/residue: 0.1315 time to fit residues: 26.8511 Evaluate side-chains 110 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 786 LYS 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 858 LEU 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 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: 2.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 272 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.130296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.082890 restraints weight = 57258.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.087199 restraints weight = 33455.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.087886 restraints weight = 20834.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089415 restraints weight = 17796.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.089217 restraints weight = 17151.149| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25485 Z= 0.209 Angle : 0.656 11.790 34833 Z= 0.322 Chirality : 0.046 0.475 4151 Planarity : 0.004 0.052 4369 Dihedral : 4.190 24.283 3257 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.90 % Favored : 93.07 % Rotamer: Outliers : 1.43 % Allowed : 12.44 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.15), residues: 3001 helix: 1.26 (0.21), residues: 686 sheet: -0.33 (0.20), residues: 680 loop : -1.76 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.020 0.001 TYR C1067 PHE 0.033 0.002 PHE C 238 TRP 0.010 0.002 TRP C 353 HIS 0.010 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (25376) covalent geometry : angle 0.62372 / 0.31 (34540) SS BOND : bond 0.00500 / 0.31 ( 34) SS BOND : angle 1.67153 / 1.08 ( 68) hydrogen bonds : bond 0.06152 / 4.15 ( 876) hydrogen bonds : angle 4.86230 / 3.37 ( 2415) link_BETA1-4 : bond 0.00530 / 0.29 ( 30) link_BETA1-4 : angle 2.24899 / 1.56 ( 90) link_NAG-ASN : bond 0.00317 / 0.20 ( 45) link_NAG-ASN : angle 2.62329 / 1.79 ( 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 133 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8687 (p90) cc_final: 0.8408 (p90) REVERT: A 441 LEU cc_start: 0.8630 (mt) cc_final: 0.8384 (tp) REVERT: A 990 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6699 (mt-10) REVERT: B 858 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8605 (pp) REVERT: B 976 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8298 (p) REVERT: C 191 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6865 (tm-30) REVERT: C 441 LEU cc_start: 0.9075 (mm) cc_final: 0.8608 (tt) REVERT: C 985 ASP cc_start: 0.7544 (t0) cc_final: 0.7166 (t0) REVERT: C 1029 MET cc_start: 0.8546 (tmm) cc_final: 0.8118 (tmm) REVERT: C 1031 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8000 (tm-30) outliers start: 38 outliers final: 23 residues processed: 129 average time/residue: 0.1353 time to fit residues: 30.1307 Evaluate side-chains 116 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 327 VAL 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 A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU 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 118 LEU 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 934 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 157 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 chunk 245 optimal weight: 8.9990 chunk 289 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 129 optimal weight: 9.9990 chunk 134 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 254 optimal weight: 0.9990 chunk 137 optimal weight: 40.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B1106 GLN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.132021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.085722 restraints weight = 57391.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090935 restraints weight = 31353.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.091929 restraints weight = 18609.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091909 restraints weight = 17750.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.092010 restraints weight = 15144.553| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25485 Z= 0.140 Angle : 0.597 11.403 34833 Z= 0.290 Chirality : 0.045 0.441 4151 Planarity : 0.004 0.060 4369 Dihedral : 4.043 24.734 3257 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.00 % Favored : 94.97 % Rotamer: Outliers : 1.39 % Allowed : 14.21 % Favored : 84.40 % 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: 1.40 (0.21), residues: 681 sheet: -0.26 (0.20), residues: 668 loop : -1.71 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 237 TYR 0.018 0.001 TYR C1067 PHE 0.032 0.001 PHE C 238 TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (25376) covalent geometry : angle 0.56530 / 0.28 (34540) SS BOND : bond 0.00436 / 0.26 ( 34) SS BOND : angle 1.45105 / 0.96 ( 68) hydrogen bonds : bond 0.05471 / 3.69 ( 876) hydrogen bonds : angle 4.67156 / 3.23 ( 2415) link_BETA1-4 : bond 0.00571 / 0.32 ( 30) link_BETA1-4 : angle 2.25483 / 1.56 ( 90) link_NAG-ASN : bond 0.00310 / 0.21 ( 45) link_NAG-ASN : angle 2.42929 / 1.67 ( 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 133 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8570 (p90) cc_final: 0.8353 (p90) REVERT: A 441 LEU cc_start: 0.8625 (mt) cc_final: 0.8382 (tp) REVERT: A 948 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7399 (mt) REVERT: B 725 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6608 (mt-10) REVERT: B 858 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8621 (pp) REVERT: B 976 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8301 (p) REVERT: C 191 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6619 (tm-30) REVERT: C 441 LEU cc_start: 0.9070 (mm) cc_final: 0.8595 (tt) REVERT: C 985 ASP cc_start: 0.7684 (t0) cc_final: 0.7299 (t0) REVERT: C 1029 MET cc_start: 0.8532 (tmm) cc_final: 0.8107 (tmm) outliers start: 37 outliers final: 22 residues processed: 128 average time/residue: 0.1420 time to fit residues: 31.1160 Evaluate side-chains 117 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 90 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 288 optimal weight: 0.9990 chunk 289 optimal weight: 0.6980 chunk 218 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 128 optimal weight: 40.0000 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 271 optimal weight: 0.0670 chunk 43 optimal weight: 9.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN B 751 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.132501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.086745 restraints weight = 57075.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.090080 restraints weight = 32232.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.092135 restraints weight = 21614.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.092110 restraints weight = 19683.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.092045 restraints weight = 16154.992| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25485 Z= 0.110 Angle : 0.579 10.838 34833 Z= 0.280 Chirality : 0.044 0.413 4151 Planarity : 0.004 0.050 4369 Dihedral : 3.867 23.141 3257 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.74 % Rotamer: Outliers : 1.35 % Allowed : 14.47 % Favored : 84.18 % 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: -0.73 (0.15), residues: 3001 helix: 1.65 (0.21), residues: 662 sheet: -0.08 (0.21), residues: 649 loop : -1.60 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 237 TYR 0.018 0.001 TYR C1067 PHE 0.030 0.001 PHE C 238 TRP 0.014 0.001 TRP B 633 HIS 0.004 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (25376) covalent geometry : angle 0.54913 / 0.27 (34540) SS BOND : bond 0.00377 / 0.23 ( 34) SS BOND : angle 1.24185 / 0.82 ( 68) hydrogen bonds : bond 0.04937 / 3.34 ( 876) hydrogen bonds : angle 4.51770 / 3.13 ( 2415) link_BETA1-4 : bond 0.00588 / 0.33 ( 30) link_BETA1-4 : angle 2.24656 / 1.56 ( 90) link_NAG-ASN : bond 0.00323 / 0.21 ( 45) link_NAG-ASN : angle 2.30230 / 1.58 ( 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 135 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8567 (p90) cc_final: 0.8349 (p90) REVERT: A 441 LEU cc_start: 0.8633 (mt) cc_final: 0.8392 (tp) REVERT: B 725 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6681 (mt-10) REVERT: B 858 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8708 (pp) REVERT: B 976 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8268 (p) REVERT: C 104 TRP cc_start: 0.6776 (m-90) cc_final: 0.6414 (m-10) REVERT: C 191 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6644 (tm-30) REVERT: C 441 LEU cc_start: 0.9081 (mm) cc_final: 0.8607 (tt) REVERT: C 985 ASP cc_start: 0.7709 (t0) cc_final: 0.7293 (t0) REVERT: C 1029 MET cc_start: 0.8515 (tmm) cc_final: 0.8121 (tmm) outliers start: 36 outliers final: 21 residues processed: 131 average time/residue: 0.1364 time to fit residues: 30.9320 Evaluate side-chains 114 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 968 SER Chi-restraints excluded: chain A residue 976 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 118 LEU Chi-restraints excluded: chain C residue 203 ILE 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 640 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1012 LEU 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: 0.9980 chunk 127 optimal weight: 30.0000 chunk 275 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 199 optimal weight: 0.5980 chunk 293 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4069 r_free = 0.4069 target = 0.131914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.085920 restraints weight = 57092.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.089086 restraints weight = 32543.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090992 restraints weight = 22359.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.091073 restraints weight = 20178.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090928 restraints weight = 16871.780| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25485 Z= 0.129 Angle : 0.590 10.746 34833 Z= 0.285 Chirality : 0.044 0.416 4151 Planarity : 0.004 0.049 4369 Dihedral : 3.885 22.997 3257 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.87 % Rotamer: Outliers : 1.24 % Allowed : 15.11 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 3001 helix: 1.61 (0.21), residues: 663 sheet: -0.06 (0.21), residues: 646 loop : -1.61 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.018 0.001 TYR C1067 PHE 0.028 0.001 PHE C 238 TRP 0.010 0.001 TRP A 436 HIS 0.006 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (25376) covalent geometry : angle 0.56035 / 0.28 (34540) SS BOND : bond 0.00512 / 0.27 ( 34) SS BOND : angle 1.26891 / 0.84 ( 68) hydrogen bonds : bond 0.05057 / 3.42 ( 876) hydrogen bonds : angle 4.52813 / 3.13 ( 2415) link_BETA1-4 : bond 0.00567 / 0.31 ( 30) link_BETA1-4 : angle 2.22610 / 1.55 ( 90) link_NAG-ASN : bond 0.00289 / 0.19 ( 45) link_NAG-ASN : angle 2.30818 / 1.59 ( 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 127 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8545 (p90) cc_final: 0.8329 (p90) REVERT: A 441 LEU cc_start: 0.8643 (mt) cc_final: 0.8403 (tp) REVERT: A 740 MET cc_start: 0.8527 (tpp) cc_final: 0.7954 (tmm) REVERT: A 948 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7328 (mt) REVERT: B 725 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6707 (mt-10) REVERT: B 858 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8704 (pp) REVERT: C 104 TRP cc_start: 0.6833 (m-90) cc_final: 0.6513 (m-10) REVERT: C 191 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6678 (tm-30) REVERT: C 441 LEU cc_start: 0.9091 (mm) cc_final: 0.8621 (tt) REVERT: C 985 ASP cc_start: 0.7726 (t0) cc_final: 0.7301 (t0) REVERT: C 1029 MET cc_start: 0.8553 (tmm) cc_final: 0.8119 (tmm) outliers start: 33 outliers final: 25 residues processed: 123 average time/residue: 0.1419 time to fit residues: 30.0644 Evaluate side-chains 118 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 705 VAL 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 C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE 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 640 SER Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 204 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 197 optimal weight: 0.8980 chunk 231 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.132031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.085541 restraints weight = 57317.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089946 restraints weight = 31643.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.092432 restraints weight = 19920.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.092304 restraints weight = 17531.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.092267 restraints weight = 14401.798| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25485 Z= 0.123 Angle : 0.588 10.708 34833 Z= 0.284 Chirality : 0.044 0.408 4151 Planarity : 0.004 0.050 4369 Dihedral : 3.862 22.740 3257 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 1.20 % Allowed : 15.60 % Favored : 83.20 % 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: -0.70 (0.15), residues: 3001 helix: 1.68 (0.21), residues: 655 sheet: -0.04 (0.21), residues: 648 loop : -1.58 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.018 0.001 TYR C1067 PHE 0.030 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/Z covalent geometry : bond 0.00282 / 0.12 (25376) covalent geometry : angle 0.55876 / 0.28 (34540) SS BOND : bond 0.00435 / 0.25 ( 34) SS BOND : angle 1.32939 / 0.86 ( 68) hydrogen bonds : bond 0.04968 / 3.36 ( 876) hydrogen bonds : angle 4.50581 / 3.12 ( 2415) link_BETA1-4 : bond 0.00576 / 0.32 ( 30) link_BETA1-4 : angle 2.21138 / 1.54 ( 90) link_NAG-ASN : bond 0.00294 / 0.19 ( 45) link_NAG-ASN : angle 2.26102 / 1.55 ( 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 128 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8530 (p90) cc_final: 0.8322 (p90) REVERT: A 441 LEU cc_start: 0.8647 (mt) cc_final: 0.8407 (tp) REVERT: A 740 MET cc_start: 0.8529 (tpp) cc_final: 0.7939 (tmm) REVERT: A 902 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7977 (mmm) REVERT: A 948 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7299 (mt) REVERT: B 725 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6682 (mt-10) REVERT: B 858 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8717 (pp) REVERT: C 104 TRP cc_start: 0.6829 (m-90) cc_final: 0.6544 (m-10) REVERT: C 191 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6585 (tm-30) REVERT: C 441 LEU cc_start: 0.9101 (mm) cc_final: 0.8622 (tt) REVERT: C 985 ASP cc_start: 0.7572 (t0) cc_final: 0.7110 (t0) REVERT: C 1029 MET cc_start: 0.8522 (tmm) cc_final: 0.8087 (tmm) outliers start: 32 outliers final: 26 residues processed: 122 average time/residue: 0.1292 time to fit residues: 27.7533 Evaluate side-chains 121 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 902 MET 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 C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE 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 640 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1012 LEU 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: 0.9980 chunk 210 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 167 optimal weight: 0.0070 chunk 119 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4092 r_free = 0.4092 target = 0.136159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.086204 restraints weight = 55819.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089936 restraints weight = 29081.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.092299 restraints weight = 20103.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.093735 restraints weight = 16145.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.094662 restraints weight = 14121.476| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25485 Z= 0.116 Angle : 0.591 11.915 34833 Z= 0.285 Chirality : 0.044 0.399 4151 Planarity : 0.004 0.049 4369 Dihedral : 3.840 22.756 3257 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.00 % Favored : 94.97 % Rotamer: Outliers : 1.35 % Allowed : 15.63 % Favored : 83.01 % 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: -0.66 (0.15), residues: 3001 helix: 1.71 (0.21), residues: 649 sheet: 0.01 (0.21), residues: 637 loop : -1.54 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.018 0.001 TYR C1067 PHE 0.034 0.001 PHE C 238 TRP 0.011 0.001 TRP A 436 HIS 0.005 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (25376) covalent geometry : angle 0.56314 / 0.28 (34540) SS BOND : bond 0.00384 / 0.23 ( 34) SS BOND : angle 1.36256 / 0.87 ( 68) hydrogen bonds : bond 0.04825 / 3.26 ( 876) hydrogen bonds : angle 4.46528 / 3.09 ( 2415) link_BETA1-4 : bond 0.00580 / 0.32 ( 30) link_BETA1-4 : angle 2.20633 / 1.54 ( 90) link_NAG-ASN : bond 0.00301 / 0.20 ( 45) link_NAG-ASN : angle 2.21669 / 1.52 ( 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 130 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8649 (mt) cc_final: 0.8399 (tp) REVERT: A 740 MET cc_start: 0.8543 (tpp) cc_final: 0.7950 (tmm) REVERT: A 902 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8020 (mmm) REVERT: A 948 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7269 (mt) REVERT: B 725 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6670 (mt-10) REVERT: B 858 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8711 (pp) REVERT: C 104 TRP cc_start: 0.6789 (m-90) cc_final: 0.6505 (m-10) REVERT: C 191 GLU cc_start: 0.6993 (tm-30) cc_final: 0.6707 (tm-30) REVERT: C 441 LEU cc_start: 0.9146 (mm) cc_final: 0.8651 (tt) REVERT: C 985 ASP cc_start: 0.7500 (t0) cc_final: 0.7032 (t0) REVERT: C 1029 MET cc_start: 0.8469 (tmm) cc_final: 0.8050 (tmm) outliers start: 36 outliers final: 28 residues processed: 125 average time/residue: 0.1297 time to fit residues: 28.6044 Evaluate side-chains 124 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 902 MET 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 270 LEU Chi-restraints excluded: chain B residue 551 VAL 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 1012 LEU 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: 3.9990 chunk 196 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 201 optimal weight: 0.8980 chunk 214 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4077 r_free = 0.4077 target = 0.135321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.085138 restraints weight = 55639.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088726 restraints weight = 29418.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.091020 restraints weight = 20611.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.092501 restraints weight = 16660.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.093411 restraints weight = 14531.866| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 25485 Z= 0.145 Angle : 0.604 10.768 34833 Z= 0.293 Chirality : 0.044 0.415 4151 Planarity : 0.004 0.049 4369 Dihedral : 3.930 22.831 3257 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.56 % Favored : 94.40 % Rotamer: Outliers : 1.20 % Allowed : 15.90 % Favored : 82.90 % 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: -0.73 (0.15), residues: 3001 helix: 1.63 (0.21), residues: 655 sheet: -0.02 (0.21), residues: 645 loop : -1.60 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.019 0.001 TYR C1067 PHE 0.037 0.001 PHE C 238 TRP 0.011 0.001 TRP C 104 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (25376) covalent geometry : angle 0.57466 / 0.29 (34540) SS BOND : bond 0.00453 / 0.27 ( 34) SS BOND : angle 1.54361 / 0.97 ( 68) hydrogen bonds : bond 0.05206 / 3.52 ( 876) hydrogen bonds : angle 4.55088 / 3.15 ( 2415) link_BETA1-4 : bond 0.00555 / 0.30 ( 30) link_BETA1-4 : angle 2.17401 / 1.52 ( 90) link_NAG-ASN : bond 0.00267 / 0.18 ( 45) link_NAG-ASN : angle 2.26686 / 1.55 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4084.76 seconds wall clock time: 71 minutes 26.32 seconds (4286.32 seconds total)