Starting phenix.real_space_refine on Sat Jul 4 20:59:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7edh_31071/07_2026/7edh_31071.cif Found real_map, /net/cci-nas-00/data/ceres_data/7edh_31071/07_2026/7edh_31071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7edh_31071/07_2026/7edh_31071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7edh_31071/07_2026/7edh_31071.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7edh_31071/07_2026/7edh_31071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7edh_31071/07_2026/7edh_31071.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7edh_31071/07_2026/7edh_31071.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7edh_31071/07_2026/7edh_31071.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.041 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 100 5.16 5 C 14801 2.51 5 N 3763 2.21 5 O 4612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s 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: 23276 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 6366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6366 Classifications: {'peptide': 819} Link IDs: {'PTRANS': 39, 'TRANS': 779} Chain breaks: 8 Chain: "B" Number of atoms: 7957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7957 Classifications: {'peptide': 1019} Link IDs: {'PTRANS': 51, 'TRANS': 967} Chain breaks: 7 Chain: "C" Number of atoms: 7878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7878 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.28, per 1000 atoms: 0.23 Number of scatterers: 23276 At special positions: 0 Unit cell: (132, 140.8, 177.1, 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 100 16.00 O 4612 8.00 N 3763 7.00 C 14801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 163 " distance=2.04 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.04 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG 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 N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 279 " " NAG A2003 " - " ASN A 600 " " NAG A2004 " - " ASN A 654 " " NAG A2005 " - " ASN A 706 " " NAG A2006 " - " ASN A1071 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 162 " " NAG B2003 " - " ASN B 231 " " NAG B2004 " - " ASN B 328 " " NAG B2005 " - " ASN B 600 " " NAG B2006 " - " ASN B 654 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 328 " " NAG C2003 " - " ASN C 600 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 162 " " NAG F 1 " - " ASN A 231 " " NAG G 1 " - " ASN A 613 " " NAG H 1 " - " ASN A 714 " " NAG I 1 " - " ASN A 798 " " NAG J 1 " - " ASN A1095 " " NAG K 1 " - " ASN A1131 " " NAG L 1 " - " ASN B 120 " " NAG M 1 " - " ASN B 279 " " NAG N 1 " - " ASN B 340 " " NAG O 1 " - " ASN B 613 " " NAG P 1 " - " ASN B 706 " " NAG Q 1 " - " ASN B 714 " " NAG R 1 " - " ASN B 798 " " NAG S 1 " - " ASN B1071 " " NAG T 1 " - " ASN B1095 " " NAG U 1 " - " ASN B1131 " " NAG V 1 " - " ASN C 120 " " NAG W 1 " - " ASN C 162 " " NAG X 1 " - " ASN C 231 " " NAG Y 1 " - " ASN C 279 " " NAG Z 1 " - " ASN C 340 " " NAG a 1 " - " ASN C 613 " " NAG b 1 " - " ASN C 706 " " NAG c 1 " - " ASN C 714 " " NAG d 1 " - " ASN C 798 " " NAG e 1 " - " ASN C1071 " " NAG f 1 " - " ASN C1095 " " NAG g 1 " - " ASN C1131 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5336 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 41 sheets defined 23.3% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.654A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 751 Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.612A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 822 Processing helix chain 'A' and resid 863 through 882 removed outlier: 3.622A pdb=" N GLY A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 912 through 915 removed outlier: 3.559A pdb=" N GLU A 915 " --> pdb=" O VAL A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 915' Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.512A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.716A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.803A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1030 removed outlier: 3.607A pdb=" N GLN A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1030 " --> pdb=" O MET A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 removed outlier: 4.415A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.738A pdb=" N GLU B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 340 removed outlier: 4.356A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.695A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 734 through 740 removed outlier: 3.621A pdb=" N TYR B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.884A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 780 removed outlier: 4.119A pdb=" N PHE B 779 " --> pdb=" O THR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.731A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.599A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 904 removed outlier: 3.555A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.744A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.706A pdb=" N GLN B 962 " --> pdb=" O THR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 4.036A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 979 " --> pdb=" O ASN B 975 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 981 " --> pdb=" O ILE B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.215A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 341 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.668A pdb=" N TYR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 419' Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.964A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.903A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 762 " --> pdb=" O THR C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 removed outlier: 3.502A pdb=" N ASP C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.788A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.682A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 915 removed outlier: 3.694A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 910 through 915' Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.557A pdb=" N GLN C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.571A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.433A pdb=" N GLU C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 3.736A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.525A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.806A pdb=" N GLN A 268 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.655A pdb=" N PHE A 104 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 89 removed outlier: 3.888A pdb=" N VAL A 190 " --> pdb=" O TYR A 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 133 through 140 removed outlier: 10.188A pdb=" N ASP A 136 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N TYR A 157 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.615A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.175A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG A 325 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY A 563 " --> pdb=" O ASP A 571 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.120A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AB2, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.716A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AB4, first strand: chain 'A' and resid 1117 through 1119 removed outlier: 3.514A pdb=" N ILE A1078 " --> pdb=" O HIS A1085 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS A1079 " --> pdb=" O VAL A1130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.725A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.783A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.635A pdb=" N PHE B 104 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 125 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 87 through 89 removed outlier: 3.520A pdb=" N VAL B 190 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 131 through 140 removed outlier: 6.525A pdb=" N GLN B 132 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS B 134 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL B 156 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N ASP B 136 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N PHE B 154 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.328A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 645 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 322 through 325 removed outlier: 6.837A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC6, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.312A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 698 through 700 removed outlier: 6.769A pdb=" N ALA B 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 714 through 725 removed outlier: 3.768A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.559A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1073 through 1075 removed outlier: 3.520A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.621A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS B1079 " --> pdb=" O VAL B1130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.611A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.753A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.526A pdb=" N SER C 169 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 221 through 227 removed outlier: 6.003A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL C 190 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 265 " --> pdb=" O TYR C 89 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.284A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 590 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 323 through 325 Processing sheet with id=AD9, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.946A pdb=" N ASN C 351 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER C 396 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU C 513 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.216A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.925A pdb=" N GLN C1068 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE C 717 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C1064 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.657A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1117 through 1119 removed outlier: 3.958A pdb=" N CYS C1079 " --> pdb=" O VAL C1130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1091 through 1094 782 hydrogen bonds defined for protein. 2181 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: 2.80 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: 7333 1.35 - 1.47: 5990 1.47 - 1.59: 10321 1.59 - 1.71: 0 1.71 - 1.83: 124 Bond restraints: 23768 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.39e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" N VAL A 141 " pdb=" CA VAL A 141 " ideal model delta sigma weight residual 1.458 1.417 0.041 1.90e-02 2.77e+03 4.71e+00 bond pdb=" C1 NAG A2001 " pdb=" O5 NAG A2001 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.29e+00 ... (remaining 23763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 31649 2.08 - 4.16: 626 4.16 - 6.23: 46 6.23 - 8.31: 7 8.31 - 10.39: 3 Bond angle restraints: 32331 Sorted by residual: angle pdb=" N VAL A 128 " pdb=" CA VAL A 128 " pdb=" C VAL A 128 " ideal model delta sigma weight residual 112.17 107.35 4.82 9.50e-01 1.11e+00 2.57e+01 angle pdb=" N LYS B 851 " pdb=" CA LYS B 851 " pdb=" C LYS B 851 " ideal model delta sigma weight residual 110.80 102.07 8.73 2.13e+00 2.20e-01 1.68e+01 angle pdb=" N THR C 122 " pdb=" CA THR C 122 " pdb=" C THR C 122 " ideal model delta sigma weight residual 114.56 109.99 4.57 1.27e+00 6.20e-01 1.30e+01 angle pdb=" N VAL B 128 " pdb=" CA VAL B 128 " pdb=" C VAL B 128 " ideal model delta sigma weight residual 111.77 108.21 3.56 1.04e+00 9.25e-01 1.17e+01 angle pdb=" CA TRP A 64 " pdb=" CB TRP A 64 " pdb=" CG TRP A 64 " ideal model delta sigma weight residual 113.60 120.07 -6.47 1.90e+00 2.77e-01 1.16e+01 ... (remaining 32326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12274 17.93 - 35.87: 1037 35.87 - 53.80: 168 53.80 - 71.74: 35 71.74 - 89.67: 24 Dihedral angle restraints: 13538 sinusoidal: 5263 harmonic: 8275 Sorted by residual: dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual -86.00 -170.87 84.87 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual 93.00 173.80 -80.80 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS B 659 " pdb=" SG CYS B 659 " pdb=" SG CYS B 668 " pdb=" CB CYS B 668 " ideal model delta sinusoidal sigma weight residual 93.00 170.94 -77.94 1 1.00e+01 1.00e-02 7.59e+01 ... (remaining 13535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3863 0.122 - 0.244: 46 0.244 - 0.367: 5 0.367 - 0.489: 3 0.489 - 0.611: 2 Chirality restraints: 3919 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN C 162 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.33e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 162 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C 340 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.91e+00 ... (remaining 3916 not shown) Planarity restraints: 4122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 140 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C GLY A 140 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY A 140 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 141 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 983 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO A 984 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 983 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO C 984 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 984 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 984 " -0.031 5.00e-02 4.00e+02 ... (remaining 4119 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1319 2.73 - 3.27: 22613 3.27 - 3.82: 35340 3.82 - 4.36: 39297 4.36 - 4.90: 70471 Nonbonded interactions: 169040 Sorted by model distance: nonbonded pdb=" OH TYR C 753 " pdb=" OD1 ASP C 991 " model vdw 2.189 3.040 nonbonded pdb=" OD2 ASP C 575 " pdb=" OG1 THR C 578 " model vdw 2.203 3.040 nonbonded pdb=" OG SER A 110 " pdb=" OE1 GLN A 132 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR B 498 " pdb=" O TYR B 502 " model vdw 2.219 3.040 nonbonded pdb=" OG SER B 110 " pdb=" OE1 GLN B 132 " model vdw 2.222 3.040 ... (remaining 169035 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 'B' and (resid 27 through 139 or resid 152 through 173 or resid 184 throu \ gh 208 or resid 214 through 240 or resid 261 through 618 or resid 638 through 20 \ 04)) selection = (chain 'C' and (resid 27 through 824 or resid 842 through 2004)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.680 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 0.054 23876 Z= 0.195 Angle : 0.717 13.991 32623 Z= 0.359 Chirality : 0.050 0.611 3919 Planarity : 0.004 0.055 4077 Dihedral : 13.660 89.671 8106 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.37 % Favored : 93.34 % Rotamer: Outliers : 0.16 % Allowed : 0.48 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.16), residues: 2794 helix: 1.88 (0.23), residues: 608 sheet: -0.68 (0.22), residues: 549 loop : -2.08 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 100 TYR 0.014 0.001 TYR A 89 PHE 0.022 0.001 PHE B 138 TRP 0.030 0.001 TRP B 102 HIS 0.003 0.000 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 (23768) covalent geometry : angle 0.66827 / 0.35 (32331) SS BOND : bond 0.00363 / 0.19 ( 32) SS BOND : angle 1.28819 / 0.92 ( 64) hydrogen bonds : bond 0.15681 / 10.16 ( 782) hydrogen bonds : angle 6.06681 / 4.03 ( 2181) link_BETA1-4 : bond 0.00806 / 0.54 ( 31) link_BETA1-4 : angle 3.10614 / 2.14 ( 93) link_NAG-ASN : bond 0.00525 / 0.31 ( 45) link_NAG-ASN : angle 3.15406 / 1.97 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 165 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 742 ASP cc_start: 0.6118 (t70) cc_final: 0.5883 (t70) REVERT: C 1028 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7399 (tm-30) REVERT: C 1132 ASN cc_start: 0.8223 (t0) cc_final: 0.7571 (t0) outliers start: 4 outliers final: 0 residues processed: 166 average time/residue: 0.1490 time to fit residues: 40.0330 Evaluate side-chains 105 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN A 952 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 79 ASN C 119 ASN C 161 ASN C 952 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.148606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.119837 restraints weight = 46578.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.122726 restraints weight = 35007.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.122419 restraints weight = 37395.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.123689 restraints weight = 23259.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.124802 restraints weight = 19729.067| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 23876 Z= 0.174 Angle : 0.661 13.374 32623 Z= 0.324 Chirality : 0.047 0.356 3919 Planarity : 0.004 0.057 4077 Dihedral : 4.246 24.313 3030 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.48 % Favored : 92.20 % Rotamer: Outliers : 0.32 % Allowed : 7.85 % Favored : 91.83 % 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: -1.26 (0.16), residues: 2794 helix: 1.81 (0.22), residues: 613 sheet: -0.59 (0.21), residues: 594 loop : -2.14 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 270 TYR 0.019 0.001 TYR C 89 PHE 0.021 0.002 PHE A 235 TRP 0.025 0.002 TRP B 102 HIS 0.003 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (23768) covalent geometry : angle 0.61829 / 0.31 (32331) SS BOND : bond 0.00422 / 0.24 ( 32) SS BOND : angle 2.08044 / 1.35 ( 64) hydrogen bonds : bond 0.05796 / 3.90 ( 782) hydrogen bonds : angle 4.95001 / 3.27 ( 2181) link_BETA1-4 : bond 0.00766 / 0.50 ( 31) link_BETA1-4 : angle 2.35928 / 1.65 ( 93) link_NAG-ASN : bond 0.00439 / 0.27 ( 45) link_NAG-ASN : angle 2.86716 / 1.80 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 405 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7458 (ttp80) REVERT: C 505 TYR cc_start: 0.7111 (m-80) cc_final: 0.6866 (m-80) REVERT: C 742 ASP cc_start: 0.6236 (t70) cc_final: 0.5925 (t70) REVERT: C 1132 ASN cc_start: 0.8299 (t0) cc_final: 0.7720 (t0) outliers start: 8 outliers final: 6 residues processed: 122 average time/residue: 0.1393 time to fit residues: 28.9330 Evaluate side-chains 105 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain C residue 846 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 101 optimal weight: 0.3980 chunk 175 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 280 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 776 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.149030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.120079 restraints weight = 46378.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.122223 restraints weight = 33625.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.122501 restraints weight = 35386.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.124292 restraints weight = 23207.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.124588 restraints weight = 19634.024| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23876 Z= 0.130 Angle : 0.605 13.102 32623 Z= 0.294 Chirality : 0.046 0.361 3919 Planarity : 0.004 0.058 4077 Dihedral : 4.140 24.185 3030 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.41 % Favored : 93.24 % Rotamer: Outliers : 0.85 % Allowed : 11.23 % Favored : 87.93 % 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: -1.17 (0.16), residues: 2794 helix: 1.96 (0.22), residues: 608 sheet: -0.53 (0.21), residues: 587 loop : -2.10 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 762 TYR 0.015 0.001 TYR C 89 PHE 0.025 0.001 PHE B 131 TRP 0.018 0.001 TRP B 102 HIS 0.002 0.000 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (23768) covalent geometry : angle 0.56715 / 0.29 (32331) SS BOND : bond 0.00429 / 0.27 ( 32) SS BOND : angle 1.21117 / 0.86 ( 64) hydrogen bonds : bond 0.04839 / 3.30 ( 782) hydrogen bonds : angle 4.65022 / 3.08 ( 2181) link_BETA1-4 : bond 0.00790 / 0.52 ( 31) link_BETA1-4 : angle 2.21027 / 1.54 ( 93) link_NAG-ASN : bond 0.00438 / 0.26 ( 45) link_NAG-ASN : angle 2.71429 / 1.71 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.233 Fit side-chains REVERT: A 187 ARG cc_start: 0.6974 (mtp180) cc_final: 0.6709 (tpp-160) REVERT: A 189 PHE cc_start: 0.7387 (m-10) cc_final: 0.6755 (m-10) REVERT: C 1132 ASN cc_start: 0.8221 (t0) cc_final: 0.7655 (t0) outliers start: 21 outliers final: 11 residues processed: 123 average time/residue: 0.1379 time to fit residues: 28.8951 Evaluate side-chains 112 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 846 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 51 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 225 optimal weight: 20.0000 chunk 250 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 222 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 HIS C 204 HIS ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN C 910 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.143999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.112982 restraints weight = 46379.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.113473 restraints weight = 30919.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.114680 restraints weight = 26248.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.115046 restraints weight = 21410.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.115313 restraints weight = 20522.347| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 23876 Z= 0.243 Angle : 0.714 12.577 32623 Z= 0.351 Chirality : 0.049 0.348 3919 Planarity : 0.005 0.059 4077 Dihedral : 4.581 23.855 3030 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.70 % Favored : 90.91 % Rotamer: Outliers : 1.81 % Allowed : 14.00 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.16), residues: 2794 helix: 1.72 (0.22), residues: 607 sheet: -0.80 (0.21), residues: 605 loop : -2.28 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B1036 TYR 0.023 0.002 TYR C 167 PHE 0.032 0.002 PHE C 235 TRP 0.028 0.002 TRP C 64 HIS 0.005 0.001 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.24 (23768) covalent geometry : angle 0.68019 / 0.34 (32331) SS BOND : bond 0.00578 / 0.33 ( 32) SS BOND : angle 1.50365 / 1.10 ( 64) hydrogen bonds : bond 0.06413 / 4.36 ( 782) hydrogen bonds : angle 4.87410 / 3.25 ( 2181) link_BETA1-4 : bond 0.00710 / 0.47 ( 31) link_BETA1-4 : angle 2.10258 / 1.47 ( 93) link_NAG-ASN : bond 0.00454 / 0.29 ( 45) link_NAG-ASN : angle 2.86106 / 1.83 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: B 131 PHE cc_start: 0.5142 (m-10) cc_final: 0.4841 (m-10) outliers start: 45 outliers final: 30 residues processed: 147 average time/residue: 0.1334 time to fit residues: 33.0346 Evaluate side-chains 126 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 239 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 218 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 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 = 0.4521 r_free = 0.4521 target = 0.147041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.118147 restraints weight = 45685.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.121609 restraints weight = 34952.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.121160 restraints weight = 36500.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.122216 restraints weight = 22874.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.124255 restraints weight = 19747.162| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23876 Z= 0.143 Angle : 0.620 12.624 32623 Z= 0.302 Chirality : 0.046 0.357 3919 Planarity : 0.004 0.059 4077 Dihedral : 4.316 23.960 3030 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.51 % Favored : 93.09 % Rotamer: Outliers : 1.61 % Allowed : 15.25 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.16), residues: 2794 helix: 1.90 (0.22), residues: 608 sheet: -0.73 (0.21), residues: 579 loop : -2.19 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.020 0.001 TYR C 89 PHE 0.018 0.001 PHE A 235 TRP 0.015 0.001 TRP C 64 HIS 0.003 0.000 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (23768) covalent geometry : angle 0.58569 / 0.29 (32331) SS BOND : bond 0.00424 / 0.25 ( 32) SS BOND : angle 1.20980 / 0.84 ( 64) hydrogen bonds : bond 0.05314 / 3.65 ( 782) hydrogen bonds : angle 4.57901 / 3.05 ( 2181) link_BETA1-4 : bond 0.00755 / 0.50 ( 31) link_BETA1-4 : angle 2.08471 / 1.46 ( 93) link_NAG-ASN : bond 0.00416 / 0.25 ( 45) link_NAG-ASN : angle 2.65978 / 1.70 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: B 389 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7685 (p90) REVERT: C 332 LEU cc_start: 0.8171 (mm) cc_final: 0.7971 (mm) outliers start: 40 outliers final: 28 residues processed: 143 average time/residue: 0.1140 time to fit residues: 28.0617 Evaluate side-chains 127 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 273 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 202 optimal weight: 0.0570 chunk 162 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1085 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** C 541 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 = 0.4493 r_free = 0.4493 target = 0.145711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.116402 restraints weight = 46220.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.118822 restraints weight = 38097.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.119211 restraints weight = 36994.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.120351 restraints weight = 23672.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.121699 restraints weight = 20827.116| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23876 Z= 0.161 Angle : 0.626 13.265 32623 Z= 0.306 Chirality : 0.047 0.376 3919 Planarity : 0.004 0.058 4077 Dihedral : 4.311 23.330 3030 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.48 % Favored : 92.13 % Rotamer: Outliers : 2.41 % Allowed : 15.41 % Favored : 82.17 % 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: -1.33 (0.16), residues: 2794 helix: 1.95 (0.22), residues: 604 sheet: -0.78 (0.21), residues: 618 loop : -2.19 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 187 TYR 0.018 0.001 TYR C 89 PHE 0.020 0.001 PHE A 235 TRP 0.016 0.002 TRP C 64 HIS 0.002 0.000 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (23768) covalent geometry : angle 0.59240 / 0.30 (32331) SS BOND : bond 0.00410 / 0.23 ( 32) SS BOND : angle 1.21201 / 0.84 ( 64) hydrogen bonds : bond 0.05348 / 3.66 ( 782) hydrogen bonds : angle 4.56042 / 3.04 ( 2181) link_BETA1-4 : bond 0.00735 / 0.49 ( 31) link_BETA1-4 : angle 2.05989 / 1.44 ( 93) link_NAG-ASN : bond 0.00439 / 0.25 ( 45) link_NAG-ASN : angle 2.64202 / 1.68 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 105 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7413 (t80) cc_final: 0.7105 (t80) REVERT: B 389 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7711 (p90) REVERT: C 332 LEU cc_start: 0.8184 (mm) cc_final: 0.7975 (mm) REVERT: C 847 ILE cc_start: 0.6800 (mt) cc_final: 0.6596 (mt) REVERT: C 915 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6857 (mp0) outliers start: 60 outliers final: 45 residues processed: 159 average time/residue: 0.1246 time to fit residues: 33.6796 Evaluate side-chains 147 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 161 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 264 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 chunk 194 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 268 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 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 = 0.4500 r_free = 0.4500 target = 0.146322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.117134 restraints weight = 46109.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.119483 restraints weight = 37615.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.119739 restraints weight = 38371.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.121097 restraints weight = 23959.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.122242 restraints weight = 20746.845| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23876 Z= 0.136 Angle : 0.608 13.149 32623 Z= 0.296 Chirality : 0.046 0.355 3919 Planarity : 0.004 0.058 4077 Dihedral : 4.237 28.013 3030 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.51 % Favored : 93.13 % Rotamer: Outliers : 2.29 % Allowed : 15.61 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.16), residues: 2794 helix: 2.04 (0.22), residues: 604 sheet: -0.70 (0.21), residues: 614 loop : -2.17 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 187 TYR 0.017 0.001 TYR C 89 PHE 0.018 0.001 PHE B 138 TRP 0.015 0.001 TRP B 102 HIS 0.002 0.000 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (23768) covalent geometry : angle 0.57478 / 0.29 (32331) SS BOND : bond 0.00361 / 0.21 ( 32) SS BOND : angle 1.22019 / 0.85 ( 64) hydrogen bonds : bond 0.04981 / 3.42 ( 782) hydrogen bonds : angle 4.49118 / 3.00 ( 2181) link_BETA1-4 : bond 0.00746 / 0.50 ( 31) link_BETA1-4 : angle 2.05297 / 1.44 ( 93) link_NAG-ASN : bond 0.00409 / 0.24 ( 45) link_NAG-ASN : angle 2.59271 / 1.65 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 106 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7316 (t80) cc_final: 0.7026 (t80) REVERT: B 131 PHE cc_start: 0.4686 (m-10) cc_final: 0.4469 (m-10) REVERT: B 187 ARG cc_start: 0.5797 (tpm170) cc_final: 0.5562 (tpm170) REVERT: B 389 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7639 (p90) REVERT: C 847 ILE cc_start: 0.6807 (mt) cc_final: 0.6568 (mt) REVERT: C 915 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.6836 (mp0) outliers start: 57 outliers final: 42 residues processed: 157 average time/residue: 0.1291 time to fit residues: 35.0830 Evaluate side-chains 146 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 614 CYS Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 61 optimal weight: 7.9990 chunk 242 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 234 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 271 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 869 GLN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 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 = 0.4502 r_free = 0.4502 target = 0.146449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.117041 restraints weight = 45870.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.119029 restraints weight = 35855.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.119391 restraints weight = 37038.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.120613 restraints weight = 23935.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.121232 restraints weight = 21057.303| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23876 Z= 0.136 Angle : 0.605 12.818 32623 Z= 0.293 Chirality : 0.046 0.351 3919 Planarity : 0.004 0.058 4077 Dihedral : 4.187 25.415 3030 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.94 % Favored : 92.70 % Rotamer: Outliers : 2.62 % Allowed : 15.86 % Favored : 81.53 % 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: -1.22 (0.16), residues: 2794 helix: 2.07 (0.22), residues: 604 sheet: -0.72 (0.20), residues: 632 loop : -2.14 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 187 TYR 0.016 0.001 TYR A 89 PHE 0.019 0.001 PHE C 90 TRP 0.013 0.001 TRP B 102 HIS 0.002 0.000 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (23768) covalent geometry : angle 0.57251 / 0.29 (32331) SS BOND : bond 0.00376 / 0.21 ( 32) SS BOND : angle 1.20309 / 0.84 ( 64) hydrogen bonds : bond 0.04887 / 3.35 ( 782) hydrogen bonds : angle 4.44751 / 2.97 ( 2181) link_BETA1-4 : bond 0.00752 / 0.50 ( 31) link_BETA1-4 : angle 2.03387 / 1.42 ( 93) link_NAG-ASN : bond 0.00398 / 0.23 ( 45) link_NAG-ASN : angle 2.53148 / 1.62 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 100 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7314 (t80) cc_final: 0.6972 (t80) REVERT: C 847 ILE cc_start: 0.6805 (mt) cc_final: 0.6564 (mt) REVERT: C 915 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.6855 (mp0) outliers start: 65 outliers final: 52 residues processed: 159 average time/residue: 0.1280 time to fit residues: 35.1657 Evaluate side-chains 154 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 101 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 TRP Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 614 CYS Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 58 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 263 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 110 optimal weight: 6.9990 chunk 13 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 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 = 0.4522 r_free = 0.4522 target = 0.148001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.119019 restraints weight = 46102.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.120708 restraints weight = 35997.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.121135 restraints weight = 37982.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.122501 restraints weight = 24319.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.123243 restraints weight = 21109.479| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23876 Z= 0.111 Angle : 0.590 12.764 32623 Z= 0.286 Chirality : 0.046 0.354 3919 Planarity : 0.004 0.058 4077 Dihedral : 4.047 23.281 3030 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.01 % Favored : 93.63 % Rotamer: Outliers : 1.85 % Allowed : 16.54 % Favored : 81.61 % 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: -1.07 (0.16), residues: 2794 helix: 2.22 (0.22), residues: 600 sheet: -0.58 (0.21), residues: 615 loop : -2.05 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 187 TYR 0.017 0.001 TYR A 89 PHE 0.032 0.001 PHE B 131 TRP 0.016 0.001 TRP B 102 HIS 0.001 0.000 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (23768) covalent geometry : angle 0.55888 / 0.28 (32331) SS BOND : bond 0.00347 / 0.19 ( 32) SS BOND : angle 1.05156 / 0.73 ( 64) hydrogen bonds : bond 0.04373 / 3.00 ( 782) hydrogen bonds : angle 4.33079 / 2.89 ( 2181) link_BETA1-4 : bond 0.00764 / 0.50 ( 31) link_BETA1-4 : angle 2.03549 / 1.42 ( 93) link_NAG-ASN : bond 0.00408 / 0.24 ( 45) link_NAG-ASN : angle 2.43497 / 1.56 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 847 ILE cc_start: 0.6810 (mt) cc_final: 0.6567 (mt) outliers start: 46 outliers final: 39 residues processed: 149 average time/residue: 0.1200 time to fit residues: 31.0565 Evaluate side-chains 141 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 614 CYS Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 42 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 158 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.145858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.116830 restraints weight = 46192.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.119802 restraints weight = 37968.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.119887 restraints weight = 36328.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.121002 restraints weight = 23206.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.122406 restraints weight = 20428.478| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23876 Z= 0.165 Angle : 0.625 12.586 32623 Z= 0.305 Chirality : 0.046 0.346 3919 Planarity : 0.004 0.058 4077 Dihedral : 4.189 23.704 3030 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.70 % Favored : 91.95 % Rotamer: Outliers : 2.13 % Allowed : 16.42 % Favored : 81.45 % 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: -1.19 (0.16), residues: 2794 helix: 2.07 (0.22), residues: 606 sheet: -0.66 (0.21), residues: 622 loop : -2.13 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 187 TYR 0.020 0.001 TYR C 89 PHE 0.033 0.002 PHE B 131 TRP 0.016 0.001 TRP C 64 HIS 0.003 0.001 HIS A1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (23768) covalent geometry : angle 0.59515 / 0.30 (32331) SS BOND : bond 0.00400 / 0.22 ( 32) SS BOND : angle 1.23355 / 0.86 ( 64) hydrogen bonds : bond 0.05050 / 3.44 ( 782) hydrogen bonds : angle 4.43562 / 2.96 ( 2181) link_BETA1-4 : bond 0.00725 / 0.48 ( 31) link_BETA1-4 : angle 2.00789 / 1.41 ( 93) link_NAG-ASN : bond 0.00381 / 0.23 ( 45) link_NAG-ASN : angle 2.49366 / 1.60 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 96 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7422 (t80) cc_final: 0.7189 (t80) REVERT: C 847 ILE cc_start: 0.6885 (mt) cc_final: 0.6634 (mt) REVERT: C 915 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.6888 (mp0) outliers start: 53 outliers final: 45 residues processed: 143 average time/residue: 0.1311 time to fit residues: 32.3047 Evaluate side-chains 142 residues out of total 2485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 96 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 919 LEU Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 614 CYS Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 202 optimal weight: 0.0470 chunk 141 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 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 = 0.4506 r_free = 0.4506 target = 0.146765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.117617 restraints weight = 46014.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.120155 restraints weight = 35423.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.120062 restraints weight = 38361.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.121332 restraints weight = 24104.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.121947 restraints weight = 20768.268| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23876 Z= 0.129 Angle : 0.605 12.538 32623 Z= 0.294 Chirality : 0.046 0.348 3919 Planarity : 0.004 0.058 4077 Dihedral : 4.125 23.229 3030 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.34 % Favored : 93.34 % Rotamer: Outliers : 2.01 % Allowed : 16.66 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.16), residues: 2794 helix: 2.20 (0.22), residues: 600 sheet: -0.61 (0.21), residues: 615 loop : -2.09 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 187 TYR 0.016 0.001 TYR A 89 PHE 0.031 0.001 PHE B 131 TRP 0.014 0.001 TRP B 102 HIS 0.002 0.000 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (23768) covalent geometry : angle 0.57538 / 0.29 (32331) SS BOND : bond 0.00370 / 0.20 ( 32) SS BOND : angle 1.14391 / 0.80 ( 64) hydrogen bonds : bond 0.04725 / 3.24 ( 782) hydrogen bonds : angle 4.37004 / 2.91 ( 2181) link_BETA1-4 : bond 0.00741 / 0.49 ( 31) link_BETA1-4 : angle 2.00363 / 1.40 ( 93) link_NAG-ASN : bond 0.00388 / 0.23 ( 45) link_NAG-ASN : angle 2.42294 / 1.55 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2892.84 seconds wall clock time: 51 minutes 22.44 seconds (3082.44 seconds total)