Starting phenix.real_space_refine on Sun Jul 5 02:38:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7edi_31072/07_2026/7edi_31072.cif Found real_map, /net/cci-nas-00/data/ceres_data/7edi_31072/07_2026/7edi_31072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7edi_31072/07_2026/7edi_31072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7edi_31072/07_2026/7edi_31072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7edi_31072/07_2026/7edi_31072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7edi_31072/07_2026/7edi_31072.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7edi_31072/07_2026/7edi_31072.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7edi_31072/07_2026/7edi_31072.cif" } resolution = 3.3 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= 0.051 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 108 5.16 5 C 15835 2.51 5 N 4034 2.21 5 O 4918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 24895 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 7992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7992 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 7 Chain: "B" Number of atoms: 7933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7933 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 51, 'TRANS': 964} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.31, per 1000 atoms: 0.21 Number of scatterers: 24895 At special positions: 0 Unit cell: (132, 140.8, 200.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4918 8.00 N 4034 7.00 C 15835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, 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 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.02 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=2.04 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=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 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=2.02 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 162 " " NAG A2003 " - " ASN A 231 " " NAG A2004 " - " ASN A 600 " " 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 120 " " NAG C2003 " - " ASN C 162 " " NAG C2004 " - " ASN C 600 " " NAG C2005 " - " ASN C 654 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 279 " " NAG F 1 " - " ASN A 328 " " NAG G 1 " - " ASN A 613 " " NAG H 1 " - " ASN A 706 " " NAG I 1 " - " ASN A 714 " " NAG J 1 " - " ASN A 798 " " NAG K 1 " - " ASN A1071 " " NAG L 1 " - " ASN A1095 " " NAG M 1 " - " ASN A1131 " " NAG N 1 " - " ASN B 120 " " NAG O 1 " - " ASN B 279 " " NAG P 1 " - " ASN B 340 " " NAG Q 1 " - " ASN B 613 " " NAG R 1 " - " ASN B 706 " " NAG S 1 " - " ASN B 714 " " NAG T 1 " - " ASN B 798 " " NAG U 1 " - " ASN B1071 " " NAG V 1 " - " ASN B1095 " " NAG W 1 " - " ASN B1131 " " NAG X 1 " - " ASN C 231 " " NAG Y 1 " - " ASN C 279 " " NAG Z 1 " - " ASN C 328 " " NAG a 1 " - " ASN C 340 " " NAG b 1 " - " ASN C 613 " " NAG c 1 " - " ASN C 706 " " NAG d 1 " - " ASN C 714 " " NAG e 1 " - " ASN C 798 " " NAG f 1 " - " ASN C1071 " " NAG g 1 " - " ASN C1095 " " NAG h 1 " - " ASN C1131 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 664.1 milliseconds 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5710 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 49 sheets defined 23.4% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.642A pdb=" N LEU A 387 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 540 through 543 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.630A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 739 " --> pdb=" O CYS A 735 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 740 " --> pdb=" O THR A 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 734 through 740' Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.588A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 780 removed outlier: 4.029A pdb=" N ASN A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 4.327A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 883 through 888' Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.649A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 962 removed outlier: 4.234A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.569A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 3.723A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N THR A 995 " --> pdb=" O ASP A 991 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 998 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A1030 " --> pdb=" O MET A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 removed outlier: 4.515A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.511A pdb=" N GLU B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.996A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 4.004A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 780 removed outlier: 4.080A pdb=" N PHE B 779 " --> pdb=" O THR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.523A pdb=" N ASP B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 3.658A 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 894 through 904 Processing helix chain 'B' and resid 905 through 907 No H-bonds generated for 'chain 'B' and resid 905 through 907' Processing helix chain 'B' and resid 910 through 916 Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.699A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 961 removed outlier: 3.555A pdb=" N GLN B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 965 removed outlier: 3.635A pdb=" N SER B 965 " --> pdb=" O GLN B 962 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 962 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.934A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 981 " --> pdb=" O ILE B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 3.996A 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 362 through 367 removed outlier: 3.706A pdb=" N TYR C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 387 removed outlier: 3.571A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 387 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 removed outlier: 3.749A pdb=" N SER C 440 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.745A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.659A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 910 through 915 removed outlier: 3.773A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.523A 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 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.770A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 1030 removed outlier: 3.748A pdb=" N ILE C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C1030 " --> pdb=" O MET C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1115 No H-bonds generated for 'chain 'C' and resid 1113 through 1115' Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 3.888A 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: 3.750A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.557A pdb=" N ARG A 270 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 226 removed outlier: 6.757A pdb=" N SER A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 224 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 205 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 7.008A pdb=" N VAL A 128 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 164 " --> pdb=" O VAL A 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.348A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 323 removed outlier: 3.930A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 removed outlier: 4.148A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359 removed outlier: 7.100A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.540A pdb=" N TYR A 486 " --> pdb=" O TYR A 470 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 562 through 563 removed outlier: 7.112A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.920A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.831A pdb=" N ALA A 698 " --> pdb=" O ILE B 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AB7, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.632A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 730 through 732 removed outlier: 4.651A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1119 removed outlier: 3.816A pdb=" N CYS A1079 " --> pdb=" O VAL A1130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AC2, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.822A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.682A pdb=" N THR B 271 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ASP B 287 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.654A pdb=" N LEU B 82 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 118 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 125 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 87 through 92 removed outlier: 3.547A pdb=" N GLU B 188 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 190 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 200 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 224 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.212A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 645 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 322 through 325 Processing sheet with id=AC8, first strand: chain 'B' and resid 351 through 355 removed outlier: 4.041A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 396 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP B 395 " --> pdb=" O VAL B 509 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.299A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 699 through 701 removed outlier: 3.677A pdb=" N LYS C 787 " --> pdb=" O ASN B 700 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 714 through 725 removed outlier: 3.506A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 714 through 725 removed outlier: 3.506A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.681A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.877A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD8, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.887A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.706A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.536A pdb=" N LEU C 238 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY C 101 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 221 through 227 removed outlier: 6.214A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 224 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 190 " --> pdb=" O TYR C 201 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.699A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 322 through 325 removed outlier: 3.675A pdb=" N ARG C 325 " --> pdb=" O ASN C 539 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 351 through 355 removed outlier: 4.048A pdb=" N ASN C 351 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 396 " --> pdb=" O ASN C 351 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 358 through 359 removed outlier: 7.238A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE8, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE9, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.029A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 709 through 725 removed outlier: 7.013A pdb=" N GLN C1068 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 6.990A 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: 6.916A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1044 through 1047 removed outlier: 6.762A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.636A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1117 through 1119 removed outlier: 3.679A pdb=" N CYS C1079 " --> pdb=" O VAL C1130 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2286 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: 5.38 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7846 1.34 - 1.46: 6299 1.46 - 1.58: 11157 1.58 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 25434 Sorted by residual: bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" C ASN A 79 " pdb=" N PRO A 80 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.81e+00 bond pdb=" C1 NAG C2003 " pdb=" O5 NAG C2003 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.90e+00 ... (remaining 25429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 33658 1.96 - 3.92: 838 3.92 - 5.87: 88 5.87 - 7.83: 14 7.83 - 9.79: 3 Bond angle restraints: 34601 Sorted by residual: angle pdb=" N THR A 615 " pdb=" CA THR A 615 " pdb=" C THR A 615 " ideal model delta sigma weight residual 114.75 107.70 7.05 1.26e+00 6.30e-01 3.13e+01 angle pdb=" N ARG A 992 " pdb=" CA ARG A 992 " pdb=" C ARG A 992 " ideal model delta sigma weight residual 113.18 106.58 6.60 1.33e+00 5.65e-01 2.46e+01 angle pdb=" C THR B 112 " pdb=" CA THR B 112 " pdb=" CB THR B 112 " ideal model delta sigma weight residual 115.79 109.93 5.86 1.19e+00 7.06e-01 2.42e+01 angle pdb=" C ASP B 567 " pdb=" CA ASP B 567 " pdb=" CB ASP B 567 " ideal model delta sigma weight residual 115.89 110.06 5.83 1.32e+00 5.74e-01 1.95e+01 angle pdb=" N ASN B1071 " pdb=" CA ASN B1071 " pdb=" C ASN B1071 " ideal model delta sigma weight residual 111.96 117.66 -5.70 1.41e+00 5.03e-01 1.63e+01 ... (remaining 34596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13176 17.94 - 35.88: 1081 35.88 - 53.83: 200 53.83 - 71.77: 42 71.77 - 89.71: 20 Dihedral angle restraints: 14519 sinusoidal: 5651 harmonic: 8868 Sorted by residual: dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual 93.00 179.82 -86.82 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual -86.00 -6.09 -79.91 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 298 " pdb=" CB CYS A 298 " ideal model delta sinusoidal sigma weight residual -86.00 -165.56 79.56 1 1.00e+01 1.00e-02 7.86e+01 ... (remaining 14516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 4136 0.163 - 0.326: 13 0.326 - 0.489: 7 0.489 - 0.651: 0 0.651 - 0.814: 2 Chirality restraints: 4158 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A1131 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN C1071 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C1 NAG B2003 " pdb=" ND2 ASN B 231 " pdb=" C2 NAG B2003 " pdb=" O5 NAG B2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 4155 not shown) Planarity restraints: 4422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1131 " 0.009 2.00e-02 2.50e+03 2.47e-02 7.63e+00 pdb=" CG ASN A1131 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A1131 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A1131 " -0.016 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1131 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" CG ASN A1131 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A1131 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A1131 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 162 " -0.020 2.00e-02 2.50e+03 1.82e-02 4.16e+00 pdb=" CG ASN C 162 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 162 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 162 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG C2003 " -0.020 2.00e-02 2.50e+03 ... (remaining 4419 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 387 2.66 - 3.22: 22689 3.22 - 3.78: 35275 3.78 - 4.34: 46341 4.34 - 4.90: 79165 Nonbonded interactions: 183857 Sorted by model distance: nonbonded pdb=" OH TYR B 89 " pdb=" OE2 GLU B 188 " model vdw 2.097 3.040 nonbonded pdb=" O ASP B 565 " pdb=" OG1 THR B 569 " model vdw 2.107 3.040 nonbonded pdb=" O THR A 390 " pdb=" OG1 THR A 520 " model vdw 2.133 3.040 nonbonded pdb=" OD1 ASP B 439 " pdb=" OH TYR B 448 " model vdw 2.134 3.040 nonbonded pdb=" O THR C 390 " pdb=" OG1 THR C 520 " model vdw 2.181 3.040 ... (remaining 183852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 139 or resid 152 through 208 or resid 214 throu \ gh 240 or resid 261 through 618 or resid 638 through 672 or resid 688 through 11 \ 43 or resid 2001 through 2005)) selection = (chain 'B' and (resid 27 through 139 or resid 152 through 208 or resid 214 throu \ gh 618 or resid 638 through 1143 or resid 2002 through 2006)) selection = (chain 'C' and (resid 27 through 824 or resid 842 through 2005)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.470 Find NCS groups from input model: 0.690 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: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.005 0.056 25548 Z= 0.217 Angle : 0.755 19.803 34906 Z= 0.377 Chirality : 0.053 0.814 4158 Planarity : 0.004 0.071 4376 Dihedral : 13.690 89.709 8698 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.10 % Favored : 93.40 % Rotamer: Outliers : 0.19 % Allowed : 0.34 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.15), residues: 2998 helix: 1.69 (0.22), residues: 622 sheet: -0.52 (0.20), residues: 654 loop : -1.72 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 234 TYR 0.017 0.001 TYR C1064 PHE 0.029 0.002 PHE B 344 TRP 0.028 0.002 TRP A 64 HIS 0.009 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.22 (25434) covalent geometry : angle 0.69530 / 0.36 (34601) SS BOND : bond 0.00385 / 0.22 ( 37) SS BOND : angle 1.39824 / 0.93 ( 74) hydrogen bonds : bond 0.15035 / 9.68 ( 821) hydrogen bonds : angle 5.89461 / 3.94 ( 2286) link_BETA1-4 : bond 0.00507 / 0.27 ( 31) link_BETA1-4 : angle 2.19726 / 1.67 ( 93) link_NAG-ASN : bond 0.00714 / 0.43 ( 46) link_NAG-ASN : angle 4.31591 / 2.75 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 173 time to evaluate : 0.725 Fit side-chains REVERT: A 188 GLU cc_start: 0.7744 (tt0) cc_final: 0.7516 (tt0) REVERT: A 226 LEU cc_start: 0.5090 (tp) cc_final: 0.4886 (tp) REVERT: A 883 TRP cc_start: 0.7891 (p90) cc_final: 0.6889 (p90) REVERT: B 357 ASN cc_start: 0.8281 (m-40) cc_final: 0.8076 (p0) REVERT: B 728 MET cc_start: 0.8402 (ptt) cc_final: 0.8072 (ptt) REVERT: B 1026 MET cc_start: 0.8125 (tmm) cc_final: 0.7798 (tpp) REVERT: B 1129 ILE cc_start: 0.8122 (pt) cc_final: 0.7683 (pt) REVERT: C 315 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8398 (p90) outliers start: 5 outliers final: 0 residues processed: 175 average time/residue: 0.1462 time to fit residues: 42.1774 Evaluate side-chains 122 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN B 950 ASN C 85 ASN C 911 ASN C 954 GLN C 966 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.195254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.131639 restraints weight = 42787.124| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 3.62 r_work: 0.3711 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25548 Z= 0.161 Angle : 0.667 17.821 34906 Z= 0.325 Chirality : 0.049 0.592 4158 Planarity : 0.004 0.045 4376 Dihedral : 4.257 40.579 3261 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.74 % Favored : 93.80 % Rotamer: Outliers : 0.49 % Allowed : 6.88 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 2998 helix: 1.72 (0.22), residues: 626 sheet: -0.43 (0.20), residues: 671 loop : -1.74 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1036 TYR 0.023 0.001 TYR C 167 PHE 0.028 0.002 PHE A1118 TRP 0.027 0.001 TRP B 64 HIS 0.007 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (25434) covalent geometry : angle 0.61828 / 0.31 (34601) SS BOND : bond 0.00580 / 0.29 ( 37) SS BOND : angle 1.49277 / 0.98 ( 74) hydrogen bonds : bond 0.05747 / 3.77 ( 821) hydrogen bonds : angle 5.01341 / 3.36 ( 2286) link_BETA1-4 : bond 0.00581 / 0.31 ( 31) link_BETA1-4 : angle 1.75879 / 1.36 ( 93) link_NAG-ASN : bond 0.00667 / 0.37 ( 46) link_NAG-ASN : angle 3.66060 / 2.33 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.709 Fit side-chains REVERT: A 188 GLU cc_start: 0.7770 (tt0) cc_final: 0.7563 (mt-10) REVERT: A 301 LYS cc_start: 0.8756 (tppt) cc_final: 0.8540 (tppp) REVERT: A 883 TRP cc_start: 0.8219 (p90) cc_final: 0.7267 (p90) REVERT: B 335 PHE cc_start: 0.8585 (m-80) cc_final: 0.8270 (m-80) REVERT: B 526 LYS cc_start: 0.8852 (pptt) cc_final: 0.8648 (mmtm) REVERT: B 529 ASN cc_start: 0.7964 (t0) cc_final: 0.7701 (t0) REVERT: B 1129 ILE cc_start: 0.8439 (pt) cc_final: 0.8094 (pt) REVERT: C 315 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8634 (p90) outliers start: 13 outliers final: 5 residues processed: 152 average time/residue: 0.1317 time to fit residues: 33.4622 Evaluate side-chains 129 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 243 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.0270 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 30.0000 chunk 105 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 217 optimal weight: 0.0070 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN B 655 ASN C 911 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.184446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.129921 restraints weight = 40848.701| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.83 r_work: 0.3766 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25548 Z= 0.108 Angle : 0.606 17.131 34906 Z= 0.292 Chirality : 0.047 0.551 4158 Planarity : 0.004 0.044 4376 Dihedral : 4.008 40.043 3261 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.20 % Favored : 94.33 % Rotamer: Outliers : 0.60 % Allowed : 8.80 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.16), residues: 2998 helix: 1.90 (0.22), residues: 633 sheet: -0.27 (0.20), residues: 681 loop : -1.65 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 234 TYR 0.015 0.001 TYR C 167 PHE 0.025 0.001 PHE B 84 TRP 0.021 0.001 TRP B 64 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (25434) covalent geometry : angle 0.55997 / 0.28 (34601) SS BOND : bond 0.00488 / 0.24 ( 37) SS BOND : angle 1.02898 / 0.69 ( 74) hydrogen bonds : bond 0.04651 / 3.04 ( 821) hydrogen bonds : angle 4.71566 / 3.18 ( 2286) link_BETA1-4 : bond 0.00572 / 0.29 ( 31) link_BETA1-4 : angle 1.73916 / 1.33 ( 93) link_NAG-ASN : bond 0.00646 / 0.37 ( 46) link_NAG-ASN : angle 3.43576 / 2.19 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.723 Fit side-chains REVERT: A 883 TRP cc_start: 0.8209 (p90) cc_final: 0.7271 (p90) REVERT: B 526 LYS cc_start: 0.8814 (pptt) cc_final: 0.8544 (mmtm) REVERT: B 529 ASN cc_start: 0.8006 (t0) cc_final: 0.7738 (t0) REVERT: B 728 MET cc_start: 0.8688 (ptt) cc_final: 0.8459 (ptm) REVERT: B 1129 ILE cc_start: 0.8286 (pt) cc_final: 0.7995 (pt) REVERT: C 170 GLN cc_start: 0.7828 (mm110) cc_final: 0.7430 (tp40) outliers start: 16 outliers final: 7 residues processed: 152 average time/residue: 0.1269 time to fit residues: 33.1091 Evaluate side-chains 138 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 0.0670 chunk 86 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 288 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 73 optimal weight: 0.0020 chunk 189 optimal weight: 0.6980 overall best weight: 0.3926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN C 911 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.185264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.130606 restraints weight = 40830.872| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 3.73 r_work: 0.3772 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25548 Z= 0.103 Angle : 0.589 16.420 34906 Z= 0.282 Chirality : 0.047 0.532 4158 Planarity : 0.004 0.045 4376 Dihedral : 3.773 23.949 3259 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.50 % Favored : 94.06 % Rotamer: Outliers : 1.17 % Allowed : 10.27 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.16), residues: 2998 helix: 1.90 (0.22), residues: 641 sheet: -0.13 (0.20), residues: 683 loop : -1.57 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 234 TYR 0.014 0.001 TYR A1064 PHE 0.024 0.001 PHE B 84 TRP 0.020 0.001 TRP A 64 HIS 0.004 0.000 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (25434) covalent geometry : angle 0.54538 / 0.27 (34601) SS BOND : bond 0.00307 / 0.17 ( 37) SS BOND : angle 0.99706 / 0.65 ( 74) hydrogen bonds : bond 0.04273 / 2.79 ( 821) hydrogen bonds : angle 4.52944 / 3.06 ( 2286) link_BETA1-4 : bond 0.00541 / 0.28 ( 31) link_BETA1-4 : angle 1.70634 / 1.30 ( 93) link_NAG-ASN : bond 0.00610 / 0.35 ( 46) link_NAG-ASN : angle 3.26249 / 2.08 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.728 Fit side-chains REVERT: A 737 MET cc_start: 0.8688 (tpp) cc_final: 0.8445 (mtp) REVERT: A 883 TRP cc_start: 0.8213 (p90) cc_final: 0.7280 (p90) REVERT: B 393 TYR cc_start: 0.7314 (m-10) cc_final: 0.7111 (m-80) REVERT: B 529 ASN cc_start: 0.7971 (t0) cc_final: 0.7725 (t0) REVERT: B 777 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 875 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8207 (tt) REVERT: B 1129 ILE cc_start: 0.8270 (pt) cc_final: 0.7994 (pt) REVERT: C 315 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8646 (p90) outliers start: 31 outliers final: 14 residues processed: 167 average time/residue: 0.1306 time to fit residues: 37.4687 Evaluate side-chains 143 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 26 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 245 optimal weight: 50.0000 chunk 83 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN A 989 GLN A1103 GLN B 204 HIS ** B 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1045 HIS B1061 HIS C 85 ASN C 268 GLN C 911 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.196142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.138880 restraints weight = 41372.442| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 4.20 r_work: 0.3501 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 25548 Z= 0.314 Angle : 0.786 15.923 34906 Z= 0.392 Chirality : 0.054 0.524 4158 Planarity : 0.005 0.053 4376 Dihedral : 4.620 30.596 3259 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.04 % Favored : 92.49 % Rotamer: Outliers : 1.65 % Allowed : 11.85 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.24 (0.15), residues: 2998 helix: 1.24 (0.21), residues: 634 sheet: -0.48 (0.19), residues: 681 loop : -1.87 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1036 TYR 0.026 0.002 TYR C 89 PHE 0.043 0.003 PHE A1118 TRP 0.024 0.002 TRP A 64 HIS 0.011 0.002 HIS A1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.31 (25434) covalent geometry : angle 0.74899 / 0.38 (34601) SS BOND : bond 0.00741 / 0.50 ( 37) SS BOND : angle 1.69643 / 1.06 ( 74) hydrogen bonds : bond 0.07582 / 4.92 ( 821) hydrogen bonds : angle 5.14614 / 3.45 ( 2286) link_BETA1-4 : bond 0.00438 / 0.24 ( 31) link_BETA1-4 : angle 1.81718 / 1.38 ( 93) link_NAG-ASN : bond 0.00557 / 0.35 ( 46) link_NAG-ASN : angle 3.42153 / 2.16 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.888 Fit side-chains REVERT: A 856 THR cc_start: 0.7931 (m) cc_final: 0.7600 (p) REVERT: A 883 TRP cc_start: 0.8187 (p90) cc_final: 0.7390 (p90) REVERT: A 998 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8743 (mm) REVERT: A 999 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8612 (mm-40) REVERT: B 167 TYR cc_start: 0.7360 (t80) cc_final: 0.6698 (t80) REVERT: B 332 LEU cc_start: 0.8981 (tp) cc_final: 0.8768 (tt) REVERT: B 393 TYR cc_start: 0.7495 (m-10) cc_final: 0.7293 (m-80) REVERT: B 526 LYS cc_start: 0.8787 (pptt) cc_final: 0.8521 (mmtm) REVERT: B 529 ASN cc_start: 0.8038 (t0) cc_final: 0.7662 (t0) REVERT: B 578 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8302 (p) REVERT: B 901 TYR cc_start: 0.8549 (m-10) cc_final: 0.8343 (m-80) REVERT: B 1129 ILE cc_start: 0.8704 (pt) cc_final: 0.8491 (pt) REVERT: C 759 GLN cc_start: 0.8411 (pm20) cc_final: 0.8133 (pm20) outliers start: 44 outliers final: 27 residues processed: 174 average time/residue: 0.1351 time to fit residues: 40.8704 Evaluate side-chains 154 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 119 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 296 optimal weight: 0.9990 chunk 252 optimal weight: 0.9980 chunk 230 optimal weight: 20.0000 chunk 175 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN C 85 ASN C 268 GLN C 911 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.193519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.136771 restraints weight = 40926.722| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 3.99 r_work: 0.3673 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25548 Z= 0.152 Angle : 0.642 14.587 34906 Z= 0.313 Chirality : 0.048 0.546 4158 Planarity : 0.004 0.049 4376 Dihedral : 4.254 27.953 3259 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.57 % Favored : 93.96 % Rotamer: Outliers : 1.09 % Allowed : 13.43 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.15), residues: 2998 helix: 1.60 (0.21), residues: 641 sheet: -0.50 (0.20), residues: 679 loop : -1.74 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 234 TYR 0.018 0.001 TYR A1064 PHE 0.027 0.001 PHE A1118 TRP 0.023 0.001 TRP A 64 HIS 0.005 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (25434) covalent geometry : angle 0.60773 / 0.31 (34601) SS BOND : bond 0.00383 / 0.22 ( 37) SS BOND : angle 1.24088 / 0.82 ( 74) hydrogen bonds : bond 0.05712 / 3.71 ( 821) hydrogen bonds : angle 4.77656 / 3.21 ( 2286) link_BETA1-4 : bond 0.00526 / 0.27 ( 31) link_BETA1-4 : angle 1.72868 / 1.33 ( 93) link_NAG-ASN : bond 0.00460 / 0.29 ( 46) link_NAG-ASN : angle 2.96301 / 1.95 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.832 Fit side-chains REVERT: A 856 THR cc_start: 0.7869 (m) cc_final: 0.7545 (p) REVERT: A 883 TRP cc_start: 0.8184 (p90) cc_final: 0.7412 (p90) REVERT: A 998 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8708 (mm) REVERT: A 999 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8547 (mm-40) REVERT: B 393 TYR cc_start: 0.7339 (m-10) cc_final: 0.7131 (m-80) REVERT: B 526 LYS cc_start: 0.8799 (pptt) cc_final: 0.8397 (mmtm) REVERT: B 529 ASN cc_start: 0.8102 (t0) cc_final: 0.7747 (t0) REVERT: B 1129 ILE cc_start: 0.8529 (pt) cc_final: 0.8325 (pt) REVERT: C 170 GLN cc_start: 0.7822 (mm110) cc_final: 0.7455 (tp40) REVERT: C 899 MET cc_start: 0.8070 (mmm) cc_final: 0.7836 (tpt) outliers start: 29 outliers final: 14 residues processed: 160 average time/residue: 0.1388 time to fit residues: 38.3445 Evaluate side-chains 141 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 279 optimal weight: 0.0870 chunk 246 optimal weight: 30.0000 chunk 33 optimal weight: 40.0000 chunk 72 optimal weight: 0.4980 chunk 280 optimal weight: 0.0570 chunk 290 optimal weight: 0.6980 chunk 300 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 252 optimal weight: 0.8980 chunk 32 optimal weight: 40.0000 chunk 247 optimal weight: 6.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN A1103 GLN B1008 GLN C 954 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.188716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.127296 restraints weight = 40434.812| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 4.09 r_work: 0.3726 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25548 Z= 0.109 Angle : 0.607 13.815 34906 Z= 0.292 Chirality : 0.047 0.524 4158 Planarity : 0.004 0.043 4376 Dihedral : 3.950 26.374 3259 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.27 % Favored : 94.23 % Rotamer: Outliers : 1.13 % Allowed : 13.76 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.16), residues: 2998 helix: 1.90 (0.22), residues: 633 sheet: -0.22 (0.19), residues: 689 loop : -1.62 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 234 TYR 0.023 0.001 TYR B 418 PHE 0.025 0.001 PHE B 84 TRP 0.025 0.001 TRP A 64 HIS 0.003 0.000 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (25434) covalent geometry : angle 0.57618 / 0.29 (34601) SS BOND : bond 0.00322 / 0.17 ( 37) SS BOND : angle 1.04717 / 0.68 ( 74) hydrogen bonds : bond 0.04603 / 3.00 ( 821) hydrogen bonds : angle 4.54426 / 3.06 ( 2286) link_BETA1-4 : bond 0.00554 / 0.29 ( 31) link_BETA1-4 : angle 1.70447 / 1.30 ( 93) link_NAG-ASN : bond 0.00476 / 0.30 ( 46) link_NAG-ASN : angle 2.74797 / 1.82 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 883 TRP cc_start: 0.8148 (p90) cc_final: 0.7400 (p90) REVERT: A 998 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8676 (mm) REVERT: A 999 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8457 (mm-40) REVERT: B 167 TYR cc_start: 0.6728 (t80) cc_final: 0.6375 (t80) REVERT: B 393 TYR cc_start: 0.7370 (m-10) cc_final: 0.7160 (m-80) REVERT: B 526 LYS cc_start: 0.8707 (pptt) cc_final: 0.8491 (mmtm) REVERT: B 529 ASN cc_start: 0.8078 (t0) cc_final: 0.7733 (t0) REVERT: C 170 GLN cc_start: 0.7904 (mm110) cc_final: 0.7567 (tp40) outliers start: 30 outliers final: 18 residues processed: 165 average time/residue: 0.1419 time to fit residues: 40.1427 Evaluate side-chains 152 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 270 optimal weight: 0.0270 chunk 95 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 chunk 269 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN B 910 GLN C 268 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.187680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.125941 restraints weight = 40387.380| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 4.09 r_work: 0.3683 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25548 Z= 0.149 Angle : 0.630 14.240 34906 Z= 0.306 Chirality : 0.048 0.512 4158 Planarity : 0.004 0.047 4376 Dihedral : 3.999 26.646 3259 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.54 % Favored : 93.96 % Rotamer: Outliers : 1.13 % Allowed : 13.92 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.16), residues: 2998 helix: 1.65 (0.22), residues: 645 sheet: -0.19 (0.20), residues: 674 loop : -1.65 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1036 TYR 0.016 0.001 TYR A1064 PHE 0.028 0.001 PHE A1118 TRP 0.026 0.001 TRP A 64 HIS 0.005 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (25434) covalent geometry : angle 0.59942 / 0.30 (34601) SS BOND : bond 0.00384 / 0.22 ( 37) SS BOND : angle 1.19346 / 0.75 ( 74) hydrogen bonds : bond 0.05256 / 3.42 ( 821) hydrogen bonds : angle 4.60059 / 3.09 ( 2286) link_BETA1-4 : bond 0.00500 / 0.26 ( 31) link_BETA1-4 : angle 1.70248 / 1.30 ( 93) link_NAG-ASN : bond 0.00432 / 0.27 ( 46) link_NAG-ASN : angle 2.76153 / 1.84 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.918 Fit side-chains REVERT: A 751 LEU cc_start: 0.9256 (tp) cc_final: 0.9017 (tp) REVERT: A 883 TRP cc_start: 0.8210 (p90) cc_final: 0.7431 (p90) REVERT: A 998 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8712 (mm) REVERT: A 999 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8561 (mm-40) REVERT: B 167 TYR cc_start: 0.6755 (t80) cc_final: 0.6411 (t80) REVERT: B 339 PHE cc_start: 0.8221 (m-80) cc_final: 0.8018 (m-80) REVERT: B 393 TYR cc_start: 0.7361 (m-10) cc_final: 0.7150 (m-80) REVERT: B 526 LYS cc_start: 0.8674 (pptt) cc_final: 0.8414 (mppt) REVERT: B 529 ASN cc_start: 0.8070 (t0) cc_final: 0.7714 (t0) REVERT: C 170 GLN cc_start: 0.7848 (mm110) cc_final: 0.7512 (tp40) outliers start: 30 outliers final: 24 residues processed: 161 average time/residue: 0.1369 time to fit residues: 38.1698 Evaluate side-chains 153 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 910 GLN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 256 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 276 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 48 optimal weight: 0.0670 chunk 251 optimal weight: 0.9980 chunk 245 optimal weight: 30.0000 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.200324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.130337 restraints weight = 41855.817| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 3.58 r_work: 0.3684 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25548 Z= 0.115 Angle : 0.613 13.724 34906 Z= 0.296 Chirality : 0.047 0.519 4158 Planarity : 0.004 0.049 4376 Dihedral : 3.899 25.996 3259 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.24 % Favored : 94.30 % Rotamer: Outliers : 0.98 % Allowed : 14.40 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2998 helix: 1.82 (0.22), residues: 639 sheet: -0.12 (0.20), residues: 659 loop : -1.59 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 234 TYR 0.015 0.001 TYR A1064 PHE 0.025 0.001 PHE B 84 TRP 0.027 0.001 TRP A 64 HIS 0.003 0.000 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (25434) covalent geometry : angle 0.58360 / 0.29 (34601) SS BOND : bond 0.00304 / 0.16 ( 37) SS BOND : angle 1.09117 / 0.69 ( 74) hydrogen bonds : bond 0.04692 / 3.06 ( 821) hydrogen bonds : angle 4.49838 / 3.02 ( 2286) link_BETA1-4 : bond 0.00537 / 0.28 ( 31) link_BETA1-4 : angle 1.68834 / 1.29 ( 93) link_NAG-ASN : bond 0.00461 / 0.29 ( 46) link_NAG-ASN : angle 2.68878 / 1.79 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 114 SER cc_start: 0.6760 (OUTLIER) cc_final: 0.6458 (t) REVERT: A 883 TRP cc_start: 0.8178 (p90) cc_final: 0.7414 (p90) REVERT: A 998 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8697 (mm) REVERT: A 999 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8545 (mm-40) REVERT: B 167 TYR cc_start: 0.6718 (t80) cc_final: 0.6381 (t80) REVERT: B 393 TYR cc_start: 0.7302 (m-10) cc_final: 0.7078 (m-80) REVERT: B 526 LYS cc_start: 0.8702 (pptt) cc_final: 0.8476 (mppt) REVERT: C 170 GLN cc_start: 0.7895 (mm110) cc_final: 0.7576 (tp40) REVERT: C 186 LEU cc_start: 0.8339 (tp) cc_final: 0.7863 (pp) outliers start: 26 outliers final: 20 residues processed: 157 average time/residue: 0.1349 time to fit residues: 36.6152 Evaluate side-chains 149 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 264 optimal weight: 0.0170 chunk 210 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 44 optimal weight: 0.0870 chunk 193 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 654 ASN ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1103 GLN B 541 ASN B 910 GLN C 999 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.188418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.126482 restraints weight = 40553.107| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 4.10 r_work: 0.3682 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25548 Z= 0.157 Angle : 0.640 14.059 34906 Z= 0.312 Chirality : 0.048 0.511 4158 Planarity : 0.004 0.047 4376 Dihedral : 4.013 26.823 3259 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.87 % Favored : 93.66 % Rotamer: Outliers : 1.05 % Allowed : 14.44 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 2998 helix: 1.67 (0.22), residues: 634 sheet: -0.19 (0.20), residues: 667 loop : -1.61 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1036 TYR 0.017 0.001 TYR A1064 PHE 0.027 0.001 PHE A1118 TRP 0.029 0.001 TRP A 64 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (25434) covalent geometry : angle 0.61092 / 0.31 (34601) SS BOND : bond 0.00392 / 0.23 ( 37) SS BOND : angle 1.21580 / 0.76 ( 74) hydrogen bonds : bond 0.05342 / 3.48 ( 821) hydrogen bonds : angle 4.59474 / 3.08 ( 2286) link_BETA1-4 : bond 0.00497 / 0.26 ( 31) link_BETA1-4 : angle 1.69268 / 1.29 ( 93) link_NAG-ASN : bond 0.00422 / 0.27 ( 46) link_NAG-ASN : angle 2.72149 / 1.81 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.815 Fit side-chains REVERT: A 883 TRP cc_start: 0.8218 (p90) cc_final: 0.7431 (p90) REVERT: A 998 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8699 (mm) REVERT: A 999 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8584 (mm-40) REVERT: B 167 TYR cc_start: 0.6764 (t80) cc_final: 0.6433 (t80) REVERT: B 335 PHE cc_start: 0.8613 (m-80) cc_final: 0.8283 (m-80) REVERT: B 393 TYR cc_start: 0.7375 (m-10) cc_final: 0.7171 (m-80) REVERT: B 526 LYS cc_start: 0.8683 (pptt) cc_final: 0.8461 (mppt) REVERT: C 186 LEU cc_start: 0.8342 (tp) cc_final: 0.8006 (pp) outliers start: 28 outliers final: 23 residues processed: 154 average time/residue: 0.1293 time to fit residues: 34.6592 Evaluate side-chains 152 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 910 GLN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 13 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 103 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 289 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN A 954 GLN A1103 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.188171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.126362 restraints weight = 40335.771| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 4.12 r_work: 0.3684 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25548 Z= 0.135 Angle : 0.635 13.855 34906 Z= 0.308 Chirality : 0.048 0.515 4158 Planarity : 0.004 0.073 4376 Dihedral : 3.979 26.589 3259 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.54 % Favored : 94.03 % Rotamer: Outliers : 0.98 % Allowed : 14.89 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 2998 helix: 1.68 (0.22), residues: 641 sheet: -0.16 (0.20), residues: 666 loop : -1.62 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 325 TYR 0.016 0.001 TYR A1064 PHE 0.025 0.001 PHE B 84 TRP 0.029 0.001 TRP A 64 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (25434) covalent geometry : angle 0.60444 / 0.30 (34601) SS BOND : bond 0.00341 / 0.19 ( 37) SS BOND : angle 1.47152 / 0.93 ( 74) hydrogen bonds : bond 0.05071 / 3.30 ( 821) hydrogen bonds : angle 4.58144 / 3.08 ( 2286) link_BETA1-4 : bond 0.00522 / 0.27 ( 31) link_BETA1-4 : angle 1.68737 / 1.29 ( 93) link_NAG-ASN : bond 0.00439 / 0.28 ( 46) link_NAG-ASN : angle 2.69093 / 1.79 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5549.17 seconds wall clock time: 95 minutes 55.12 seconds (5755.12 seconds total)