Starting phenix.real_space_refine on Mon Sep 14 00:41:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zgi_11207/09_2026/6zgi_11207.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zgi_11207/09_2026/6zgi_11207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6zgi_11207/09_2026/6zgi_11207.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zgi_11207/09_2026/6zgi_11207.cif" model { file = "/net/cci-nas-00/data/ceres_data/6zgi_11207/09_2026/6zgi_11207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zgi_11207/09_2026/6zgi_11207.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zgi_11207/09_2026/6zgi_11207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zgi_11207/09_2026/6zgi_11207.map" } resolution = 2.9 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= 0.003 sd= 0.086 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 120 5.16 5 C 17097 2.51 5 N 4392 2.21 5 O 5292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 190 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26901 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 Chain: "B" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 Chain: "C" Number of atoms: 8603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1098, 8587 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 4 bond proxies already assigned to first conformer: 8768 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 11.77, per 1000 atoms: 0.44 Number of scatterers: 26901 At special positions: 0 Unit cell: (154.154, 144.452, 178.948, 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 120 16.00 O 5292 8.00 N 4392 7.00 C 17097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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-ASN " NAG A1305 " - " ASN A 149 " " NAG A1310 " - " ASN A 282 " " NAG A1311 " - " ASN A 331 " " NAG A1312 " - " ASN A 343 " " NAG A1315 " - " ASN A 657 " " NAG A1316 " - " ASN A 709 " " NAG A1321 " - " ASN A1074 " " NAG A1324 " - " ASN A1134 " " NAG B1305 " - " ASN B 149 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 331 " " NAG B1312 " - " ASN B 343 " " NAG B1315 " - " ASN B 657 " " NAG B1316 " - " ASN B 709 " " NAG B1321 " - " ASN B1074 " " NAG B1324 " - " ASN B1134 " " NAG C1305 " - " ASN C 149 " " NAG C1310 " - " ASN C 282 " " NAG C1311 " - " ASN C 331 " " NAG C1312 " - " ASN C 343 " " NAG C1315 " - " ASN C 657 " " NAG C1316 " - " ASN C 709 " " NAG C1321 " - " ASN C1074 " " NAG C1324 " - " ASN C1134 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A 61 " " NAG M 1 " - " ASN B 17 " " NAG N 1 " - " ASN B 122 " " NAG O 1 " - " ASN B 165 " " NAG P 1 " - " ASN B 234 " " NAG Q 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B 61 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 801 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN C 61 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 2.4 seconds 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6168 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 42 sheets defined 23.8% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.645A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.676A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.048A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.713A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.066A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.278A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.530A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.645A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.676A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.048A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.713A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.065A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.278A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.530A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.645A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.676A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.048A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.713A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.066A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.278A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.530A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.199A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.003A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.832A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 163 removed outlier: 6.721A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.361A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.122A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.137A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.581A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.079A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.540A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.200A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.004A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.832A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 151 through 163 removed outlier: 6.721A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.749A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.361A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.122A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.137A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.581A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.079A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.540A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.199A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.003A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.832A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 151 through 163 removed outlier: 6.720A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.749A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.361A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.122A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.137A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.581A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.080A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.540A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 1044 hydrogen bonds defined for protein. 2847 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: 7.74 Time building geometry restraints manager: 3.61 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: 8492 1.34 - 1.46: 6913 1.46 - 1.59: 11955 1.59 - 1.71: 0 1.71 - 1.84: 150 Bond restraints: 27510 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.20e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 27505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 35332 1.63 - 3.26: 1845 3.26 - 4.88: 218 4.88 - 6.51: 30 6.51 - 8.14: 12 Bond angle restraints: 37437 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.06 -3.36 1.22e+00 6.72e-01 7.59e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.05 -3.35 1.22e+00 6.72e-01 7.53e+00 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.04 -3.34 1.22e+00 6.72e-01 7.51e+00 angle pdb=" C THR A 76 " pdb=" N LYS A 77 " pdb=" CA LYS A 77 " ideal model delta sigma weight residual 121.54 126.55 -5.01 1.91e+00 2.74e-01 6.88e+00 angle pdb=" C THR C 76 " pdb=" N LYS C 77 " pdb=" CA LYS C 77 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.81e+00 ... (remaining 37432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 14710 17.57 - 35.14: 833 35.14 - 52.71: 132 52.71 - 70.28: 60 70.28 - 87.84: 27 Dihedral angle restraints: 15762 sinusoidal: 6156 harmonic: 9606 Sorted by residual: dihedral pdb=" CA HIS B 66 " pdb=" C HIS B 66 " pdb=" N ALA B 67 " pdb=" CA ALA B 67 " ideal model delta harmonic sigma weight residual 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA HIS A 66 " pdb=" C HIS A 66 " pdb=" N ALA A 67 " pdb=" CA ALA A 67 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA HIS C 66 " pdb=" C HIS C 66 " pdb=" N ALA C 67 " pdb=" CA ALA C 67 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 15759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2923 0.050 - 0.100: 1200 0.100 - 0.150: 310 0.150 - 0.199: 4 0.199 - 0.249: 6 Chirality restraints: 4443 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 149 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 149 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 4440 not shown) Planarity restraints: 4803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 60 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.76e+00 pdb=" C SER C 60 " 0.054 2.00e-02 2.50e+03 pdb=" O SER C 60 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN C 61 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 60 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.71e+00 pdb=" C SER B 60 " -0.054 2.00e-02 2.50e+03 pdb=" O SER B 60 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN B 61 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 60 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.61e+00 pdb=" C SER A 60 " 0.054 2.00e-02 2.50e+03 pdb=" O SER A 60 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN A 61 " -0.018 2.00e-02 2.50e+03 ... (remaining 4800 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 8155 2.83 - 3.35: 22014 3.35 - 3.87: 42041 3.87 - 4.38: 49229 4.38 - 4.90: 86430 Nonbonded interactions: 207869 Sorted by model distance: nonbonded pdb=" OE2 GLU C 96 " pdb=" N ILE C 101 " model vdw 2.317 3.120 nonbonded pdb=" OE2 GLU A 96 " pdb=" N ILE A 101 " model vdw 2.317 3.120 nonbonded pdb=" OE2 GLU B 96 " pdb=" N ILE B 101 " model vdw 2.318 3.120 nonbonded pdb=" OE1 GLN A 787 " pdb=" ND2 ASN C 703 " model vdw 2.334 3.120 nonbonded pdb=" ND2 ASN B 703 " pdb=" OE1 GLN C 787 " model vdw 2.334 3.120 ... (remaining 207864 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: 0.07 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1324)) selection = (chain 'B' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1324)) selection = (chain 'C' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1324)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 6.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 36.990 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 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:8.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 : 0.007 0.044 27633 Z= 0.283 Angle : 0.830 10.975 37761 Z= 0.443 Chirality : 0.054 0.249 4443 Planarity : 0.005 0.035 4752 Dihedral : 12.592 87.844 9459 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 0.73 % Allowed : 3.17 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3270 helix: 1.01 (0.20), residues: 702 sheet: 0.46 (0.18), residues: 786 loop : -1.91 (0.12), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1039 TYR 0.029 0.003 TYR B 756 PHE 0.028 0.003 PHE C 55 TRP 0.014 0.002 TRP C 886 HIS 0.007 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.28 (27510) covalent geometry : angle 0.80080 / 0.44 (37437) SS BOND : bond 0.00498 / 0.34 ( 45) SS BOND : angle 1.90114 / 1.34 ( 90) hydrogen bonds : bond 0.12145 / 7.99 ( 1044) hydrogen bonds : angle 6.31169 / 4.50 ( 2847) link_BETA1-4 : bond 0.00451 / 0.29 ( 27) link_BETA1-4 : angle 1.71011 / 1.23 ( 81) link_NAG-ASN : bond 0.00385 / 0.20 ( 51) link_NAG-ASN : angle 3.05623 / 2.06 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 390 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: 0.7145 (m90) cc_final: 0.6797 (m-70) REVERT: A 428 ASP cc_start: 0.7203 (p0) cc_final: 0.6819 (p0) REVERT: A 878 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8142 (mp) REVERT: A 1038 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8152 (mmtp) REVERT: B 146 HIS cc_start: 0.7081 (m90) cc_final: 0.6865 (m-70) REVERT: B 319 ARG cc_start: 0.7722 (mtt-85) cc_final: 0.7450 (mmt180) REVERT: B 321 GLN cc_start: 0.8206 (mm110) cc_final: 0.7835 (mm-40) REVERT: B 389 ASP cc_start: 0.7748 (m-30) cc_final: 0.7532 (m-30) REVERT: B 474 GLN cc_start: 0.8128 (tt0) cc_final: 0.7788 (tt0) REVERT: B 878 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8297 (mp) REVERT: B 947 LYS cc_start: 0.8146 (mttm) cc_final: 0.7362 (mptt) REVERT: B 1038 LYS cc_start: 0.8510 (mtpp) cc_final: 0.8192 (mmtp) REVERT: B 1101 HIS cc_start: 0.7509 (m90) cc_final: 0.7182 (m90) REVERT: C 319 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.7357 (mmt180) REVERT: C 428 ASP cc_start: 0.7217 (p0) cc_final: 0.6919 (p0) REVERT: C 462 LYS cc_start: 0.8647 (mmtp) cc_final: 0.7810 (mtmt) REVERT: C 878 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8132 (mp) REVERT: C 1017 GLU cc_start: 0.7366 (tt0) cc_final: 0.7144 (tt0) REVERT: C 1038 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8200 (mmtp) outliers start: 21 outliers final: 3 residues processed: 408 average time/residue: 0.7412 time to fit residues: 348.3203 Evaluate side-chains 207 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 201 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 146 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 239 GLN A 245 HIS A 314 GLN A 501 ASN A 540 ASN A 580 GLN A 607 GLN A 613 GLN A 641 ASN A 658 ASN A 675 GLN A 703 ASN A 751 ASN A 804 GLN A 925 ASN A 954 GLN A1023 ASN A1036 GLN A1064 HIS B 99 ASN B 207 HIS B 239 GLN B 245 HIS B 314 GLN B 440 ASN B 501 ASN B 540 ASN B 563 GLN B 580 GLN B 613 GLN B 641 ASN B 658 ASN B 675 GLN B 703 ASN B 751 ASN B 925 ASN B 954 GLN B1023 ASN B1036 GLN B1064 HIS C 66 HIS C 99 ASN C 146 HIS C 207 HIS C 239 GLN C 314 GLN C 501 ASN C 540 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 606 ASN C 613 GLN C 641 ASN C 658 ASN C 675 GLN C 703 ASN C 710 ASN C 751 ASN C 779 GLN C 925 ASN C 954 GLN C1010 GLN C1023 ASN C1036 GLN C1064 HIS Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.095554 restraints weight = 43085.707| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.72 r_work: 0.2948 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27633 Z= 0.150 Angle : 0.663 13.855 37761 Z= 0.336 Chirality : 0.047 0.296 4443 Planarity : 0.004 0.039 4752 Dihedral : 5.475 59.379 3566 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 1.77 % Allowed : 8.46 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3270 helix: 1.33 (0.20), residues: 708 sheet: 0.57 (0.18), residues: 792 loop : -1.89 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 567 TYR 0.020 0.002 TYR A 756 PHE 0.018 0.002 PHE A 55 TRP 0.011 0.001 TRP C 152 HIS 0.013 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (27510) covalent geometry : angle 0.61835 / 0.33 (37437) SS BOND : bond 0.00326 / 0.21 ( 45) SS BOND : angle 1.52505 / 1.09 ( 90) hydrogen bonds : bond 0.06675 / 4.51 ( 1044) hydrogen bonds : angle 5.45917 / 3.78 ( 2847) link_BETA1-4 : bond 0.00443 / 0.28 ( 27) link_BETA1-4 : angle 1.09215 / 0.76 ( 81) link_NAG-ASN : bond 0.00466 / 0.24 ( 51) link_NAG-ASN : angle 3.57671 / 2.19 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7610 (ttt-90) REVERT: A 428 ASP cc_start: 0.7811 (p0) cc_final: 0.7436 (p0) REVERT: A 462 LYS cc_start: 0.8863 (mmtp) cc_final: 0.8601 (mmtm) REVERT: A 804 GLN cc_start: 0.8208 (mm110) cc_final: 0.7987 (mt0) REVERT: A 820 ASP cc_start: 0.8325 (m-30) cc_final: 0.7963 (m-30) REVERT: A 1029 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8808 (tpp) REVERT: A 1038 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8267 (mmtp) REVERT: B 319 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7717 (mmt180) REVERT: B 474 GLN cc_start: 0.8504 (tt0) cc_final: 0.8213 (tt0) REVERT: B 567 ARG cc_start: 0.8573 (mtt90) cc_final: 0.8367 (mtt-85) REVERT: B 571 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8076 (t70) REVERT: B 947 LYS cc_start: 0.8370 (mttm) cc_final: 0.7468 (mptt) REVERT: B 1038 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8332 (mmtp) REVERT: B 1101 HIS cc_start: 0.8119 (m90) cc_final: 0.7703 (m90) REVERT: C 88 ASP cc_start: 0.8204 (t70) cc_final: 0.7900 (t70) REVERT: C 96 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7605 (mt-10) REVERT: C 202 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8713 (mttp) REVERT: C 319 ARG cc_start: 0.8039 (mtt-85) cc_final: 0.7635 (mmt180) REVERT: C 389 ASP cc_start: 0.8106 (m-30) cc_final: 0.7839 (m-30) REVERT: C 428 ASP cc_start: 0.7864 (p0) cc_final: 0.7551 (p0) REVERT: C 462 LYS cc_start: 0.8787 (mmtp) cc_final: 0.7837 (mtmt) REVERT: C 525 CYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6782 (m) REVERT: C 537 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7886 (mtpp) REVERT: C 1017 GLU cc_start: 0.8216 (tt0) cc_final: 0.8005 (tt0) REVERT: C 1038 LYS cc_start: 0.8787 (mtpp) cc_final: 0.8298 (mptt) REVERT: C 1113 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7557 (mm-40) outliers start: 51 outliers final: 23 residues processed: 240 average time/residue: 0.7296 time to fit residues: 203.0926 Evaluate side-chains 207 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 110 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 304 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 257 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 607 GLN B 563 GLN B 606 ASN B 644 GLN C 188 ASN C 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 710 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.095777 restraints weight = 59647.576| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.38 r_work: 0.2917 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 27633 Z= 0.152 Angle : 0.624 10.153 37761 Z= 0.318 Chirality : 0.047 0.293 4443 Planarity : 0.004 0.041 4752 Dihedral : 5.144 55.370 3562 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.71 % Rotamer: Outliers : 1.77 % Allowed : 8.84 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3270 helix: 1.33 (0.20), residues: 711 sheet: 0.78 (0.19), residues: 777 loop : -1.83 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 567 TYR 0.019 0.002 TYR B 756 PHE 0.016 0.002 PHE A 55 TRP 0.012 0.001 TRP C 152 HIS 0.009 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (27510) covalent geometry : angle 0.59291 / 0.31 (37437) SS BOND : bond 0.00398 / 0.22 ( 45) SS BOND : angle 1.45786 / 1.04 ( 90) hydrogen bonds : bond 0.06503 / 4.40 ( 1044) hydrogen bonds : angle 5.28840 / 3.64 ( 2847) link_BETA1-4 : bond 0.00422 / 0.27 ( 27) link_BETA1-4 : angle 1.08446 / 0.77 ( 81) link_NAG-ASN : bond 0.00435 / 0.22 ( 51) link_NAG-ASN : angle 2.84791 / 1.83 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7694 (p0) cc_final: 0.7307 (p0) REVERT: A 462 LYS cc_start: 0.8803 (mmtp) cc_final: 0.8520 (mmtm) REVERT: A 820 ASP cc_start: 0.8122 (m-30) cc_final: 0.7722 (m-30) REVERT: A 1029 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8758 (tpp) REVERT: A 1038 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8199 (mmtp) REVERT: B 214 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7704 (ptm-80) REVERT: B 319 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.7657 (mmt180) REVERT: B 321 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7800 (mm-40) REVERT: B 474 GLN cc_start: 0.8403 (tt0) cc_final: 0.8155 (tt0) REVERT: B 567 ARG cc_start: 0.8417 (mtt90) cc_final: 0.8178 (mtt-85) REVERT: B 582 LEU cc_start: 0.8640 (mp) cc_final: 0.8426 (mm) REVERT: B 675 GLN cc_start: 0.7396 (mm-40) cc_final: 0.7128 (mt0) REVERT: B 740 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8663 (ttm) REVERT: B 964 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7577 (mttt) REVERT: B 1038 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8244 (mmtp) REVERT: B 1101 HIS cc_start: 0.8068 (m90) cc_final: 0.7653 (m90) REVERT: C 68 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7433 (pp) REVERT: C 146 HIS cc_start: 0.7140 (m-70) cc_final: 0.6919 (m-70) REVERT: C 153 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7324 (mtp) REVERT: C 202 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8634 (mttp) REVERT: C 428 ASP cc_start: 0.7763 (p0) cc_final: 0.7418 (p0) REVERT: C 525 CYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6979 (m) REVERT: C 537 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7785 (mtpp) REVERT: C 567 ARG cc_start: 0.8460 (mtt-85) cc_final: 0.8107 (mtt90) REVERT: C 1017 GLU cc_start: 0.7904 (tt0) cc_final: 0.7677 (tt0) REVERT: C 1038 LYS cc_start: 0.8712 (mtpp) cc_final: 0.8246 (mptt) REVERT: C 1113 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7544 (mm-40) outliers start: 51 outliers final: 24 residues processed: 222 average time/residue: 0.7045 time to fit residues: 182.6404 Evaluate side-chains 204 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 120 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 262 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 164 ASN B 188 ASN B 563 GLN B 606 ASN B 644 GLN B 784 GLN C 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.094817 restraints weight = 54352.992| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.90 r_work: 0.2901 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 27633 Z= 0.185 Angle : 0.653 9.262 37761 Z= 0.334 Chirality : 0.048 0.322 4443 Planarity : 0.005 0.045 4752 Dihedral : 5.301 51.707 3562 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 2.09 % Allowed : 9.53 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3270 helix: 1.19 (0.20), residues: 711 sheet: 0.74 (0.19), residues: 777 loop : -1.86 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 357 TYR 0.022 0.002 TYR B 756 PHE 0.018 0.002 PHE B1121 TRP 0.018 0.002 TRP A 152 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (27510) covalent geometry : angle 0.62512 / 0.33 (37437) SS BOND : bond 0.00476 / 0.27 ( 45) SS BOND : angle 1.59528 / 1.12 ( 90) hydrogen bonds : bond 0.07064 / 4.78 ( 1044) hydrogen bonds : angle 5.34176 / 3.67 ( 2847) link_BETA1-4 : bond 0.00428 / 0.28 ( 27) link_BETA1-4 : angle 1.00376 / 0.72 ( 81) link_NAG-ASN : bond 0.00386 / 0.19 ( 51) link_NAG-ASN : angle 2.73125 / 1.77 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 183 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7764 (ttt-90) REVERT: A 428 ASP cc_start: 0.7933 (p0) cc_final: 0.7554 (p0) REVERT: A 820 ASP cc_start: 0.8237 (m-30) cc_final: 0.7863 (m-30) REVERT: A 1038 LYS cc_start: 0.8952 (mtpp) cc_final: 0.8278 (mmtp) REVERT: A 1039 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7207 (ptm160) REVERT: B 214 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7867 (ptm-80) REVERT: B 319 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7745 (mtt180) REVERT: B 474 GLN cc_start: 0.8441 (tt0) cc_final: 0.8149 (tt0) REVERT: B 567 ARG cc_start: 0.8610 (mtt90) cc_final: 0.8401 (mtt-85) REVERT: B 582 LEU cc_start: 0.8686 (mp) cc_final: 0.8460 (mm) REVERT: B 675 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7248 (mt0) REVERT: B 740 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8942 (ttm) REVERT: B 814 LYS cc_start: 0.7036 (mttt) cc_final: 0.6708 (ptmt) REVERT: B 1038 LYS cc_start: 0.8887 (mtpp) cc_final: 0.8321 (mmtp) REVERT: B 1101 HIS cc_start: 0.8216 (m90) cc_final: 0.7804 (m90) REVERT: C 138 ASP cc_start: 0.7970 (t0) cc_final: 0.7624 (t0) REVERT: C 146 HIS cc_start: 0.7220 (m-70) cc_final: 0.6971 (m-70) REVERT: C 182 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6232 (mptt) REVERT: C 202 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8707 (mttp) REVERT: C 309 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7912 (mp0) REVERT: C 428 ASP cc_start: 0.7971 (p0) cc_final: 0.7633 (p0) REVERT: C 474 GLN cc_start: 0.8646 (tt0) cc_final: 0.8418 (tt0) REVERT: C 537 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7910 (mtpp) REVERT: C 567 ARG cc_start: 0.8719 (mtt-85) cc_final: 0.8340 (mtt90) REVERT: C 1017 GLU cc_start: 0.8221 (tt0) cc_final: 0.8010 (tt0) REVERT: C 1038 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8355 (mptt) REVERT: C 1113 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7707 (mm-40) outliers start: 60 outliers final: 35 residues processed: 224 average time/residue: 0.6998 time to fit residues: 182.3481 Evaluate side-chains 218 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 221 optimal weight: 0.8980 chunk 313 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 chunk 240 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 644 GLN B 935 GLN B1054 GLN C 99 ASN C 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.092813 restraints weight = 66220.818| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.27 r_work: 0.2864 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 27633 Z= 0.163 Angle : 0.618 9.110 37761 Z= 0.317 Chirality : 0.047 0.312 4443 Planarity : 0.004 0.046 4752 Dihedral : 5.199 56.264 3562 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.95 % Allowed : 10.16 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.14), residues: 3270 helix: 1.28 (0.20), residues: 711 sheet: 0.75 (0.19), residues: 777 loop : -1.85 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 357 TYR 0.020 0.002 TYR B 756 PHE 0.016 0.002 PHE B1121 TRP 0.013 0.001 TRP C 436 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 (27510) covalent geometry : angle 0.59128 / 0.31 (37437) SS BOND : bond 0.00400 / 0.24 ( 45) SS BOND : angle 1.42266 / 1.00 ( 90) hydrogen bonds : bond 0.06614 / 4.48 ( 1044) hydrogen bonds : angle 5.26246 / 3.61 ( 2847) link_BETA1-4 : bond 0.00428 / 0.28 ( 27) link_BETA1-4 : angle 1.01976 / 0.73 ( 81) link_NAG-ASN : bond 0.00386 / 0.19 ( 51) link_NAG-ASN : angle 2.64834 / 1.73 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7779 (p0) cc_final: 0.7356 (p0) REVERT: A 820 ASP cc_start: 0.8051 (m-30) cc_final: 0.7641 (m-30) REVERT: A 1038 LYS cc_start: 0.8882 (mtpp) cc_final: 0.8147 (mmtp) REVERT: A 1039 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7042 (ptm160) REVERT: B 214 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7843 (ptm-80) REVERT: B 319 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7758 (mtt180) REVERT: B 321 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7810 (mm-40) REVERT: B 474 GLN cc_start: 0.8222 (tt0) cc_final: 0.7978 (tt0) REVERT: B 567 ARG cc_start: 0.8424 (mtt90) cc_final: 0.8182 (mtt-85) REVERT: B 582 LEU cc_start: 0.8584 (mp) cc_final: 0.8342 (mm) REVERT: B 675 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7211 (mt0) REVERT: B 814 LYS cc_start: 0.6897 (mttt) cc_final: 0.6663 (ptmt) REVERT: B 1038 LYS cc_start: 0.8828 (mtpp) cc_final: 0.8198 (mmtp) REVERT: B 1039 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7970 (ptm160) REVERT: B 1101 HIS cc_start: 0.8072 (m90) cc_final: 0.7638 (m90) REVERT: C 138 ASP cc_start: 0.7881 (t0) cc_final: 0.7572 (t0) REVERT: C 182 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6155 (mptt) REVERT: C 202 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8593 (mttp) REVERT: C 213 VAL cc_start: 0.7970 (t) cc_final: 0.7567 (m) REVERT: C 428 ASP cc_start: 0.7858 (p0) cc_final: 0.7479 (p0) REVERT: C 474 GLN cc_start: 0.8490 (tt0) cc_final: 0.8216 (tt0) REVERT: C 537 LYS cc_start: 0.7852 (mtpt) cc_final: 0.7576 (mtpp) REVERT: C 567 ARG cc_start: 0.8494 (mtt-85) cc_final: 0.8126 (mtt90) REVERT: C 1038 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8185 (mptt) REVERT: C 1113 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7602 (mm-40) outliers start: 56 outliers final: 33 residues processed: 224 average time/residue: 0.6938 time to fit residues: 180.1410 Evaluate side-chains 214 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 157 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 242 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 224 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 563 GLN B 644 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.096183 restraints weight = 54873.898| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.98 r_work: 0.2872 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27633 Z= 0.148 Angle : 0.597 9.437 37761 Z= 0.306 Chirality : 0.046 0.311 4443 Planarity : 0.004 0.046 4752 Dihedral : 5.102 56.438 3562 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.70 % Allowed : 10.93 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3270 helix: 1.36 (0.20), residues: 711 sheet: 0.73 (0.19), residues: 777 loop : -1.82 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 357 TYR 0.020 0.002 TYR B 756 PHE 0.014 0.002 PHE B1121 TRP 0.014 0.001 TRP C 152 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (27510) covalent geometry : angle 0.57094 / 0.30 (37437) SS BOND : bond 0.00375 / 0.22 ( 45) SS BOND : angle 1.33749 / 0.93 ( 90) hydrogen bonds : bond 0.06293 / 4.27 ( 1044) hydrogen bonds : angle 5.20520 / 3.57 ( 2847) link_BETA1-4 : bond 0.00442 / 0.29 ( 27) link_BETA1-4 : angle 1.01636 / 0.73 ( 81) link_NAG-ASN : bond 0.00398 / 0.20 ( 51) link_NAG-ASN : angle 2.58664 / 1.69 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7835 (p0) cc_final: 0.7413 (p0) REVERT: A 820 ASP cc_start: 0.8065 (m-30) cc_final: 0.7666 (m-30) REVERT: A 964 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7808 (mttt) REVERT: A 1038 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8158 (mmtp) REVERT: A 1039 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.6988 (ptm160) REVERT: B 319 ARG cc_start: 0.8105 (mtt-85) cc_final: 0.7772 (mtt180) REVERT: B 321 GLN cc_start: 0.8423 (mm-40) cc_final: 0.7845 (mm-40) REVERT: B 474 GLN cc_start: 0.8216 (tt0) cc_final: 0.8001 (tt0) REVERT: B 567 ARG cc_start: 0.8464 (mtt90) cc_final: 0.8234 (mtt-85) REVERT: B 582 LEU cc_start: 0.8604 (mp) cc_final: 0.8383 (mm) REVERT: B 675 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7232 (mt0) REVERT: B 814 LYS cc_start: 0.6994 (mttt) cc_final: 0.6664 (ptmt) REVERT: B 1038 LYS cc_start: 0.8866 (mtpp) cc_final: 0.8237 (mmtp) REVERT: B 1039 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7949 (ptm160) REVERT: B 1101 HIS cc_start: 0.8133 (m90) cc_final: 0.7679 (m90) REVERT: C 182 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6106 (mptt) REVERT: C 202 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8616 (mttp) REVERT: C 213 VAL cc_start: 0.8005 (t) cc_final: 0.7589 (m) REVERT: C 428 ASP cc_start: 0.7919 (p0) cc_final: 0.7549 (p0) REVERT: C 474 GLN cc_start: 0.8509 (tt0) cc_final: 0.8226 (tt0) REVERT: C 537 LYS cc_start: 0.7929 (mtpt) cc_final: 0.7661 (mtpp) REVERT: C 567 ARG cc_start: 0.8540 (mtt-85) cc_final: 0.8117 (mtt90) REVERT: C 964 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7516 (mttt) REVERT: C 1038 LYS cc_start: 0.8756 (mtpp) cc_final: 0.8164 (mmtp) REVERT: C 1113 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7664 (mm-40) outliers start: 49 outliers final: 34 residues processed: 219 average time/residue: 0.6802 time to fit residues: 173.9493 Evaluate side-chains 214 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 82 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 275 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 307 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.095481 restraints weight = 52785.223| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.07 r_work: 0.2884 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27633 Z= 0.145 Angle : 0.592 9.271 37761 Z= 0.304 Chirality : 0.046 0.311 4443 Planarity : 0.004 0.045 4752 Dihedral : 5.057 56.660 3562 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.74 % Allowed : 11.13 % Favored : 87.13 % 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: -0.61 (0.14), residues: 3270 helix: 1.43 (0.20), residues: 711 sheet: 0.72 (0.19), residues: 777 loop : -1.80 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 357 TYR 0.019 0.001 TYR B 756 PHE 0.014 0.001 PHE B1121 TRP 0.016 0.001 TRP C 152 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (27510) covalent geometry : angle 0.56628 / 0.30 (37437) SS BOND : bond 0.00376 / 0.22 ( 45) SS BOND : angle 1.32802 / 0.92 ( 90) hydrogen bonds : bond 0.06233 / 4.23 ( 1044) hydrogen bonds : angle 5.16952 / 3.54 ( 2847) link_BETA1-4 : bond 0.00434 / 0.28 ( 27) link_BETA1-4 : angle 1.01616 / 0.72 ( 81) link_NAG-ASN : bond 0.00392 / 0.19 ( 51) link_NAG-ASN : angle 2.52848 / 1.66 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7822 (p0) cc_final: 0.7399 (p0) REVERT: A 820 ASP cc_start: 0.8059 (m-30) cc_final: 0.7661 (m-30) REVERT: A 964 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7812 (mttt) REVERT: A 1038 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8156 (mmtp) REVERT: A 1039 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.6982 (ptm160) REVERT: B 474 GLN cc_start: 0.8241 (tt0) cc_final: 0.8008 (tt0) REVERT: B 567 ARG cc_start: 0.8458 (mtt90) cc_final: 0.8222 (mtt-85) REVERT: B 582 LEU cc_start: 0.8593 (mp) cc_final: 0.8357 (mm) REVERT: B 675 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7247 (mt0) REVERT: B 740 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8816 (ttm) REVERT: B 814 LYS cc_start: 0.6989 (mttt) cc_final: 0.6664 (ptmt) REVERT: B 1038 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8225 (mmtp) REVERT: B 1039 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7902 (ptm160) REVERT: B 1101 HIS cc_start: 0.8123 (m90) cc_final: 0.7682 (m90) REVERT: C 138 ASP cc_start: 0.7731 (t70) cc_final: 0.7487 (t0) REVERT: C 182 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6136 (mptt) REVERT: C 202 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8612 (mttp) REVERT: C 213 VAL cc_start: 0.7992 (t) cc_final: 0.7628 (m) REVERT: C 428 ASP cc_start: 0.7887 (p0) cc_final: 0.7523 (p0) REVERT: C 474 GLN cc_start: 0.8518 (tt0) cc_final: 0.8240 (tt0) REVERT: C 525 CYS cc_start: 0.7294 (OUTLIER) cc_final: 0.7026 (m) REVERT: C 537 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7621 (mtpp) REVERT: C 567 ARG cc_start: 0.8535 (mtt-85) cc_final: 0.8115 (mtt90) REVERT: C 964 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7522 (mttt) REVERT: C 1038 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8172 (mmtp) REVERT: C 1113 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7658 (mm-40) outliers start: 50 outliers final: 37 residues processed: 214 average time/residue: 0.6587 time to fit residues: 164.7640 Evaluate side-chains 212 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 317 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 188 optimal weight: 0.2980 chunk 265 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 563 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.091962 restraints weight = 57258.728| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.08 r_work: 0.2859 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27633 Z= 0.174 Angle : 0.627 8.778 37761 Z= 0.323 Chirality : 0.047 0.308 4443 Planarity : 0.005 0.047 4752 Dihedral : 5.167 56.457 3562 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.74 % Allowed : 11.38 % Favored : 86.88 % 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: -0.67 (0.14), residues: 3270 helix: 1.35 (0.20), residues: 711 sheet: 0.69 (0.19), residues: 777 loop : -1.83 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 357 TYR 0.022 0.002 TYR B 756 PHE 0.017 0.002 PHE B1121 TRP 0.013 0.002 TRP C 152 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.17 (27510) covalent geometry : angle 0.60220 / 0.32 (37437) SS BOND : bond 0.00452 / 0.27 ( 45) SS BOND : angle 1.52382 / 1.05 ( 90) hydrogen bonds : bond 0.06781 / 4.60 ( 1044) hydrogen bonds : angle 5.23388 / 3.59 ( 2847) link_BETA1-4 : bond 0.00428 / 0.28 ( 27) link_BETA1-4 : angle 1.00909 / 0.72 ( 81) link_NAG-ASN : bond 0.00386 / 0.18 ( 51) link_NAG-ASN : angle 2.55170 / 1.68 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7787 (p0) cc_final: 0.7356 (p0) REVERT: A 820 ASP cc_start: 0.8038 (m-30) cc_final: 0.7617 (m-30) REVERT: A 1038 LYS cc_start: 0.8873 (mtpp) cc_final: 0.8144 (mmtp) REVERT: A 1039 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7046 (ptm160) REVERT: B 214 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7971 (ptm-80) REVERT: B 321 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7856 (mm-40) REVERT: B 474 GLN cc_start: 0.8240 (tt0) cc_final: 0.8001 (tt0) REVERT: B 567 ARG cc_start: 0.8440 (mtt90) cc_final: 0.8206 (mtt-85) REVERT: B 582 LEU cc_start: 0.8606 (mp) cc_final: 0.8367 (mm) REVERT: B 675 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7298 (mt0) REVERT: B 740 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8812 (ttm) REVERT: B 814 LYS cc_start: 0.6879 (mttt) cc_final: 0.6657 (ptmt) REVERT: B 964 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7592 (mttt) REVERT: B 1038 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8205 (mmtp) REVERT: B 1039 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7903 (ptm160) REVERT: B 1101 HIS cc_start: 0.8124 (m90) cc_final: 0.7685 (m90) REVERT: C 138 ASP cc_start: 0.7655 (t70) cc_final: 0.7309 (t0) REVERT: C 182 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6204 (mptt) REVERT: C 202 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8605 (mttp) REVERT: C 213 VAL cc_start: 0.8089 (t) cc_final: 0.7718 (m) REVERT: C 428 ASP cc_start: 0.7863 (p0) cc_final: 0.7493 (p0) REVERT: C 537 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7645 (mtpp) REVERT: C 567 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.8032 (mtt90) REVERT: C 964 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7395 (mttt) REVERT: C 1038 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8147 (mmtp) REVERT: C 1113 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7636 (mm-40) outliers start: 50 outliers final: 35 residues processed: 206 average time/residue: 0.6658 time to fit residues: 160.1627 Evaluate side-chains 205 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 175 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 317 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 257 optimal weight: 0.0470 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 563 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.097231 restraints weight = 57058.710| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.07 r_work: 0.2914 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27633 Z= 0.131 Angle : 0.572 9.446 37761 Z= 0.294 Chirality : 0.046 0.310 4443 Planarity : 0.004 0.044 4752 Dihedral : 4.984 56.923 3562 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.01 % Favored : 95.96 % Rotamer: Outliers : 1.57 % Allowed : 11.59 % Favored : 86.85 % 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: -0.56 (0.14), residues: 3270 helix: 1.55 (0.20), residues: 711 sheet: 0.67 (0.19), residues: 762 loop : -1.74 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.016 0.001 TYR B 756 PHE 0.011 0.001 PHE C 592 TRP 0.012 0.001 TRP C 152 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (27510) covalent geometry : angle 0.54805 / 0.29 (37437) SS BOND : bond 0.00322 / 0.19 ( 45) SS BOND : angle 1.17772 / 0.82 ( 90) hydrogen bonds : bond 0.05898 / 4.00 ( 1044) hydrogen bonds : angle 5.11445 / 3.51 ( 2847) link_BETA1-4 : bond 0.00450 / 0.29 ( 27) link_BETA1-4 : angle 1.01623 / 0.73 ( 81) link_NAG-ASN : bond 0.00401 / 0.19 ( 51) link_NAG-ASN : angle 2.45618 / 1.61 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7933 (tt0) cc_final: 0.7610 (mm-30) REVERT: A 428 ASP cc_start: 0.7728 (p0) cc_final: 0.7347 (p0) REVERT: A 820 ASP cc_start: 0.8067 (m-30) cc_final: 0.7667 (m-30) REVERT: A 1038 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8153 (mmtp) REVERT: A 1039 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7015 (ptm160) REVERT: B 474 GLN cc_start: 0.8269 (tt0) cc_final: 0.8031 (tt0) REVERT: B 567 ARG cc_start: 0.8476 (mtt90) cc_final: 0.8242 (mtt-85) REVERT: B 582 LEU cc_start: 0.8580 (mp) cc_final: 0.8364 (mm) REVERT: B 675 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7223 (mt0) REVERT: B 740 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8816 (ttm) REVERT: B 814 LYS cc_start: 0.6968 (mttt) cc_final: 0.6683 (ptmt) REVERT: B 964 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7547 (mttt) REVERT: B 1038 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8221 (mmtp) REVERT: B 1039 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.7949 (ptm160) REVERT: B 1101 HIS cc_start: 0.8122 (m90) cc_final: 0.7662 (m90) REVERT: C 138 ASP cc_start: 0.7597 (t70) cc_final: 0.7309 (t0) REVERT: C 202 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8603 (mttp) REVERT: C 213 VAL cc_start: 0.8028 (t) cc_final: 0.7643 (m) REVERT: C 428 ASP cc_start: 0.7845 (p0) cc_final: 0.7481 (p0) REVERT: C 525 CYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6989 (m) REVERT: C 537 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7620 (mtpp) REVERT: C 567 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.8095 (mtt90) REVERT: C 964 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7489 (mttt) REVERT: C 1038 LYS cc_start: 0.8777 (mtpp) cc_final: 0.8169 (mmtp) outliers start: 45 outliers final: 36 residues processed: 207 average time/residue: 0.6614 time to fit residues: 160.4120 Evaluate side-chains 209 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 95 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 192 optimal weight: 0.0980 chunk 125 optimal weight: 2.9990 chunk 219 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 935 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.095958 restraints weight = 62860.817| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.21 r_work: 0.2940 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27633 Z= 0.114 Angle : 0.547 9.365 37761 Z= 0.281 Chirality : 0.045 0.308 4443 Planarity : 0.004 0.043 4752 Dihedral : 4.810 57.634 3562 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 1.43 % Allowed : 11.90 % Favored : 86.67 % 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: -0.46 (0.14), residues: 3270 helix: 1.67 (0.20), residues: 711 sheet: 0.68 (0.19), residues: 762 loop : -1.68 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 357 TYR 0.016 0.001 TYR B1067 PHE 0.011 0.001 PHE B 133 TRP 0.012 0.001 TRP C 436 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (27510) covalent geometry : angle 0.52346 / 0.28 (37437) SS BOND : bond 0.00287 / 0.17 ( 45) SS BOND : angle 1.06938 / 0.75 ( 90) hydrogen bonds : bond 0.05361 / 3.65 ( 1044) hydrogen bonds : angle 5.00203 / 3.43 ( 2847) link_BETA1-4 : bond 0.00437 / 0.28 ( 27) link_BETA1-4 : angle 1.02699 / 0.73 ( 81) link_NAG-ASN : bond 0.00400 / 0.19 ( 51) link_NAG-ASN : angle 2.33502 / 1.53 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7703 (p0) cc_final: 0.7326 (p0) REVERT: A 820 ASP cc_start: 0.8016 (m-30) cc_final: 0.7593 (m-30) REVERT: A 1038 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8109 (mmtp) REVERT: A 1039 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7033 (ptm160) REVERT: B 321 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7794 (mm-40) REVERT: B 474 GLN cc_start: 0.8233 (tt0) cc_final: 0.8009 (tt0) REVERT: B 567 ARG cc_start: 0.8431 (mtt90) cc_final: 0.8205 (mtt-85) REVERT: B 582 LEU cc_start: 0.8565 (mp) cc_final: 0.8345 (mm) REVERT: B 675 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7270 (mt0) REVERT: B 740 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8757 (ttm) REVERT: B 964 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7527 (mttt) REVERT: B 1038 LYS cc_start: 0.8830 (mtpp) cc_final: 0.8204 (mptt) REVERT: B 1039 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.7895 (ptm160) REVERT: B 1101 HIS cc_start: 0.8115 (m90) cc_final: 0.7648 (m90) REVERT: C 138 ASP cc_start: 0.7563 (t70) cc_final: 0.7305 (t0) REVERT: C 202 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8585 (mttp) REVERT: C 213 VAL cc_start: 0.7999 (t) cc_final: 0.7591 (m) REVERT: C 309 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7436 (mp0) REVERT: C 389 ASP cc_start: 0.7712 (m-30) cc_final: 0.7397 (m-30) REVERT: C 428 ASP cc_start: 0.7874 (p0) cc_final: 0.7514 (p0) REVERT: C 525 CYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6916 (m) REVERT: C 567 ARG cc_start: 0.8443 (mtt-85) cc_final: 0.8053 (mtt90) REVERT: C 964 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7391 (mttt) REVERT: C 1038 LYS cc_start: 0.8715 (mtpp) cc_final: 0.8070 (mmtp) outliers start: 41 outliers final: 32 residues processed: 205 average time/residue: 0.6401 time to fit residues: 153.4641 Evaluate side-chains 200 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1039 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 114 optimal weight: 0.7980 chunk 318 optimal weight: 0.0270 chunk 278 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 299 optimal weight: 0.0770 chunk 188 optimal weight: 0.0670 chunk 325 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 199 optimal weight: 0.6980 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 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 = 0.3503 r_free = 0.3503 target = 0.131299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.100419 restraints weight = 54505.501| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.99 r_work: 0.2945 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27633 Z= 0.102 Angle : 0.522 9.481 37761 Z= 0.268 Chirality : 0.044 0.311 4443 Planarity : 0.004 0.042 4752 Dihedral : 4.639 57.470 3562 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.45 % Rotamer: Outliers : 1.04 % Allowed : 12.49 % Favored : 86.46 % 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: -0.34 (0.15), residues: 3270 helix: 1.88 (0.21), residues: 708 sheet: 0.71 (0.19), residues: 762 loop : -1.61 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.015 0.001 TYR A1067 PHE 0.013 0.001 PHE B 643 TRP 0.012 0.001 TRP C 152 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (27510) covalent geometry : angle 0.49978 / 0.26 (37437) SS BOND : bond 0.00243 / 0.16 ( 45) SS BOND : angle 0.90545 / 0.64 ( 90) hydrogen bonds : bond 0.04833 / 3.29 ( 1044) hydrogen bonds : angle 4.91652 / 3.37 ( 2847) link_BETA1-4 : bond 0.00446 / 0.29 ( 27) link_BETA1-4 : angle 1.02048 / 0.73 ( 81) link_NAG-ASN : bond 0.00413 / 0.20 ( 51) link_NAG-ASN : angle 2.26411 / 1.48 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9392.37 seconds wall clock time: 160 minutes 45.06 seconds (9645.06 seconds total)