Starting phenix.real_space_refine on Mon Jul 6 03:07:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ls9_23506/07_2026/7ls9_23506.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ls9_23506/07_2026/7ls9_23506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ls9_23506/07_2026/7ls9_23506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ls9_23506/07_2026/7ls9_23506.map" model { file = "/net/cci-nas-00/data/ceres_data/7ls9_23506/07_2026/7ls9_23506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ls9_23506/07_2026/7ls9_23506.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ls9_23506/07_2026/7ls9_23506.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ls9_23506/07_2026/7ls9_23506.cif" } resolution = 3.42 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= 0.021 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 144 5.16 5 C 20436 2.51 5 N 5304 2.21 5 O 6342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 234 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32226 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8574 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 54, 'TRANS': 1042} Chain breaks: 5 Chain: "H" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "B" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8574 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 54, 'TRANS': 1042} Chain breaks: 5 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "F" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8574 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 54, 'TRANS': 1042} Chain breaks: 5 Chain: "E" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: "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: "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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.37, per 1000 atoms: 0.23 Number of scatterers: 32226 At special positions: 0 Unit cell: (140.17, 140.17, 206.51, 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 144 16.00 O 6342 8.00 N 5304 7.00 C 20436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100A" - pdb=" SG CYS H 100F" distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.03 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 D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 100A" - pdb=" SG CYS D 100F" distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 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=2.03 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=2.03 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 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 100A" - pdb=" SG CYS E 100F" distance=2.05 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 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 I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 P 2 " - " BMA P 3 " " 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 A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 17 " " NAG A1310 " - " ASN A 343 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 17 " " NAG B1310 " - " ASN B 343 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 17 " " NAG C1310 " - " ASN C 343 " " NAG I 1 " - " ASN A 165 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN B 165 " " NAG M 1 " - " ASN B 234 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN C 165 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN C 234 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN B 122 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " " NAG Y 1 " - " ASN C 122 " " NAG Z 1 " - " ASN A 717 " " NAG a 1 " - " ASN A 801 " " NAG b 1 " - " ASN A1098 " " NAG c 1 " - " ASN A1134 " " NAG d 1 " - " ASN A 122 " Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.4 seconds 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7446 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 69 sheets defined 22.5% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.040A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.306A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 749 through 757 Processing helix chain 'A' and resid 757 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 832 through 838 Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.929A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.970A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.254A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.713A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.846A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.215A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.871A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.766A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 31 removed outlier: 4.248A pdb=" N SER L 31 " --> pdb=" O VAL L 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.090A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.050A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.300A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.650A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.161A 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 502 through 506 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 630 through 636 removed outlier: 3.626A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 749 through 757 Processing helix chain 'B' and resid 757 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 832 through 838 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.782A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 889 removed outlier: 3.702A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 889' Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.100A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.618A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.822A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.006A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.900A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 52A through 54 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.900A pdb=" N THR D 87 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 removed outlier: 3.906A pdb=" N SER F 31 " --> pdb=" O VAL F 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 31' Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.077A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.882A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.296A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.737A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.285A 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 502 through 506 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 630 through 636 removed outlier: 3.601A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 749 through 783 removed outlier: 6.415A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 832 through 838 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.810A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.236A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.174A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.642A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.806A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.287A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.924A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.801A pdb=" N THR E 87 " --> pdb=" O THR E 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 31 removed outlier: 4.202A pdb=" N SER G 31 " --> pdb=" O VAL G 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 31' Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.155A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.083A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.814A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.519A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 144 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 354 through 358 removed outlier: 3.996A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.996A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (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 538 through 543 removed outlier: 3.891A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.616A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.230A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.674A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.674A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.791A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.755A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP H 72 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.647A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.647A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 100 through 100B Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.594A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.511A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.511A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.124A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.806A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.819A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 141 through 144 Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.008A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.008A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD7, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.192A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.719A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.175A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.676A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.676A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.512A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.733A pdb=" N THR D 107 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.733A pdb=" N THR D 107 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 100 through 100B removed outlier: 3.522A pdb=" N ILE D 100B" --> pdb=" O VAL D 100E" (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.587A pdb=" N SER F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.608A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN F 37 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.608A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.124A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.810A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.787A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 141 through 144 Processing sheet with id=AF7, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AF8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.038A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.038A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AG3, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.750A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.684A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.684A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.794A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 1094 through 1098 Processing sheet with id=AG9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AH1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.912A pdb=" N THR E 107 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.912A pdb=" N THR E 107 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 100 through 100B Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.593A pdb=" N SER G 22 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS G 23 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.674A pdb=" N GLN G 89 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN G 37 " --> pdb=" O ARG G 45 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.699A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) 1303 hydrogen bonds defined for protein. 3528 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: 8.98 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5373 1.32 - 1.46: 11551 1.46 - 1.59: 15840 1.59 - 1.73: 2 1.73 - 1.86: 180 Bond restraints: 32946 Sorted by residual: bond pdb=" CG PRO F 40 " pdb=" CD PRO F 40 " ideal model delta sigma weight residual 1.503 1.244 0.259 3.40e-02 8.65e+02 5.79e+01 bond pdb=" CG PRO G 59 " pdb=" CD PRO G 59 " ideal model delta sigma weight residual 1.503 1.309 0.194 3.40e-02 8.65e+02 3.26e+01 bond pdb=" CA ALA D 99 " pdb=" CB ALA D 99 " ideal model delta sigma weight residual 1.530 1.463 0.066 1.48e-02 4.57e+03 2.01e+01 bond pdb=" CA ALA H 99 " pdb=" CB ALA H 99 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.66e-02 3.63e+03 1.61e+01 bond pdb=" C PHE E 100G" pdb=" O PHE E 100G" ideal model delta sigma weight residual 1.236 1.189 0.046 1.17e-02 7.31e+03 1.58e+01 ... (remaining 32941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 44321 3.29 - 6.58: 435 6.58 - 9.88: 50 9.88 - 13.17: 4 13.17 - 16.46: 4 Bond angle restraints: 44814 Sorted by residual: angle pdb=" CA PRO F 40 " pdb=" N PRO F 40 " pdb=" CD PRO F 40 " ideal model delta sigma weight residual 112.00 95.54 16.46 1.40e+00 5.10e-01 1.38e+02 angle pdb=" N PRO F 40 " pdb=" CD PRO F 40 " pdb=" CG PRO F 40 " ideal model delta sigma weight residual 103.20 87.93 15.27 1.50e+00 4.44e-01 1.04e+02 angle pdb=" CA GLY C 447 " pdb=" C GLY C 447 " pdb=" O GLY C 447 " ideal model delta sigma weight residual 121.88 114.92 6.96 7.80e-01 1.64e+00 7.97e+01 angle pdb=" N PRO G 59 " pdb=" CD PRO G 59 " pdb=" CG PRO G 59 " ideal model delta sigma weight residual 103.20 90.02 13.18 1.50e+00 4.44e-01 7.72e+01 angle pdb=" C PHE A 140 " pdb=" CA PHE A 140 " pdb=" CB PHE A 140 " ideal model delta sigma weight residual 111.17 95.96 15.21 1.96e+00 2.60e-01 6.02e+01 ... (remaining 44809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 17478 17.56 - 35.11: 1239 35.11 - 52.67: 222 52.67 - 70.23: 35 70.23 - 87.78: 22 Dihedral angle restraints: 18996 sinusoidal: 7380 harmonic: 11616 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.51 -80.49 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -9.81 -76.19 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -10.44 -75.56 1 1.00e+01 1.00e-02 7.21e+01 ... (remaining 18993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4792 0.096 - 0.192: 416 0.192 - 0.288: 44 0.288 - 0.384: 3 0.384 - 0.479: 4 Chirality restraints: 5259 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.33e+01 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.10e+01 ... (remaining 5256 not shown) Planarity restraints: 5751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.244 2.00e-02 2.50e+03 2.07e-01 5.37e+02 pdb=" C7 NAG I 2 " 0.051 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.342 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.232 2.00e-02 2.50e+03 1.97e-01 4.86e+02 pdb=" C7 NAG K 2 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.323 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 2 " -0.221 2.00e-02 2.50e+03 1.88e-01 4.42e+02 pdb=" C7 NAG P 2 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG P 2 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG P 2 " 0.308 2.00e-02 2.50e+03 pdb=" O7 NAG P 2 " -0.171 2.00e-02 2.50e+03 ... (remaining 5748 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5085 2.77 - 3.30: 28806 3.30 - 3.83: 52493 3.83 - 4.37: 59924 4.37 - 4.90: 106489 Nonbonded interactions: 252797 Sorted by model distance: nonbonded pdb=" OG SER B 494 " pdb=" OH TYR F 32 " model vdw 2.232 3.040 nonbonded pdb=" OE1 GLN B 314 " pdb=" OG SER C 735 " model vdw 2.282 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 21 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.315 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.331 3.040 ... (remaining 252792 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.440 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: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.710 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.259 33075 Z= 0.288 Angle : 0.900 16.459 45147 Z= 0.521 Chirality : 0.057 0.479 5259 Planarity : 0.008 0.207 5700 Dihedral : 12.553 87.785 11388 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 3.17 % 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: -0.75 (0.12), residues: 3954 helix: -0.05 (0.18), residues: 741 sheet: 0.48 (0.17), residues: 963 loop : -1.11 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 61 TYR 0.035 0.002 TYR B 741 PHE 0.043 0.002 PHE C 817 TRP 0.034 0.002 TRP G 35 HIS 0.012 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.29 (32946) covalent geometry : angle 0.88817 / 0.52 (44814) SS BOND : bond 0.00599 / 0.43 ( 54) SS BOND : angle 1.48435 / 0.98 ( 108) hydrogen bonds : bond 0.21728 / 14.23 ( 1235) hydrogen bonds : angle 8.67611 / 5.96 ( 3528) link_BETA1-4 : bond 0.00589 / 0.32 ( 24) link_BETA1-4 : angle 1.74236 / 1.18 ( 72) link_NAG-ASN : bond 0.00610 / 0.28 ( 51) link_NAG-ASN : angle 2.18990 / 1.46 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 725 GLU cc_start: 0.7602 (pp20) cc_final: 0.7284 (pp20) REVERT: A 864 LEU cc_start: 0.7503 (tp) cc_final: 0.7118 (tp) REVERT: H 4 LEU cc_start: 0.8613 (mm) cc_final: 0.8249 (mm) REVERT: H 57 THR cc_start: 0.8853 (p) cc_final: 0.8553 (m) REVERT: L 53 SER cc_start: 0.7978 (t) cc_final: 0.7589 (p) REVERT: B 406 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6757 (mm-30) REVERT: D 4 LEU cc_start: 0.8327 (mm) cc_final: 0.7838 (mm) REVERT: F 2 ILE cc_start: 0.8291 (mp) cc_final: 0.8029 (mp) REVERT: F 27 GLN cc_start: 0.7368 (pt0) cc_final: 0.6528 (pp30) REVERT: F 53 SER cc_start: 0.8263 (t) cc_final: 0.7733 (p) REVERT: F 54 ARG cc_start: 0.7958 (mpt90) cc_final: 0.7534 (mtt90) REVERT: E 4 LEU cc_start: 0.8408 (mm) cc_final: 0.8158 (mm) REVERT: E 101 ASP cc_start: 0.8075 (t0) cc_final: 0.7805 (t0) REVERT: G 49 TYR cc_start: 0.8182 (p90) cc_final: 0.7798 (p90) REVERT: G 53 SER cc_start: 0.7441 (t) cc_final: 0.7026 (t) REVERT: G 79 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7176 (pm20) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.2107 time to fit residues: 150.2103 Evaluate side-chains 312 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 498 GLN A 519 HIS A 613 GLN A 644 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 498 GLN B 519 HIS B 613 GLN B 644 GLN B1011 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 519 HIS ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.128659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.099971 restraints weight = 67123.375| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.12 r_work: 0.3515 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33075 Z= 0.160 Angle : 0.607 10.868 45147 Z= 0.312 Chirality : 0.044 0.167 5259 Planarity : 0.004 0.058 5700 Dihedral : 4.604 23.336 4326 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.93 % Allowed : 7.53 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.27 (0.13), residues: 3954 helix: 0.84 (0.19), residues: 744 sheet: 0.49 (0.16), residues: 1056 loop : -0.88 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 77 TYR 0.023 0.001 TYR B1067 PHE 0.021 0.001 PHE A 140 TRP 0.019 0.002 TRP F 35 HIS 0.005 0.001 HIS D 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (32946) covalent geometry : angle 0.59972 / 0.31 (44814) SS BOND : bond 0.00351 / 0.23 ( 54) SS BOND : angle 1.05095 / 0.69 ( 108) hydrogen bonds : bond 0.04658 / 3.10 ( 1235) hydrogen bonds : angle 6.25596 / 4.31 ( 3528) link_BETA1-4 : bond 0.00356 / 0.24 ( 24) link_BETA1-4 : angle 1.30867 / 0.86 ( 72) link_NAG-ASN : bond 0.00271 / 0.16 ( 51) link_NAG-ASN : angle 1.32778 / 0.89 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 345 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7147 (p0) cc_final: 0.6843 (p0) REVERT: A 864 LEU cc_start: 0.8571 (tp) cc_final: 0.8318 (tp) REVERT: H 107 THR cc_start: 0.7817 (p) cc_final: 0.7515 (t) REVERT: L 27 GLN cc_start: 0.7987 (pp30) cc_final: 0.7596 (pp30) REVERT: L 42 GLN cc_start: 0.7950 (pm20) cc_final: 0.7683 (tm-30) REVERT: L 77 ARG cc_start: 0.8651 (ttp80) cc_final: 0.8368 (ttp80) REVERT: B 131 CYS cc_start: 0.6590 (m) cc_final: 0.6341 (m) REVERT: B 869 MET cc_start: 0.8710 (mtm) cc_final: 0.8456 (ttm) REVERT: B 1005 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7332 (tm-30) REVERT: D 58 GLU cc_start: 0.8106 (mp0) cc_final: 0.7839 (mp0) REVERT: F 2 ILE cc_start: 0.8516 (mp) cc_final: 0.8090 (mp) REVERT: F 27 GLN cc_start: 0.8217 (pt0) cc_final: 0.7529 (pp30) REVERT: F 53 SER cc_start: 0.7654 (t) cc_final: 0.7319 (p) REVERT: F 77 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8395 (ttp-110) REVERT: C 131 CYS cc_start: 0.6763 (m) cc_final: 0.6534 (m) REVERT: C 389 ASP cc_start: 0.6401 (p0) cc_final: 0.5968 (p0) REVERT: C 390 LEU cc_start: 0.7579 (mt) cc_final: 0.7368 (mt) REVERT: C 740 MET cc_start: 0.8802 (mmm) cc_final: 0.8498 (tpt) REVERT: C 965 GLN cc_start: 0.8094 (tp40) cc_final: 0.7533 (mm110) REVERT: C 1005 GLN cc_start: 0.7593 (tm-30) cc_final: 0.7231 (tm-30) REVERT: E 101 ASP cc_start: 0.8323 (t0) cc_final: 0.7989 (t0) REVERT: G 77 ARG cc_start: 0.8365 (ttp-110) cc_final: 0.7983 (ttp80) outliers start: 32 outliers final: 18 residues processed: 367 average time/residue: 0.2112 time to fit residues: 123.1212 Evaluate side-chains 315 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 297 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 256 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 343 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS A 935 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 519 HIS C 613 GLN C 901 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.131061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.100024 restraints weight = 73391.427| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.18 r_work: 0.3465 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33075 Z= 0.139 Angle : 0.554 8.502 45147 Z= 0.284 Chirality : 0.043 0.152 5259 Planarity : 0.004 0.041 5700 Dihedral : 4.387 20.487 4326 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.22 % Allowed : 9.47 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.12 (0.13), residues: 3954 helix: 1.21 (0.20), residues: 738 sheet: 0.57 (0.16), residues: 1005 loop : -0.85 (0.12), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 45 TYR 0.021 0.001 TYR B1067 PHE 0.012 0.001 PHE L 62 TRP 0.021 0.001 TRP F 35 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (32946) covalent geometry : angle 0.54703 / 0.28 (44814) SS BOND : bond 0.00273 / 0.18 ( 54) SS BOND : angle 0.99395 / 0.65 ( 108) hydrogen bonds : bond 0.04234 / 2.84 ( 1235) hydrogen bonds : angle 5.74769 / 3.96 ( 3528) link_BETA1-4 : bond 0.00376 / 0.24 ( 24) link_BETA1-4 : angle 1.12821 / 0.72 ( 72) link_NAG-ASN : bond 0.00223 / 0.14 ( 51) link_NAG-ASN : angle 1.22647 / 0.83 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 326 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7134 (p0) cc_final: 0.6832 (p0) REVERT: A 740 MET cc_start: 0.8879 (mtp) cc_final: 0.8619 (tpp) REVERT: H 101 ASP cc_start: 0.8279 (t0) cc_final: 0.8011 (t0) REVERT: H 107 THR cc_start: 0.7868 (p) cc_final: 0.7609 (t) REVERT: L 27 GLN cc_start: 0.8084 (pp30) cc_final: 0.7618 (pp30) REVERT: L 77 ARG cc_start: 0.8849 (ttp80) cc_final: 0.8502 (ttp80) REVERT: L 103 LYS cc_start: 0.8277 (tppt) cc_final: 0.7932 (tppt) REVERT: B 131 CYS cc_start: 0.6609 (m) cc_final: 0.6318 (m) REVERT: B 740 MET cc_start: 0.8796 (tpt) cc_final: 0.8571 (tpp) REVERT: B 900 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7800 (mtm) REVERT: F 2 ILE cc_start: 0.8504 (mp) cc_final: 0.8108 (mp) REVERT: F 27 GLN cc_start: 0.8239 (pt0) cc_final: 0.7662 (pp30) REVERT: F 49 TYR cc_start: 0.8472 (p90) cc_final: 0.7954 (p90) REVERT: F 53 SER cc_start: 0.7514 (t) cc_final: 0.6781 (t) REVERT: F 54 ARG cc_start: 0.8100 (mtt90) cc_final: 0.7252 (mtt90) REVERT: F 77 ARG cc_start: 0.8689 (ttp-110) cc_final: 0.8371 (ttp-110) REVERT: C 131 CYS cc_start: 0.6924 (m) cc_final: 0.6690 (m) REVERT: C 389 ASP cc_start: 0.6290 (p0) cc_final: 0.5808 (p0) REVERT: C 390 LEU cc_start: 0.7620 (mt) cc_final: 0.7314 (mt) REVERT: C 740 MET cc_start: 0.8689 (mmm) cc_final: 0.8394 (tpt) REVERT: C 965 GLN cc_start: 0.8038 (tp40) cc_final: 0.7527 (mm110) REVERT: E 101 ASP cc_start: 0.8424 (t0) cc_final: 0.7983 (t0) REVERT: E 105 GLN cc_start: 0.8703 (mp10) cc_final: 0.8441 (mp10) REVERT: G 77 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8389 (ttp-110) outliers start: 42 outliers final: 29 residues processed: 354 average time/residue: 0.2078 time to fit residues: 118.2325 Evaluate side-chains 321 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 291 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 9 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 351 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 265 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 935 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN G 42 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.122221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.093097 restraints weight = 66948.453| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.15 r_work: 0.3418 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33075 Z= 0.176 Angle : 0.577 9.705 45147 Z= 0.295 Chirality : 0.043 0.153 5259 Planarity : 0.004 0.047 5700 Dihedral : 4.410 20.713 4326 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.97 % Allowed : 10.63 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.10 (0.13), residues: 3954 helix: 1.07 (0.19), residues: 765 sheet: 0.60 (0.16), residues: 984 loop : -0.79 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 45 TYR 0.020 0.002 TYR B1067 PHE 0.019 0.001 PHE C 347 TRP 0.026 0.001 TRP F 35 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (32946) covalent geometry : angle 0.57033 / 0.29 (44814) SS BOND : bond 0.00317 / 0.21 ( 54) SS BOND : angle 1.09237 / 0.71 ( 108) hydrogen bonds : bond 0.04189 / 2.81 ( 1235) hydrogen bonds : angle 5.57536 / 3.84 ( 3528) link_BETA1-4 : bond 0.00271 / 0.17 ( 24) link_BETA1-4 : angle 1.10301 / 0.72 ( 72) link_NAG-ASN : bond 0.00258 / 0.17 ( 51) link_NAG-ASN : angle 1.27346 / 0.87 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 304 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7174 (p0) cc_final: 0.6859 (p0) REVERT: A 740 MET cc_start: 0.8949 (mtp) cc_final: 0.8678 (tpp) REVERT: H 20 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8422 (mt) REVERT: H 101 ASP cc_start: 0.8392 (t0) cc_final: 0.8029 (t0) REVERT: H 107 THR cc_start: 0.7807 (p) cc_final: 0.7582 (t) REVERT: B 131 CYS cc_start: 0.6725 (m) cc_final: 0.6403 (m) REVERT: B 495 TYR cc_start: 0.8614 (m-10) cc_final: 0.8282 (m-10) REVERT: B 740 MET cc_start: 0.8812 (tpt) cc_final: 0.8564 (tpp) REVERT: B 900 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8008 (mtm) REVERT: B 1005 GLN cc_start: 0.8235 (tt0) cc_final: 0.7933 (tm-30) REVERT: B 1029 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8180 (tpp) REVERT: D 102 TYR cc_start: 0.7752 (t80) cc_final: 0.7459 (t80) REVERT: F 2 ILE cc_start: 0.8569 (mp) cc_final: 0.8141 (mp) REVERT: F 27 GLN cc_start: 0.8273 (pt0) cc_final: 0.7689 (pp30) REVERT: F 77 ARG cc_start: 0.8741 (ttp-110) cc_final: 0.8394 (ttp-110) REVERT: C 131 CYS cc_start: 0.6930 (m) cc_final: 0.6693 (m) REVERT: C 389 ASP cc_start: 0.6425 (p0) cc_final: 0.5900 (p0) REVERT: C 390 LEU cc_start: 0.7796 (mt) cc_final: 0.7459 (mt) REVERT: C 740 MET cc_start: 0.8709 (mmm) cc_final: 0.8347 (tpt) REVERT: E 82 MET cc_start: 0.7713 (mmm) cc_final: 0.7441 (mmt) REVERT: E 101 ASP cc_start: 0.8478 (t0) cc_final: 0.8035 (t0) REVERT: E 105 GLN cc_start: 0.8713 (mp10) cc_final: 0.8468 (mp10) REVERT: G 48 ILE cc_start: 0.7968 (mt) cc_final: 0.7687 (mm) REVERT: G 103 LYS cc_start: 0.8291 (tptt) cc_final: 0.8058 (tptp) outliers start: 68 outliers final: 52 residues processed: 358 average time/residue: 0.2037 time to fit residues: 118.4819 Evaluate side-chains 339 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 284 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 164 optimal weight: 4.9990 chunk 296 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 193 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 338 optimal weight: 3.9990 chunk 308 optimal weight: 0.0670 chunk 242 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 37 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 777 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.131277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.099886 restraints weight = 70447.464| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.92 r_work: 0.3471 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33075 Z= 0.118 Angle : 0.532 8.442 45147 Z= 0.272 Chirality : 0.042 0.150 5259 Planarity : 0.003 0.045 5700 Dihedral : 4.250 20.567 4326 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.91 % Allowed : 11.82 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.05 (0.13), residues: 3954 helix: 1.27 (0.20), residues: 765 sheet: 0.53 (0.16), residues: 1023 loop : -0.79 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 97 TYR 0.020 0.001 TYR B1067 PHE 0.015 0.001 PHE A 133 TRP 0.025 0.001 TRP F 35 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (32946) covalent geometry : angle 0.52587 / 0.27 (44814) SS BOND : bond 0.00267 / 0.17 ( 54) SS BOND : angle 1.06968 / 0.67 ( 108) hydrogen bonds : bond 0.03776 / 2.54 ( 1235) hydrogen bonds : angle 5.34422 / 3.69 ( 3528) link_BETA1-4 : bond 0.00331 / 0.21 ( 24) link_BETA1-4 : angle 1.02808 / 0.66 ( 72) link_NAG-ASN : bond 0.00186 / 0.11 ( 51) link_NAG-ASN : angle 1.16291 / 0.79 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 318 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7050 (p0) cc_final: 0.6698 (p0) REVERT: A 740 MET cc_start: 0.8861 (mtp) cc_final: 0.8638 (tpp) REVERT: H 59 TYR cc_start: 0.8891 (m-80) cc_final: 0.8632 (m-80) REVERT: H 101 ASP cc_start: 0.8204 (t0) cc_final: 0.7830 (t0) REVERT: L 27 GLN cc_start: 0.8017 (pp30) cc_final: 0.7569 (pp30) REVERT: L 39 LYS cc_start: 0.8308 (mtmm) cc_final: 0.8073 (mtpt) REVERT: B 131 CYS cc_start: 0.6488 (m) cc_final: 0.6199 (m) REVERT: B 495 TYR cc_start: 0.8552 (m-10) cc_final: 0.8109 (m-10) REVERT: B 740 MET cc_start: 0.8696 (tpt) cc_final: 0.8477 (tpp) REVERT: B 900 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7711 (mtm) REVERT: F 2 ILE cc_start: 0.8513 (mp) cc_final: 0.8059 (mp) REVERT: F 27 GLN cc_start: 0.8320 (pt0) cc_final: 0.7732 (pp30) REVERT: F 42 GLN cc_start: 0.8173 (mm110) cc_final: 0.7953 (tm-30) REVERT: F 48 ILE cc_start: 0.8091 (mt) cc_final: 0.7717 (mm) REVERT: C 131 CYS cc_start: 0.6754 (m) cc_final: 0.6539 (m) REVERT: C 389 ASP cc_start: 0.6425 (p0) cc_final: 0.5858 (p0) REVERT: C 390 LEU cc_start: 0.7579 (mt) cc_final: 0.7188 (mt) REVERT: C 740 MET cc_start: 0.8648 (mmm) cc_final: 0.8307 (tpt) REVERT: C 1138 TYR cc_start: 0.7948 (t80) cc_final: 0.7663 (m-10) REVERT: E 101 ASP cc_start: 0.8432 (t0) cc_final: 0.8013 (t0) REVERT: E 105 GLN cc_start: 0.8680 (mp10) cc_final: 0.8266 (mp10) REVERT: G 48 ILE cc_start: 0.8014 (mt) cc_final: 0.7648 (mm) outliers start: 66 outliers final: 46 residues processed: 366 average time/residue: 0.2130 time to fit residues: 125.8906 Evaluate side-chains 340 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 293 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 125 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 161 optimal weight: 0.0270 chunk 105 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 314 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 519 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.127784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095815 restraints weight = 72411.752| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.11 r_work: 0.3405 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33075 Z= 0.184 Angle : 0.588 10.592 45147 Z= 0.298 Chirality : 0.043 0.156 5259 Planarity : 0.004 0.052 5700 Dihedral : 4.358 20.535 4326 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.11 % Allowed : 13.18 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.03 (0.13), residues: 3954 helix: 1.12 (0.19), residues: 765 sheet: 0.67 (0.16), residues: 957 loop : -0.74 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 77 TYR 0.020 0.001 TYR D 102 PHE 0.021 0.002 PHE B 347 TRP 0.033 0.002 TRP F 35 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (32946) covalent geometry : angle 0.58095 / 0.30 (44814) SS BOND : bond 0.00316 / 0.21 ( 54) SS BOND : angle 1.13567 / 0.73 ( 108) hydrogen bonds : bond 0.04135 / 2.78 ( 1235) hydrogen bonds : angle 5.39119 / 3.73 ( 3528) link_BETA1-4 : bond 0.00272 / 0.17 ( 24) link_BETA1-4 : angle 1.07382 / 0.70 ( 72) link_NAG-ASN : bond 0.00250 / 0.16 ( 51) link_NAG-ASN : angle 1.27325 / 0.86 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 300 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8944 (mtp) cc_final: 0.8677 (tpp) REVERT: H 59 TYR cc_start: 0.8935 (m-80) cc_final: 0.8673 (m-80) REVERT: H 101 ASP cc_start: 0.8236 (t0) cc_final: 0.7825 (t0) REVERT: H 105 GLN cc_start: 0.8741 (mp10) cc_final: 0.8508 (pm20) REVERT: L 27 GLN cc_start: 0.8105 (pp30) cc_final: 0.7561 (pp30) REVERT: L 77 ARG cc_start: 0.8821 (ttp-110) cc_final: 0.8583 (ttp-110) REVERT: B 131 CYS cc_start: 0.6682 (m) cc_final: 0.6338 (m) REVERT: B 389 ASP cc_start: 0.6679 (p0) cc_final: 0.6385 (p0) REVERT: B 495 TYR cc_start: 0.8694 (m-10) cc_final: 0.8273 (m-10) REVERT: B 740 MET cc_start: 0.8766 (tpt) cc_final: 0.8523 (tpp) REVERT: B 900 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7994 (mtm) REVERT: D 102 TYR cc_start: 0.7797 (t80) cc_final: 0.7557 (t80) REVERT: F 2 ILE cc_start: 0.8631 (mp) cc_final: 0.8194 (mp) REVERT: F 27 GLN cc_start: 0.8285 (pt0) cc_final: 0.7662 (pp30) REVERT: F 48 ILE cc_start: 0.8274 (mt) cc_final: 0.7984 (mm) REVERT: F 81 GLU cc_start: 0.6797 (pm20) cc_final: 0.6491 (pm20) REVERT: C 131 CYS cc_start: 0.6720 (m) cc_final: 0.6477 (m) REVERT: C 389 ASP cc_start: 0.6571 (p0) cc_final: 0.5950 (p0) REVERT: C 390 LEU cc_start: 0.7820 (mt) cc_final: 0.7397 (mt) REVERT: C 740 MET cc_start: 0.8786 (mmm) cc_final: 0.8411 (tpt) REVERT: C 1138 TYR cc_start: 0.8011 (t80) cc_final: 0.7687 (m-10) REVERT: E 19 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7049 (tpt170) REVERT: E 101 ASP cc_start: 0.8441 (t0) cc_final: 0.7885 (t0) REVERT: G 48 ILE cc_start: 0.8017 (mt) cc_final: 0.7778 (mm) outliers start: 73 outliers final: 65 residues processed: 356 average time/residue: 0.2160 time to fit residues: 123.9510 Evaluate side-chains 347 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 281 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 80 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 358 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 81 optimal weight: 0.8980 chunk 298 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.127928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.096212 restraints weight = 72316.933| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.11 r_work: 0.3412 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33075 Z= 0.140 Angle : 0.556 8.785 45147 Z= 0.282 Chirality : 0.042 0.149 5259 Planarity : 0.004 0.044 5700 Dihedral : 4.269 20.208 4326 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.06 % Allowed : 13.76 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 0.04 (0.13), residues: 3954 helix: 1.11 (0.19), residues: 783 sheet: 0.61 (0.16), residues: 987 loop : -0.64 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 45 TYR 0.019 0.001 TYR B1067 PHE 0.014 0.001 PHE B 347 TRP 0.034 0.001 TRP F 35 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (32946) covalent geometry : angle 0.55023 / 0.28 (44814) SS BOND : bond 0.00273 / 0.18 ( 54) SS BOND : angle 1.00824 / 0.65 ( 108) hydrogen bonds : bond 0.03839 / 2.59 ( 1235) hydrogen bonds : angle 5.24983 / 3.63 ( 3528) link_BETA1-4 : bond 0.00314 / 0.20 ( 24) link_BETA1-4 : angle 1.00216 / 0.64 ( 72) link_NAG-ASN : bond 0.00195 / 0.12 ( 51) link_NAG-ASN : angle 1.18098 / 0.80 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 288 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8942 (mtp) cc_final: 0.8665 (tpp) REVERT: H 59 TYR cc_start: 0.8942 (m-80) cc_final: 0.8664 (m-80) REVERT: H 101 ASP cc_start: 0.8194 (t0) cc_final: 0.7802 (t0) REVERT: H 105 GLN cc_start: 0.8741 (mp10) cc_final: 0.8526 (pm20) REVERT: L 27 GLN cc_start: 0.8091 (pp30) cc_final: 0.7602 (pp30) REVERT: L 54 ARG cc_start: 0.8137 (mtt90) cc_final: 0.7414 (mtt90) REVERT: B 131 CYS cc_start: 0.6615 (m) cc_final: 0.6268 (m) REVERT: B 389 ASP cc_start: 0.6681 (p0) cc_final: 0.6477 (p0) REVERT: B 495 TYR cc_start: 0.8714 (m-10) cc_final: 0.8267 (m-10) REVERT: B 740 MET cc_start: 0.8722 (tpt) cc_final: 0.8506 (tpp) REVERT: B 900 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7845 (mtm) REVERT: B 1029 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8179 (tpp) REVERT: D 102 TYR cc_start: 0.7822 (t80) cc_final: 0.7560 (t80) REVERT: F 2 ILE cc_start: 0.8561 (mp) cc_final: 0.8264 (mp) REVERT: F 27 GLN cc_start: 0.8291 (pt0) cc_final: 0.7703 (pp30) REVERT: F 42 GLN cc_start: 0.8220 (mm110) cc_final: 0.7970 (tm-30) REVERT: F 48 ILE cc_start: 0.8370 (mt) cc_final: 0.8093 (mm) REVERT: C 131 CYS cc_start: 0.6835 (m) cc_final: 0.6584 (m) REVERT: C 389 ASP cc_start: 0.6559 (p0) cc_final: 0.6010 (p0) REVERT: C 390 LEU cc_start: 0.7759 (mt) cc_final: 0.7329 (mt) REVERT: C 740 MET cc_start: 0.8762 (mmm) cc_final: 0.8445 (tpt) REVERT: C 1005 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7466 (tm-30) REVERT: C 1138 TYR cc_start: 0.7990 (t80) cc_final: 0.7694 (m-10) REVERT: E 101 ASP cc_start: 0.8439 (t0) cc_final: 0.7866 (t0) REVERT: G 27 GLN cc_start: 0.8068 (pp30) cc_final: 0.7404 (pp30) REVERT: G 47 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7190 (mp) REVERT: G 48 ILE cc_start: 0.8039 (mt) cc_final: 0.7779 (mm) REVERT: G 103 LYS cc_start: 0.8545 (tppt) cc_final: 0.8219 (tptt) outliers start: 71 outliers final: 61 residues processed: 342 average time/residue: 0.2130 time to fit residues: 117.9408 Evaluate side-chains 344 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 280 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 376 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.0970 chunk 323 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 356 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 352 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 519 HIS ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.127096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.095159 restraints weight = 72043.340| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.08 r_work: 0.3400 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33075 Z= 0.166 Angle : 0.574 9.512 45147 Z= 0.291 Chirality : 0.043 0.161 5259 Planarity : 0.004 0.045 5700 Dihedral : 4.313 19.934 4326 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.14 % Allowed : 13.96 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.02 (0.13), residues: 3954 helix: 1.09 (0.19), residues: 765 sheet: 0.54 (0.16), residues: 1017 loop : -0.68 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 45 TYR 0.020 0.001 TYR B1067 PHE 0.017 0.001 PHE B 347 TRP 0.039 0.002 TRP F 35 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (32946) covalent geometry : angle 0.56810 / 0.29 (44814) SS BOND : bond 0.00292 / 0.19 ( 54) SS BOND : angle 1.05493 / 0.68 ( 108) hydrogen bonds : bond 0.03978 / 2.69 ( 1235) hydrogen bonds : angle 5.24131 / 3.63 ( 3528) link_BETA1-4 : bond 0.00295 / 0.18 ( 24) link_BETA1-4 : angle 1.03496 / 0.67 ( 72) link_NAG-ASN : bond 0.00216 / 0.14 ( 51) link_NAG-ASN : angle 1.23062 / 0.83 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 288 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8920 (mtp) cc_final: 0.8623 (tpp) REVERT: H 58 GLU cc_start: 0.7983 (mp0) cc_final: 0.7513 (tt0) REVERT: H 59 TYR cc_start: 0.8949 (m-80) cc_final: 0.8584 (m-80) REVERT: H 101 ASP cc_start: 0.8203 (t0) cc_final: 0.7785 (t0) REVERT: L 27 GLN cc_start: 0.8048 (pp30) cc_final: 0.7554 (pp30) REVERT: B 131 CYS cc_start: 0.6744 (m) cc_final: 0.6515 (m) REVERT: B 313 TYR cc_start: 0.8179 (m-80) cc_final: 0.7932 (m-80) REVERT: B 389 ASP cc_start: 0.6881 (p0) cc_final: 0.6676 (p0) REVERT: B 495 TYR cc_start: 0.8784 (m-10) cc_final: 0.8359 (m-10) REVERT: B 740 MET cc_start: 0.8768 (tpt) cc_final: 0.8564 (mmm) REVERT: B 900 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7987 (mtm) REVERT: B 1029 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8208 (tpp) REVERT: D 102 TYR cc_start: 0.7843 (t80) cc_final: 0.7575 (t80) REVERT: F 27 GLN cc_start: 0.8353 (pt0) cc_final: 0.7742 (pp30) REVERT: F 42 GLN cc_start: 0.8261 (mm110) cc_final: 0.7990 (tm-30) REVERT: C 131 CYS cc_start: 0.6746 (m) cc_final: 0.6483 (m) REVERT: C 389 ASP cc_start: 0.6743 (p0) cc_final: 0.6152 (p0) REVERT: C 390 LEU cc_start: 0.7753 (mt) cc_final: 0.7296 (mt) REVERT: C 467 ASP cc_start: 0.8436 (p0) cc_final: 0.8110 (p0) REVERT: C 740 MET cc_start: 0.8790 (mmm) cc_final: 0.8361 (tmm) REVERT: C 1138 TYR cc_start: 0.7985 (t80) cc_final: 0.7703 (m-10) REVERT: E 34 MET cc_start: 0.6748 (mmt) cc_final: 0.6478 (mmt) REVERT: E 101 ASP cc_start: 0.8339 (t0) cc_final: 0.7797 (t0) REVERT: G 47 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7241 (mp) REVERT: G 48 ILE cc_start: 0.8096 (mt) cc_final: 0.7718 (mm) REVERT: G 54 ARG cc_start: 0.7725 (mpt180) cc_final: 0.7277 (mpt180) REVERT: G 103 LYS cc_start: 0.8544 (tppt) cc_final: 0.8241 (tptt) outliers start: 74 outliers final: 64 residues processed: 343 average time/residue: 0.2122 time to fit residues: 117.8966 Evaluate side-chains 345 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 278 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 328 optimal weight: 1.9990 chunk 386 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 109 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 189 optimal weight: 0.0370 chunk 384 optimal weight: 0.5980 chunk 231 optimal weight: 0.7980 chunk 299 optimal weight: 0.8980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C1005 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 = 0.4019 r_free = 0.4019 target = 0.128697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.097162 restraints weight = 71115.372| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.07 r_work: 0.3434 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33075 Z= 0.108 Angle : 0.543 9.825 45147 Z= 0.276 Chirality : 0.042 0.164 5259 Planarity : 0.004 0.042 5700 Dihedral : 4.157 19.938 4326 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.77 % Allowed : 14.60 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 0.09 (0.13), residues: 3954 helix: 1.31 (0.19), residues: 765 sheet: 0.57 (0.16), residues: 1020 loop : -0.64 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 77 TYR 0.019 0.001 TYR B1067 PHE 0.009 0.001 PHE A 133 TRP 0.023 0.001 TRP F 35 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (32946) covalent geometry : angle 0.53822 / 0.27 (44814) SS BOND : bond 0.00251 / 0.16 ( 54) SS BOND : angle 0.94406 / 0.60 ( 108) hydrogen bonds : bond 0.03590 / 2.43 ( 1235) hydrogen bonds : angle 5.06995 / 3.51 ( 3528) link_BETA1-4 : bond 0.00346 / 0.22 ( 24) link_BETA1-4 : angle 0.97260 / 0.62 ( 72) link_NAG-ASN : bond 0.00167 / 0.10 ( 51) link_NAG-ASN : angle 1.11079 / 0.75 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 294 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 GLU cc_start: 0.7960 (mp0) cc_final: 0.7535 (tt0) REVERT: H 59 TYR cc_start: 0.8932 (m-80) cc_final: 0.8567 (m-80) REVERT: H 101 ASP cc_start: 0.8198 (t0) cc_final: 0.7784 (t0) REVERT: L 27 GLN cc_start: 0.7996 (pp30) cc_final: 0.7674 (pp30) REVERT: B 131 CYS cc_start: 0.6613 (m) cc_final: 0.6393 (m) REVERT: B 313 TYR cc_start: 0.8163 (m-80) cc_final: 0.7952 (m-80) REVERT: B 389 ASP cc_start: 0.6791 (p0) cc_final: 0.6567 (p0) REVERT: B 740 MET cc_start: 0.8705 (tpt) cc_final: 0.8016 (tmm) REVERT: B 900 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7800 (mtm) REVERT: B 1029 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8177 (tpp) REVERT: D 102 TYR cc_start: 0.7804 (t80) cc_final: 0.7542 (t80) REVERT: F 27 GLN cc_start: 0.8364 (pt0) cc_final: 0.7751 (pp30) REVERT: F 42 GLN cc_start: 0.8212 (mm110) cc_final: 0.7935 (tm-30) REVERT: C 131 CYS cc_start: 0.6779 (m) cc_final: 0.6516 (m) REVERT: C 389 ASP cc_start: 0.6665 (p0) cc_final: 0.6108 (p0) REVERT: C 390 LEU cc_start: 0.7709 (mt) cc_final: 0.7220 (mt) REVERT: C 740 MET cc_start: 0.8752 (mmm) cc_final: 0.8401 (tmm) REVERT: C 902 MET cc_start: 0.8663 (mmt) cc_final: 0.8389 (mmp) REVERT: C 965 GLN cc_start: 0.8001 (tp40) cc_final: 0.7706 (tp40) REVERT: C 1005 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7479 (tm-30) REVERT: C 1138 TYR cc_start: 0.7910 (t80) cc_final: 0.7560 (m-10) REVERT: E 79 TYR cc_start: 0.8451 (m-10) cc_final: 0.8086 (m-10) REVERT: E 101 ASP cc_start: 0.8334 (t0) cc_final: 0.7784 (t0) REVERT: G 27 GLN cc_start: 0.8063 (pp30) cc_final: 0.7748 (pp30) REVERT: G 47 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7235 (mp) REVERT: G 48 ILE cc_start: 0.8111 (mt) cc_final: 0.7783 (mm) REVERT: G 103 LYS cc_start: 0.8515 (tppt) cc_final: 0.8239 (tptt) outliers start: 61 outliers final: 51 residues processed: 340 average time/residue: 0.2151 time to fit residues: 118.0435 Evaluate side-chains 341 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 287 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 62 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 345 optimal weight: 0.0980 chunk 309 optimal weight: 2.9990 chunk 348 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 207 HIS ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.118551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.088292 restraints weight = 68895.421| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.42 r_work: 0.3353 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33075 Z= 0.183 Angle : 0.589 9.602 45147 Z= 0.298 Chirality : 0.044 0.255 5259 Planarity : 0.004 0.044 5700 Dihedral : 4.287 19.650 4326 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.11 % Allowed : 14.39 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 0.02 (0.13), residues: 3954 helix: 1.11 (0.19), residues: 765 sheet: 0.58 (0.16), residues: 1032 loop : -0.66 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 45 TYR 0.020 0.001 TYR B1067 PHE 0.016 0.001 PHE B 347 TRP 0.021 0.002 TRP F 35 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (32946) covalent geometry : angle 0.58252 / 0.30 (44814) SS BOND : bond 0.00308 / 0.20 ( 54) SS BOND : angle 1.05243 / 0.67 ( 108) hydrogen bonds : bond 0.04020 / 2.71 ( 1235) hydrogen bonds : angle 5.19744 / 3.59 ( 3528) link_BETA1-4 : bond 0.00275 / 0.17 ( 24) link_BETA1-4 : angle 1.03943 / 0.67 ( 72) link_NAG-ASN : bond 0.00214 / 0.14 ( 51) link_NAG-ASN : angle 1.23353 / 0.83 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 289 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9014 (mtp) cc_final: 0.8639 (tpp) REVERT: H 59 TYR cc_start: 0.8947 (m-80) cc_final: 0.8682 (m-80) REVERT: H 79 TYR cc_start: 0.8555 (m-80) cc_final: 0.8346 (m-10) REVERT: H 101 ASP cc_start: 0.8288 (t0) cc_final: 0.7843 (t0) REVERT: L 27 GLN cc_start: 0.7966 (pp30) cc_final: 0.7420 (pp30) REVERT: B 131 CYS cc_start: 0.6890 (m) cc_final: 0.6597 (m) REVERT: B 313 TYR cc_start: 0.8230 (m-80) cc_final: 0.7851 (m-80) REVERT: B 389 ASP cc_start: 0.7023 (p0) cc_final: 0.6775 (p0) REVERT: B 740 MET cc_start: 0.8892 (tpt) cc_final: 0.8635 (mmm) REVERT: B 900 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8093 (mtm) REVERT: D 102 TYR cc_start: 0.7894 (t80) cc_final: 0.7600 (t80) REVERT: F 27 GLN cc_start: 0.8362 (pt0) cc_final: 0.7649 (pp30) REVERT: F 54 ARG cc_start: 0.8100 (mmt90) cc_final: 0.7842 (mpt180) REVERT: C 131 CYS cc_start: 0.6962 (m) cc_final: 0.6644 (m) REVERT: C 389 ASP cc_start: 0.6900 (p0) cc_final: 0.6280 (p0) REVERT: C 390 LEU cc_start: 0.7918 (mt) cc_final: 0.7457 (mt) REVERT: C 467 ASP cc_start: 0.8526 (p0) cc_final: 0.8172 (p0) REVERT: C 740 MET cc_start: 0.8874 (mmm) cc_final: 0.8461 (tmm) REVERT: C 1138 TYR cc_start: 0.8009 (t80) cc_final: 0.7525 (m-10) REVERT: E 79 TYR cc_start: 0.8624 (m-10) cc_final: 0.8392 (m-10) REVERT: E 87 THR cc_start: 0.7426 (OUTLIER) cc_final: 0.6945 (m) REVERT: E 101 ASP cc_start: 0.8369 (t0) cc_final: 0.7776 (t0) REVERT: G 27 GLN cc_start: 0.8081 (pp30) cc_final: 0.7334 (pp30) REVERT: G 47 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7278 (mp) REVERT: G 48 ILE cc_start: 0.8212 (mt) cc_final: 0.7818 (mm) REVERT: G 103 LYS cc_start: 0.8514 (tppt) cc_final: 0.8189 (tptt) outliers start: 73 outliers final: 66 residues processed: 341 average time/residue: 0.2121 time to fit residues: 117.4782 Evaluate side-chains 353 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 284 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 59 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 369 optimal weight: 0.4980 chunk 240 optimal weight: 2.9990 chunk 314 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 120 optimal weight: 0.3980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 207 HIS ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.128017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.097642 restraints weight = 70611.274| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.75 r_work: 0.3431 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 33075 Z= 0.198 Angle : 0.696 58.715 45147 Z= 0.377 Chirality : 0.043 0.257 5259 Planarity : 0.004 0.044 5700 Dihedral : 4.306 25.238 4326 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.09 % Allowed : 14.57 % Favored : 83.35 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.17 % 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: 0.01 (0.13), residues: 3954 helix: 1.11 (0.19), residues: 765 sheet: 0.57 (0.16), residues: 1032 loop : -0.66 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 45 TYR 0.020 0.001 TYR B1067 PHE 0.015 0.001 PHE B 347 TRP 0.019 0.001 TRP F 35 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (32946) covalent geometry : angle 0.69176 / 0.38 (44814) SS BOND : bond 0.00305 / 0.20 ( 54) SS BOND : angle 1.03951 / 0.66 ( 108) hydrogen bonds : bond 0.04044 / 2.74 ( 1235) hydrogen bonds : angle 5.21899 / 3.60 ( 3528) link_BETA1-4 : bond 0.00277 / 0.18 ( 24) link_BETA1-4 : angle 1.05110 / 0.68 ( 72) link_NAG-ASN : bond 0.00213 / 0.14 ( 51) link_NAG-ASN : angle 1.23159 / 0.83 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7095.82 seconds wall clock time: 123 minutes 5.17 seconds (7385.17 seconds total)