Starting phenix.real_space_refine on Mon Jul 6 04:19:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l2e_23126/07_2026/7l2e_23126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2e_23126/07_2026/7l2e_23126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l2e_23126/07_2026/7l2e_23126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2e_23126/07_2026/7l2e_23126.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7l2e_23126/07_2026/7l2e_23126.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l2e_23126/07_2026/7l2e_23126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l2e_23126/07_2026/7l2e_23126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2e_23126/07_2026/7l2e_23126.map" } resolution = 2.97 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= 0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 20689 2.51 5 N 5349 2.21 5 O 6465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 252 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32641 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 bond proxies already assigned to first conformer: 8918 Chain: "B" Number of atoms: 8743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 bond proxies already assigned to first conformer: 8918 Chain: "C" Number of atoms: 8744 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 bond proxies already assigned to first conformer: 8916 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "G" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "I" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR A 365 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 365 " occ=0.50 residue: pdb=" N ATYR B 365 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 365 " occ=0.50 residue: pdb=" N ATYR C 365 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 365 " occ=0.50 Time building chain proxies: 10.94, per 1000 atoms: 0.34 Number of scatterers: 32641 At special positions: 0 Unit cell: (194.74, 179.76, 184.04, 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 138 16.00 O 6465 8.00 N 5349 7.00 C 20689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, 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=1.77 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.81 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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 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=1.80 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.04 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 343 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 603 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 149 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 343 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 603 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 149 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 603 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 122 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 17 " " NAG Q 1 " - " ASN A 165 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN B 122 " " NAG W 1 " - " ASN B 234 " " NAG X 1 " - " ASN B 17 " " NAG Y 1 " - " ASN B 165 " " NAG Z 1 " - " ASN C 717 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " " NAG d 1 " - " ASN C 122 " " NAG e 1 " - " ASN C 234 " " NAG f 1 " - " ASN C 17 " " NAG g 1 " - " ASN C 165 " Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 2.2 seconds 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7530 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 69 sheets defined 20.7% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 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 364 through 371 removed outlier: 3.961A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.107A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.433A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 626 through 629 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 748 through 783 removed outlier: 6.085A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.519A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.576A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.230A 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 948 through 966 removed outlier: 3.572A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.831A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.077A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.011A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.959A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.135A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.406A 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 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 626 through 629 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 749 through 783 removed outlier: 6.140A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.593A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 838 removed outlier: 4.185A pdb=" N GLN B 836 " --> pdb=" O GLY B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 removed outlier: 3.767A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.657A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.166A 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 948 through 966 removed outlier: 3.590A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.851A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.113A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.989A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.983A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.143A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.447A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 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 737 through 743 Processing helix chain 'C' and resid 749 through 783 removed outlier: 5.964A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.658A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 838 removed outlier: 4.266A pdb=" N GLN C 836 " --> pdb=" O GLY C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 removed outlier: 3.843A pdb=" N GLN C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.575A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.195A 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 948 through 966 removed outlier: 3.555A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.753A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.050A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.967A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.763A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.762A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.763A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.288A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.559A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.909A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.768A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.422A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.703A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.659A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.776A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.803A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.919A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 5.901A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.584A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.584A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.229A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.065A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.288A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.560A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.910A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.768A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.422A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.766A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.827A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.956A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.578A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.578A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.253A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.288A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.560A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.098A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.909A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.768A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.422A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.701A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.098A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.770A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.792A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.916A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.203A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AG1, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.560A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.560A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AG4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'G' and resid 11 through 12 removed outlier: 7.203A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AG7, first strand: chain 'J' and resid 9 through 12 removed outlier: 3.560A pdb=" N TYR J 86 " --> pdb=" O THR J 102 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 9 through 12 removed outlier: 3.560A pdb=" N TYR J 86 " --> pdb=" O THR J 102 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 21 through 24 Processing sheet with id=AH1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.203A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AH4, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.561A pdb=" N TYR K 86 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.561A pdb=" N TYR K 86 " --> pdb=" O THR K 102 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 21 through 24 1259 hydrogen bonds defined for protein. 3324 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: 9.33 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5283 1.30 - 1.43: 9405 1.43 - 1.56: 18537 1.56 - 1.69: 2 1.69 - 1.82: 174 Bond restraints: 33401 Sorted by residual: bond pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 1.465 1.404 0.061 1.15e-02 7.56e+03 2.81e+01 bond pdb=" N PRO C 82 " pdb=" CA PRO C 82 " ideal model delta sigma weight residual 1.465 1.404 0.061 1.15e-02 7.56e+03 2.78e+01 bond pdb=" N PRO B 82 " pdb=" CA PRO B 82 " ideal model delta sigma weight residual 1.465 1.404 0.060 1.15e-02 7.56e+03 2.76e+01 bond pdb=" C TYR B 248 " pdb=" O TYR B 248 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.26e-02 6.30e+03 2.46e+01 bond pdb=" C PRO B 82 " pdb=" O PRO B 82 " ideal model delta sigma weight residual 1.233 1.178 0.055 1.12e-02 7.97e+03 2.39e+01 ... (remaining 33396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 44505 3.40 - 6.80: 898 6.80 - 10.20: 68 10.20 - 13.59: 11 13.59 - 16.99: 5 Bond angle restraints: 45487 Sorted by residual: angle pdb=" CA ASP A 294 " pdb=" C ASP A 294 " pdb=" N PRO A 295 " ideal model delta sigma weight residual 117.59 134.58 -16.99 9.90e-01 1.02e+00 2.95e+02 angle pdb=" O ASP A 294 " pdb=" C ASP A 294 " pdb=" N PRO A 295 " ideal model delta sigma weight residual 121.32 107.49 13.83 8.50e-01 1.38e+00 2.65e+02 angle pdb=" O ASP B 294 " pdb=" C ASP B 294 " pdb=" N PRO B 295 " ideal model delta sigma weight residual 121.32 107.39 13.93 1.15e+00 7.56e-01 1.47e+02 angle pdb=" C ASP A 294 " pdb=" N PRO A 295 " pdb=" CA PRO A 295 " ideal model delta sigma weight residual 119.19 132.01 -12.82 1.06e+00 8.90e-01 1.46e+02 angle pdb=" C ASP B 294 " pdb=" N PRO B 295 " pdb=" CA PRO B 295 " ideal model delta sigma weight residual 119.19 131.65 -12.46 1.06e+00 8.90e-01 1.38e+02 ... (remaining 45482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 17734 17.99 - 35.99: 1189 35.99 - 53.98: 197 53.98 - 71.98: 42 71.98 - 89.97: 25 Dihedral angle restraints: 19187 sinusoidal: 7413 harmonic: 11774 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -21.46 -64.54 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -22.19 -63.81 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -24.42 -61.58 1 1.00e+01 1.00e-02 5.03e+01 ... (remaining 19184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4951 0.128 - 0.256: 289 0.256 - 0.383: 52 0.383 - 0.511: 11 0.511 - 0.639: 13 Chirality restraints: 5316 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.06e+02 ... (remaining 5313 not shown) Planarity restraints: 5851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1303 " -0.318 2.00e-02 2.50e+03 2.74e-01 9.40e+02 pdb=" C7 NAG B1303 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B1303 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG B1303 " 0.488 2.00e-02 2.50e+03 pdb=" O7 NAG B1303 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.318 2.00e-02 2.50e+03 2.74e-01 9.38e+02 pdb=" C7 NAG C1303 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.153 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.488 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " -0.258 2.00e-02 2.50e+03 2.17e-01 5.87e+02 pdb=" C7 NAG b 2 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " 0.364 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " -0.001 2.00e-02 2.50e+03 ... (remaining 5848 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3623 2.75 - 3.29: 30062 3.29 - 3.83: 53304 3.83 - 4.36: 65376 4.36 - 4.90: 113550 Nonbonded interactions: 265915 Sorted by model distance: nonbonded pdb=" OH TYR K 36 " pdb=" OE1 GLN K 89 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR J 36 " pdb=" OE1 GLN J 89 " model vdw 2.218 3.040 nonbonded pdb=" O GLY A 545 " pdb=" OG SER B 982 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR A 553 " pdb=" OD1 ASP A 586 " model vdw 2.246 3.040 ... (remaining 265910 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 364 or resid 366 through 476 or resid 478 throu \ gh 1310)) selection = (chain 'B' and (resid 14 through 364 or resid 366 through 476 or resid 478 throu \ gh 1310)) selection = (chain 'C' and (resid 14 through 364 or resid 366 through 476 or resid 478 throu \ gh 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 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: 5.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 38.940 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.259 33530 Z= 0.472 Angle : 1.131 16.992 45823 Z= 0.742 Chirality : 0.079 0.639 5316 Planarity : 0.015 0.274 5797 Dihedral : 12.764 89.973 11504 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.34 % Allowed : 2.54 % Favored : 97.11 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 4030 helix: -0.14 (0.18), residues: 717 sheet: 0.16 (0.16), residues: 1092 loop : -0.82 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.043 0.002 TYR C 495 PHE 0.031 0.002 PHE A 906 TRP 0.024 0.003 TRP B 64 HIS 0.016 0.002 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.46 (33401) covalent geometry : angle 1.10980 / 0.74 (45487) SS BOND : bond 0.05734 / 3.70 ( 51) SS BOND : angle 1.21511 / 0.80 ( 102) hydrogen bonds : bond 0.16450 / 11.02 ( 1190) hydrogen bonds : angle 7.75260 / 5.42 ( 3324) link_BETA1-4 : bond 0.00442 / 0.27 ( 24) link_BETA1-4 : angle 1.61422 / 1.12 ( 72) link_NAG-ASN : bond 0.00845 / 0.51 ( 54) link_NAG-ASN : angle 3.74325 / 2.92 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 354 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6526 (mtt) cc_final: 0.6301 (mtt) REVERT: A 697 MET cc_start: 0.7600 (ttt) cc_final: 0.7262 (ttt) REVERT: A 814 LYS cc_start: 0.8266 (tptt) cc_final: 0.8033 (mmmt) REVERT: A 817 PHE cc_start: 0.7995 (t80) cc_final: 0.7708 (t80) REVERT: A 841 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6817 (mt) REVERT: B 817 PHE cc_start: 0.7729 (t80) cc_final: 0.7404 (t80) REVERT: C 200 TYR cc_start: 0.8336 (m-80) cc_final: 0.7904 (m-80) REVERT: C 854 LYS cc_start: 0.7369 (tptt) cc_final: 0.6897 (mttm) outliers start: 12 outliers final: 3 residues processed: 359 average time/residue: 0.5721 time to fit residues: 249.7270 Evaluate side-chains 219 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 215 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1092 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 188 ASN A 211 ASN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 957 GLN A 960 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 804 GLN B 856 ASN B 935 GLN B 960 ASN C 188 ASN C 207 HIS C 211 ASN C 804 GLN C 856 ASN C 960 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 105 GLN L 31 GLN L 42 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 105 GLN J 31 GLN J 42 GLN I 73 ASN I 76 ASN I 105 GLN K 31 GLN K 42 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.147505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097483 restraints weight = 76973.748| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.48 r_work: 0.3094 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33530 Z= 0.151 Angle : 0.595 8.207 45823 Z= 0.304 Chirality : 0.045 0.220 5316 Planarity : 0.005 0.084 5797 Dihedral : 4.770 52.555 4395 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.86 % Allowed : 6.83 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.13), residues: 4030 helix: 0.69 (0.19), residues: 741 sheet: 0.20 (0.16), residues: 1044 loop : -0.77 (0.13), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 646 TYR 0.031 0.002 TYR G 52A PHE 0.024 0.002 PHE A 906 TRP 0.018 0.002 TRP A 64 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (33401) covalent geometry : angle 0.58445 / 0.30 (45487) SS BOND : bond 0.00365 / 0.26 ( 51) SS BOND : angle 0.77353 / 0.52 ( 102) hydrogen bonds : bond 0.04134 / 2.73 ( 1190) hydrogen bonds : angle 5.80305 / 4.07 ( 3324) link_BETA1-4 : bond 0.00418 / 0.26 ( 24) link_BETA1-4 : angle 1.39955 / 0.94 ( 72) link_NAG-ASN : bond 0.00309 / 0.21 ( 54) link_NAG-ASN : angle 1.73015 / 1.20 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 247 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6654 (mtt) cc_final: 0.6348 (mtp) REVERT: A 258 TRP cc_start: 0.6143 (m100) cc_final: 0.5025 (t60) REVERT: A 697 MET cc_start: 0.7750 (ttt) cc_final: 0.7310 (ttt) REVERT: A 765 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7998 (ttm110) REVERT: A 789 TYR cc_start: 0.7443 (m-80) cc_final: 0.6890 (m-10) REVERT: A 814 LYS cc_start: 0.8263 (tptt) cc_final: 0.8058 (tppt) REVERT: A 841 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6749 (mt) REVERT: B 96 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7605 (pt0) REVERT: B 175 PHE cc_start: 0.7751 (m-10) cc_final: 0.7548 (m-10) REVERT: B 258 TRP cc_start: 0.6165 (m100) cc_final: 0.5244 (t60) REVERT: B 789 TYR cc_start: 0.7774 (m-80) cc_final: 0.7522 (m-80) REVERT: B 814 LYS cc_start: 0.8445 (tppt) cc_final: 0.7854 (mptp) REVERT: C 96 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: C 258 TRP cc_start: 0.6102 (m100) cc_final: 0.5190 (t60) REVERT: C 551 VAL cc_start: 0.7216 (p) cc_final: 0.6961 (m) REVERT: C 789 TYR cc_start: 0.7685 (m-80) cc_final: 0.7440 (m-10) REVERT: C 817 PHE cc_start: 0.8197 (t80) cc_final: 0.7987 (t80) REVERT: C 854 LYS cc_start: 0.7646 (tptt) cc_final: 0.7146 (mttp) REVERT: H 2 VAL cc_start: 0.6738 (m) cc_final: 0.6478 (t) REVERT: H 58 HIS cc_start: 0.6087 (OUTLIER) cc_final: 0.5131 (m-70) REVERT: H 94 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7074 (pttm) REVERT: L 95 TYR cc_start: 0.8701 (m-80) cc_final: 0.8460 (m-80) REVERT: G 46 GLU cc_start: 0.7818 (tt0) cc_final: 0.7406 (tt0) REVERT: I 38 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7200 (ttm170) REVERT: I 46 GLU cc_start: 0.8040 (tt0) cc_final: 0.7541 (pt0) REVERT: I 94 LYS cc_start: 0.7604 (tttm) cc_final: 0.7379 (tttm) outliers start: 65 outliers final: 22 residues processed: 289 average time/residue: 0.5052 time to fit residues: 182.4798 Evaluate side-chains 245 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 90 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 94 LYS Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 260 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 341 optimal weight: 1.9990 chunk 388 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN A 856 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN B 804 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 487 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 73 ASN I 76 ASN I 82AASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.141919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.091207 restraints weight = 78615.850| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.29 r_work: 0.3004 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 33530 Z= 0.242 Angle : 0.625 8.741 45823 Z= 0.321 Chirality : 0.047 0.177 5316 Planarity : 0.005 0.069 5797 Dihedral : 4.799 48.170 4387 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.03 % Allowed : 9.35 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.13), residues: 4030 helix: 0.80 (0.19), residues: 717 sheet: 0.01 (0.16), residues: 1062 loop : -0.71 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 646 TYR 0.033 0.002 TYR G 52A PHE 0.035 0.002 PHE A 906 TRP 0.018 0.002 TRP B 64 HIS 0.010 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.24 (33401) covalent geometry : angle 0.61731 / 0.32 (45487) SS BOND : bond 0.00477 / 0.32 ( 51) SS BOND : angle 0.86065 / 0.58 ( 102) hydrogen bonds : bond 0.04439 / 2.91 ( 1190) hydrogen bonds : angle 5.74596 / 4.03 ( 3324) link_BETA1-4 : bond 0.00333 / 0.23 ( 24) link_BETA1-4 : angle 1.18373 / 0.79 ( 72) link_NAG-ASN : bond 0.00308 / 0.21 ( 54) link_NAG-ASN : angle 1.60383 / 1.12 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 215 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7897 (tp) cc_final: 0.7601 (tt) REVERT: A 96 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: A 153 MET cc_start: 0.6747 (mtt) cc_final: 0.6505 (mtp) REVERT: A 258 TRP cc_start: 0.6129 (OUTLIER) cc_final: 0.4970 (t60) REVERT: A 697 MET cc_start: 0.7736 (ttt) cc_final: 0.7373 (ttt) REVERT: A 814 LYS cc_start: 0.8336 (tptt) cc_final: 0.8030 (tppt) REVERT: A 841 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6856 (mt) REVERT: B 24 LEU cc_start: 0.7773 (tp) cc_final: 0.7449 (tt) REVERT: B 96 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: B 258 TRP cc_start: 0.6129 (m100) cc_final: 0.5104 (t60) REVERT: B 814 LYS cc_start: 0.8345 (tppt) cc_final: 0.7745 (mptp) REVERT: B 855 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7368 (m-10) REVERT: C 200 TYR cc_start: 0.8555 (m-80) cc_final: 0.8231 (m-80) REVERT: C 258 TRP cc_start: 0.6041 (OUTLIER) cc_final: 0.5124 (t60) REVERT: C 532 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.7237 (p0) REVERT: C 814 LYS cc_start: 0.8294 (tppt) cc_final: 0.7796 (mptp) REVERT: C 841 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7429 (pt) REVERT: C 854 LYS cc_start: 0.7696 (tptt) cc_final: 0.7112 (mttp) REVERT: C 904 TYR cc_start: 0.6852 (m-80) cc_final: 0.6175 (t80) REVERT: C 1005 GLN cc_start: 0.8419 (tt0) cc_final: 0.8110 (tp40) REVERT: H 2 VAL cc_start: 0.6896 (m) cc_final: 0.6690 (t) REVERT: H 32 TYR cc_start: 0.7868 (m-80) cc_final: 0.7522 (m-80) REVERT: H 58 HIS cc_start: 0.6391 (OUTLIER) cc_final: 0.5216 (m-70) REVERT: H 82 MET cc_start: 0.7578 (ttp) cc_final: 0.7292 (tpp) REVERT: G 46 GLU cc_start: 0.7842 (tt0) cc_final: 0.7551 (tt0) REVERT: G 82 MET cc_start: 0.7246 (ttp) cc_final: 0.7014 (tpp) REVERT: J 32 TYR cc_start: 0.8084 (m-10) cc_final: 0.7797 (m-10) REVERT: I 32 TYR cc_start: 0.8086 (m-80) cc_final: 0.7699 (m-80) REVERT: I 58 HIS cc_start: 0.6253 (OUTLIER) cc_final: 0.5907 (m90) REVERT: I 94 LYS cc_start: 0.7671 (tttm) cc_final: 0.7319 (tttm) outliers start: 71 outliers final: 33 residues processed: 260 average time/residue: 0.5244 time to fit residues: 169.0113 Evaluate side-chains 250 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 244 optimal weight: 0.7980 chunk 210 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 120 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 804 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.094373 restraints weight = 67177.967| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.09 r_work: 0.3056 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33530 Z= 0.127 Angle : 0.545 8.502 45823 Z= 0.279 Chirality : 0.044 0.191 5316 Planarity : 0.004 0.060 5797 Dihedral : 4.568 44.702 4387 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.74 % Allowed : 10.69 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4030 helix: 1.09 (0.20), residues: 717 sheet: 0.04 (0.16), residues: 1038 loop : -0.71 (0.12), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 646 TYR 0.033 0.001 TYR G 52A PHE 0.021 0.001 PHE C 759 TRP 0.017 0.002 TRP C 64 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (33401) covalent geometry : angle 0.53817 / 0.28 (45487) SS BOND : bond 0.00310 / 0.21 ( 51) SS BOND : angle 0.67966 / 0.47 ( 102) hydrogen bonds : bond 0.03761 / 2.50 ( 1190) hydrogen bonds : angle 5.45759 / 3.83 ( 3324) link_BETA1-4 : bond 0.00368 / 0.24 ( 24) link_BETA1-4 : angle 1.08607 / 0.72 ( 72) link_NAG-ASN : bond 0.00221 / 0.14 ( 54) link_NAG-ASN : angle 1.42543 / 0.98 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7639 (tt) REVERT: A 150 LYS cc_start: 0.8118 (mptt) cc_final: 0.7732 (mppt) REVERT: A 153 MET cc_start: 0.6743 (mtt) cc_final: 0.6473 (mtp) REVERT: A 697 MET cc_start: 0.7711 (ttt) cc_final: 0.7375 (ttt) REVERT: A 740 MET cc_start: 0.9016 (ttp) cc_final: 0.8656 (tpp) REVERT: A 765 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7893 (ttm110) REVERT: A 789 TYR cc_start: 0.7654 (m-80) cc_final: 0.7440 (m-10) REVERT: A 814 LYS cc_start: 0.8364 (tptt) cc_final: 0.7961 (tppt) REVERT: A 841 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6885 (mt) REVERT: B 24 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7325 (tt) REVERT: B 96 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7477 (pt0) REVERT: B 153 MET cc_start: 0.6538 (mtt) cc_final: 0.6280 (mtp) REVERT: B 258 TRP cc_start: 0.6140 (m100) cc_final: 0.4980 (t60) REVERT: B 814 LYS cc_start: 0.8299 (tppt) cc_final: 0.7687 (mptp) REVERT: B 841 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7199 (pt) REVERT: B 855 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7286 (m-10) REVERT: C 69 HIS cc_start: 0.6720 (OUTLIER) cc_final: 0.6489 (t-170) REVERT: C 258 TRP cc_start: 0.6007 (OUTLIER) cc_final: 0.5168 (t60) REVERT: C 532 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7274 (p0) REVERT: C 814 LYS cc_start: 0.8269 (tppt) cc_final: 0.7758 (mptp) REVERT: C 841 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7365 (pt) REVERT: C 854 LYS cc_start: 0.7818 (tptt) cc_final: 0.7184 (mttp) REVERT: C 904 TYR cc_start: 0.6774 (m-80) cc_final: 0.6152 (t80) REVERT: H 32 TYR cc_start: 0.7896 (m-80) cc_final: 0.7615 (m-80) REVERT: H 58 HIS cc_start: 0.6297 (OUTLIER) cc_final: 0.5136 (m-70) REVERT: G 46 GLU cc_start: 0.7798 (tt0) cc_final: 0.7549 (tt0) REVERT: G 94 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7462 (pttp) REVERT: I 58 HIS cc_start: 0.6359 (OUTLIER) cc_final: 0.6026 (m90) REVERT: I 82 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.5832 (ptm) REVERT: K 35 TRP cc_start: 0.6997 (m100) cc_final: 0.6719 (m100) REVERT: K 95 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.8074 (t) outliers start: 61 outliers final: 28 residues processed: 244 average time/residue: 0.5322 time to fit residues: 161.2718 Evaluate side-chains 243 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 191 optimal weight: 0.0030 chunk 3 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 339 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 333 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 392 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1119 ASN C 207 HIS C1106 GLN H 76 ASN G 76 ASN I 82AASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093820 restraints weight = 84530.333| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.42 r_work: 0.3040 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33530 Z= 0.123 Angle : 0.523 8.566 45823 Z= 0.267 Chirality : 0.043 0.186 5316 Planarity : 0.004 0.055 5797 Dihedral : 4.391 40.390 4387 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.74 % Allowed : 11.12 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.13), residues: 4030 helix: 1.18 (0.20), residues: 729 sheet: 0.06 (0.15), residues: 1080 loop : -0.67 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 646 TYR 0.033 0.001 TYR G 52A PHE 0.023 0.001 PHE C 759 TRP 0.016 0.001 TRP C 64 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (33401) covalent geometry : angle 0.51692 / 0.27 (45487) SS BOND : bond 0.00293 / 0.20 ( 51) SS BOND : angle 0.61309 / 0.43 ( 102) hydrogen bonds : bond 0.03588 / 2.38 ( 1190) hydrogen bonds : angle 5.28460 / 3.71 ( 3324) link_BETA1-4 : bond 0.00359 / 0.24 ( 24) link_BETA1-4 : angle 1.06787 / 0.71 ( 72) link_NAG-ASN : bond 0.00182 / 0.12 ( 54) link_NAG-ASN : angle 1.27617 / 0.88 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7576 (tt) REVERT: A 96 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7787 (pt0) REVERT: A 150 LYS cc_start: 0.7948 (mptt) cc_final: 0.7681 (mppt) REVERT: A 153 MET cc_start: 0.6753 (mtt) cc_final: 0.6469 (mtp) REVERT: A 697 MET cc_start: 0.7725 (ttt) cc_final: 0.7397 (ttt) REVERT: A 740 MET cc_start: 0.8974 (ttp) cc_final: 0.8614 (tpp) REVERT: A 765 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7952 (ttm110) REVERT: A 789 TYR cc_start: 0.7567 (m-80) cc_final: 0.7356 (m-10) REVERT: A 814 LYS cc_start: 0.8441 (tptt) cc_final: 0.7987 (tppt) REVERT: B 24 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7446 (tt) REVERT: B 68 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8194 (tt) REVERT: B 96 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7525 (pt0) REVERT: B 814 LYS cc_start: 0.8245 (tppt) cc_final: 0.8002 (tptm) REVERT: B 823 PHE cc_start: 0.8047 (m-10) cc_final: 0.7703 (m-80) REVERT: B 841 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7274 (pt) REVERT: B 855 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7257 (m-10) REVERT: C 69 HIS cc_start: 0.6699 (OUTLIER) cc_final: 0.6458 (t-170) REVERT: C 258 TRP cc_start: 0.5905 (m100) cc_final: 0.5099 (t60) REVERT: C 532 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.7298 (p0) REVERT: C 841 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7261 (pt) REVERT: C 854 LYS cc_start: 0.7829 (tptt) cc_final: 0.7175 (mttp) REVERT: H 32 TYR cc_start: 0.7898 (m-80) cc_final: 0.7471 (m-80) REVERT: H 34 MET cc_start: 0.7208 (mtp) cc_final: 0.6844 (mtp) REVERT: H 58 HIS cc_start: 0.6265 (OUTLIER) cc_final: 0.5114 (m-70) REVERT: H 82 MET cc_start: 0.7423 (ttp) cc_final: 0.7050 (tpp) REVERT: G 46 GLU cc_start: 0.7796 (tt0) cc_final: 0.7552 (tt0) REVERT: G 94 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7498 (pttp) REVERT: I 46 GLU cc_start: 0.7689 (tt0) cc_final: 0.7445 (pt0) REVERT: I 58 HIS cc_start: 0.6423 (OUTLIER) cc_final: 0.6012 (m90) REVERT: I 82 MET cc_start: 0.6397 (OUTLIER) cc_final: 0.5691 (ptm) REVERT: K 35 TRP cc_start: 0.6969 (m100) cc_final: 0.6689 (m100) REVERT: K 95 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8076 (t) outliers start: 61 outliers final: 32 residues processed: 251 average time/residue: 0.5327 time to fit residues: 165.9657 Evaluate side-chains 254 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 124 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 293 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 339 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 357 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN C1106 GLN H 39 GLN G 76 ASN I 39 GLN I 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.141980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.090985 restraints weight = 87256.849| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.46 r_work: 0.2997 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 33530 Z= 0.205 Angle : 0.572 9.353 45823 Z= 0.290 Chirality : 0.045 0.177 5316 Planarity : 0.004 0.053 5797 Dihedral : 4.464 19.569 4385 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.29 % Allowed : 10.92 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 4030 helix: 1.08 (0.20), residues: 717 sheet: 0.05 (0.16), residues: 1050 loop : -0.68 (0.13), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 646 TYR 0.037 0.002 TYR H 52A PHE 0.024 0.002 PHE C 906 TRP 0.016 0.002 TRP L 35 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.20 (33401) covalent geometry : angle 0.56476 / 0.29 (45487) SS BOND : bond 0.00411 / 0.28 ( 51) SS BOND : angle 0.73486 / 0.51 ( 102) hydrogen bonds : bond 0.03955 / 2.61 ( 1190) hydrogen bonds : angle 5.40768 / 3.80 ( 3324) link_BETA1-4 : bond 0.00330 / 0.23 ( 24) link_BETA1-4 : angle 1.11482 / 0.74 ( 72) link_NAG-ASN : bond 0.00224 / 0.14 ( 54) link_NAG-ASN : angle 1.41102 / 0.98 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 217 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7743 (tt) REVERT: A 96 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7799 (pt0) REVERT: A 150 LYS cc_start: 0.7947 (mptt) cc_final: 0.7637 (mppt) REVERT: A 153 MET cc_start: 0.6728 (mtt) cc_final: 0.6410 (mtp) REVERT: A 697 MET cc_start: 0.7757 (ttt) cc_final: 0.7424 (ttt) REVERT: A 740 MET cc_start: 0.9016 (ttp) cc_final: 0.8657 (tpp) REVERT: A 789 TYR cc_start: 0.7716 (m-80) cc_final: 0.7395 (m-10) REVERT: A 814 LYS cc_start: 0.8435 (tptt) cc_final: 0.7939 (tppt) REVERT: A 843 ASP cc_start: 0.5986 (OUTLIER) cc_final: 0.5601 (p0) REVERT: B 24 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7395 (tt) REVERT: B 96 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: B 153 MET cc_start: 0.6581 (mtt) cc_final: 0.6258 (mtp) REVERT: B 814 LYS cc_start: 0.8195 (tppt) cc_final: 0.7671 (mptp) REVERT: B 823 PHE cc_start: 0.8248 (m-10) cc_final: 0.7923 (m-80) REVERT: B 841 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7389 (pt) REVERT: B 855 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7278 (m-10) REVERT: C 69 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6569 (t-170) REVERT: C 258 TRP cc_start: 0.5923 (m100) cc_final: 0.5091 (t60) REVERT: C 532 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.7318 (p0) REVERT: C 841 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7299 (pt) REVERT: C 854 LYS cc_start: 0.7877 (tptt) cc_final: 0.7194 (mttp) REVERT: C 904 TYR cc_start: 0.7071 (m-80) cc_final: 0.6390 (t80) REVERT: C 1005 GLN cc_start: 0.8417 (tt0) cc_final: 0.8109 (tp40) REVERT: C 1072 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: H 34 MET cc_start: 0.7383 (mtp) cc_final: 0.7001 (mtp) REVERT: H 58 HIS cc_start: 0.6369 (OUTLIER) cc_final: 0.5070 (m-70) REVERT: H 82 MET cc_start: 0.7322 (ttp) cc_final: 0.6991 (tpp) REVERT: L 95 TYR cc_start: 0.8798 (m-80) cc_final: 0.8545 (m-80) REVERT: G 46 GLU cc_start: 0.7850 (tt0) cc_final: 0.7604 (tt0) REVERT: G 94 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7477 (pttp) REVERT: I 38 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.6895 (ttm170) REVERT: I 46 GLU cc_start: 0.7717 (tt0) cc_final: 0.7434 (pt0) REVERT: I 58 HIS cc_start: 0.6416 (OUTLIER) cc_final: 0.6075 (m90) REVERT: I 82 MET cc_start: 0.6519 (OUTLIER) cc_final: 0.5845 (ptm) REVERT: K 35 TRP cc_start: 0.7055 (m100) cc_final: 0.6761 (m100) REVERT: K 95 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8084 (t) outliers start: 80 outliers final: 42 residues processed: 269 average time/residue: 0.5543 time to fit residues: 184.2100 Evaluate side-chains 263 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 204 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 83 optimal weight: 0.2980 chunk 178 optimal weight: 0.0040 chunk 290 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 207 HIS C1083 HIS C1106 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 76 ASN G 76 ASN J 31 GLN I 82AASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.094162 restraints weight = 82020.372| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.36 r_work: 0.3047 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33530 Z= 0.112 Angle : 0.520 9.220 45823 Z= 0.264 Chirality : 0.043 0.186 5316 Planarity : 0.004 0.050 5797 Dihedral : 4.281 18.073 4385 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.03 % Allowed : 11.75 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 4030 helix: 1.26 (0.20), residues: 729 sheet: 0.11 (0.16), residues: 1044 loop : -0.68 (0.12), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 646 TYR 0.036 0.001 TYR H 52A PHE 0.024 0.001 PHE C 759 TRP 0.019 0.002 TRP J 35 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (33401) covalent geometry : angle 0.51380 / 0.26 (45487) SS BOND : bond 0.00267 / 0.19 ( 51) SS BOND : angle 0.60745 / 0.43 ( 102) hydrogen bonds : bond 0.03476 / 2.31 ( 1190) hydrogen bonds : angle 5.17651 / 3.64 ( 3324) link_BETA1-4 : bond 0.00375 / 0.25 ( 24) link_BETA1-4 : angle 1.02097 / 0.68 ( 72) link_NAG-ASN : bond 0.00168 / 0.11 ( 54) link_NAG-ASN : angle 1.23290 / 0.85 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 207 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7754 (pt0) REVERT: A 150 LYS cc_start: 0.7841 (mptt) cc_final: 0.7603 (mmtm) REVERT: A 153 MET cc_start: 0.6759 (mtt) cc_final: 0.6432 (mtp) REVERT: A 697 MET cc_start: 0.7786 (ttt) cc_final: 0.7474 (ttt) REVERT: A 740 MET cc_start: 0.8963 (ttp) cc_final: 0.8589 (tpp) REVERT: A 765 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7954 (ttm110) REVERT: A 814 LYS cc_start: 0.8438 (tptt) cc_final: 0.7919 (tppt) REVERT: A 843 ASP cc_start: 0.5976 (OUTLIER) cc_final: 0.5587 (p0) REVERT: B 24 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7306 (tt) REVERT: B 96 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7585 (pt0) REVERT: B 741 TYR cc_start: 0.9111 (t80) cc_final: 0.8876 (t80) REVERT: B 814 LYS cc_start: 0.8216 (tppt) cc_final: 0.7683 (mptp) REVERT: B 823 PHE cc_start: 0.8211 (m-10) cc_final: 0.7804 (m-80) REVERT: B 841 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7338 (pt) REVERT: B 855 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7219 (m-10) REVERT: C 258 TRP cc_start: 0.5941 (m100) cc_final: 0.5140 (t60) REVERT: C 532 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7333 (p0) REVERT: C 814 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7180 (tmtm) REVERT: C 841 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7259 (pt) REVERT: C 854 LYS cc_start: 0.7913 (tptt) cc_final: 0.7219 (mttp) REVERT: C 1072 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: H 34 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.7017 (mtp) REVERT: H 82 MET cc_start: 0.7358 (ttp) cc_final: 0.6928 (tpp) REVERT: G 46 GLU cc_start: 0.7813 (tt0) cc_final: 0.7512 (tt0) REVERT: G 53 ASP cc_start: 0.7990 (p0) cc_final: 0.7761 (p0) REVERT: J 35 TRP cc_start: 0.6990 (m100) cc_final: 0.6750 (m100) REVERT: I 46 GLU cc_start: 0.7658 (tt0) cc_final: 0.7373 (pt0) REVERT: I 58 HIS cc_start: 0.6512 (OUTLIER) cc_final: 0.6075 (m90) REVERT: I 82 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.5770 (ptm) REVERT: K 35 TRP cc_start: 0.7041 (m100) cc_final: 0.6764 (m100) outliers start: 71 outliers final: 38 residues processed: 257 average time/residue: 0.5358 time to fit residues: 169.4810 Evaluate side-chains 251 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 143 optimal weight: 0.7980 chunk 323 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 328 optimal weight: 0.7980 chunk 232 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN B1119 ASN C1106 GLN H 39 GLN L 31 GLN G 76 ASN J 31 GLN I 39 GLN I 73 ASN I 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.142356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.092293 restraints weight = 73907.426| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.21 r_work: 0.3023 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33530 Z= 0.177 Angle : 0.552 9.260 45823 Z= 0.280 Chirality : 0.044 0.175 5316 Planarity : 0.004 0.049 5797 Dihedral : 4.357 19.787 4385 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.94 % Allowed : 12.35 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4030 helix: 1.20 (0.20), residues: 726 sheet: 0.05 (0.16), residues: 1044 loop : -0.65 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 646 TYR 0.036 0.002 TYR H 52A PHE 0.020 0.002 PHE A 759 TRP 0.019 0.002 TRP K 96 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (33401) covalent geometry : angle 0.54538 / 0.28 (45487) SS BOND : bond 0.00362 / 0.25 ( 51) SS BOND : angle 0.67066 / 0.47 ( 102) hydrogen bonds : bond 0.03784 / 2.50 ( 1190) hydrogen bonds : angle 5.28770 / 3.71 ( 3324) link_BETA1-4 : bond 0.00322 / 0.22 ( 24) link_BETA1-4 : angle 1.07135 / 0.71 ( 72) link_NAG-ASN : bond 0.00171 / 0.11 ( 54) link_NAG-ASN : angle 1.32427 / 0.91 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 209 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7752 (pt0) REVERT: A 150 LYS cc_start: 0.7919 (mptt) cc_final: 0.7662 (mmtm) REVERT: A 153 MET cc_start: 0.6785 (mtt) cc_final: 0.6452 (mtp) REVERT: A 697 MET cc_start: 0.7751 (ttt) cc_final: 0.7417 (ttt) REVERT: A 740 MET cc_start: 0.8999 (ttp) cc_final: 0.8616 (tpp) REVERT: A 765 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7961 (ttm110) REVERT: A 814 LYS cc_start: 0.8503 (tptt) cc_final: 0.7975 (tppt) REVERT: A 843 ASP cc_start: 0.6012 (OUTLIER) cc_final: 0.5614 (p0) REVERT: B 24 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7297 (tt) REVERT: B 96 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7643 (pt0) REVERT: B 814 LYS cc_start: 0.8199 (tppt) cc_final: 0.7662 (mptp) REVERT: B 823 PHE cc_start: 0.8277 (m-10) cc_final: 0.7887 (m-80) REVERT: B 841 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7356 (pt) REVERT: B 855 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7274 (m-10) REVERT: C 69 HIS cc_start: 0.6860 (OUTLIER) cc_final: 0.6547 (t-170) REVERT: C 258 TRP cc_start: 0.5957 (m100) cc_final: 0.5160 (t60) REVERT: C 532 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7352 (p0) REVERT: C 814 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7150 (tmtm) REVERT: C 841 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7308 (pt) REVERT: C 854 LYS cc_start: 0.7936 (tptt) cc_final: 0.7243 (mttp) REVERT: C 904 TYR cc_start: 0.7015 (m-80) cc_final: 0.6348 (t80) REVERT: C 1072 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: H 34 MET cc_start: 0.7348 (mtp) cc_final: 0.7109 (mtp) REVERT: H 38 ARG cc_start: 0.7979 (tmm160) cc_final: 0.7583 (tmm160) REVERT: H 82 MET cc_start: 0.7448 (ttp) cc_final: 0.6968 (tpp) REVERT: G 53 ASP cc_start: 0.7983 (p0) cc_final: 0.7762 (p0) REVERT: G 82 MET cc_start: 0.7068 (mmt) cc_final: 0.6810 (tpt) REVERT: J 35 TRP cc_start: 0.7033 (m100) cc_final: 0.6739 (m100) REVERT: J 49 TYR cc_start: 0.7614 (p90) cc_final: 0.7389 (p90) REVERT: I 46 GLU cc_start: 0.7753 (tt0) cc_final: 0.7514 (pt0) REVERT: I 58 HIS cc_start: 0.6431 (OUTLIER) cc_final: 0.6089 (m90) REVERT: K 35 TRP cc_start: 0.7082 (m100) cc_final: 0.6776 (m100) REVERT: K 95 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8097 (t) outliers start: 68 outliers final: 43 residues processed: 258 average time/residue: 0.5330 time to fit residues: 169.0495 Evaluate side-chains 261 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 205 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 366 optimal weight: 0.9990 chunk 369 optimal weight: 4.9990 chunk 353 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 305 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 225 optimal weight: 0.8980 chunk 27 optimal weight: 0.0770 chunk 71 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN H 39 GLN H 76 ASN L 31 GLN G 39 GLN G 76 ASN J 31 GLN I 39 GLN I 82AASN K 31 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.143378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093173 restraints weight = 65131.784| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.28 r_work: 0.3074 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33530 Z= 0.118 Angle : 0.521 9.368 45823 Z= 0.265 Chirality : 0.043 0.185 5316 Planarity : 0.004 0.048 5797 Dihedral : 4.255 18.875 4385 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.77 % Allowed : 12.52 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 4030 helix: 1.27 (0.20), residues: 729 sheet: 0.12 (0.16), residues: 1044 loop : -0.65 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 646 TYR 0.025 0.001 TYR J 49 PHE 0.015 0.001 PHE C 906 TRP 0.022 0.002 TRP K 96 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (33401) covalent geometry : angle 0.51600 / 0.26 (45487) SS BOND : bond 0.00271 / 0.19 ( 51) SS BOND : angle 0.59889 / 0.42 ( 102) hydrogen bonds : bond 0.03507 / 2.33 ( 1190) hydrogen bonds : angle 5.15723 / 3.62 ( 3324) link_BETA1-4 : bond 0.00357 / 0.24 ( 24) link_BETA1-4 : angle 1.02270 / 0.68 ( 72) link_NAG-ASN : bond 0.00152 / 0.10 ( 54) link_NAG-ASN : angle 1.21087 / 0.83 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7793 (pt0) REVERT: A 150 LYS cc_start: 0.7880 (mptt) cc_final: 0.7671 (mppt) REVERT: A 153 MET cc_start: 0.6780 (mtt) cc_final: 0.6427 (mtp) REVERT: A 697 MET cc_start: 0.7755 (ttt) cc_final: 0.7442 (ttt) REVERT: A 740 MET cc_start: 0.8960 (ttp) cc_final: 0.8578 (tpp) REVERT: A 765 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7979 (ttm110) REVERT: A 789 TYR cc_start: 0.7502 (m-80) cc_final: 0.7245 (m-10) REVERT: A 843 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5580 (p0) REVERT: B 24 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7262 (tt) REVERT: B 96 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: B 220 PHE cc_start: 0.8796 (t80) cc_final: 0.8370 (t80) REVERT: B 741 TYR cc_start: 0.9088 (t80) cc_final: 0.8862 (t80) REVERT: B 814 LYS cc_start: 0.8125 (tppt) cc_final: 0.7615 (mptp) REVERT: B 823 PHE cc_start: 0.8297 (m-10) cc_final: 0.7916 (m-80) REVERT: B 841 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7306 (pt) REVERT: B 855 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7224 (m-10) REVERT: C 69 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.6454 (t-170) REVERT: C 258 TRP cc_start: 0.5901 (m100) cc_final: 0.5127 (t60) REVERT: C 532 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.7325 (p0) REVERT: C 740 MET cc_start: 0.9200 (mmm) cc_final: 0.8985 (tpp) REVERT: C 814 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7092 (tmtm) REVERT: C 841 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7278 (pt) REVERT: C 854 LYS cc_start: 0.7920 (tptt) cc_final: 0.7231 (mttp) REVERT: C 1072 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: H 82 MET cc_start: 0.7569 (ttp) cc_final: 0.7115 (tpp) REVERT: G 82 MET cc_start: 0.7288 (mmt) cc_final: 0.6905 (tpt) REVERT: J 49 TYR cc_start: 0.7523 (p90) cc_final: 0.7304 (p90) REVERT: I 58 HIS cc_start: 0.6508 (OUTLIER) cc_final: 0.6044 (m90) REVERT: I 71 ARG cc_start: 0.7541 (ptm160) cc_final: 0.7322 (ptm160) REVERT: I 82 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.5824 (ptm) REVERT: K 35 TRP cc_start: 0.6978 (m100) cc_final: 0.6694 (m100) outliers start: 62 outliers final: 40 residues processed: 251 average time/residue: 0.5762 time to fit residues: 178.5577 Evaluate side-chains 256 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 157 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 150 optimal weight: 0.3980 chunk 178 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 387 optimal weight: 1.9990 chunk 318 optimal weight: 0.6980 chunk 276 optimal weight: 2.9990 chunk 246 optimal weight: 7.9990 chunk 213 optimal weight: 0.6980 chunk 271 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1083 HIS B1119 ASN C1002 GLN C1106 GLN H 39 GLN L 31 GLN G 76 ASN J 31 GLN I 76 ASN K 31 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.143879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092864 restraints weight = 81771.512| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.59 r_work: 0.3065 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33530 Z= 0.112 Angle : 0.515 9.431 45823 Z= 0.262 Chirality : 0.043 0.182 5316 Planarity : 0.004 0.048 5797 Dihedral : 4.166 18.629 4385 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.43 % Allowed : 12.95 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4030 helix: 1.33 (0.20), residues: 729 sheet: 0.17 (0.16), residues: 1044 loop : -0.64 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 646 TYR 0.031 0.001 TYR H 52A PHE 0.013 0.001 PHE C 906 TRP 0.036 0.002 TRP K 96 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (33401) covalent geometry : angle 0.50994 / 0.26 (45487) SS BOND : bond 0.00245 / 0.17 ( 51) SS BOND : angle 0.56717 / 0.41 ( 102) hydrogen bonds : bond 0.03417 / 2.27 ( 1190) hydrogen bonds : angle 5.09843 / 3.58 ( 3324) link_BETA1-4 : bond 0.00356 / 0.24 ( 24) link_BETA1-4 : angle 1.02884 / 0.68 ( 72) link_NAG-ASN : bond 0.00140 / 0.09 ( 54) link_NAG-ASN : angle 1.15688 / 0.80 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 1.314 Fit side-chains REVERT: A 99 ASN cc_start: 0.8098 (m110) cc_final: 0.7647 (m-40) REVERT: A 150 LYS cc_start: 0.7862 (mptt) cc_final: 0.7647 (mppt) REVERT: A 153 MET cc_start: 0.6750 (mtt) cc_final: 0.6400 (mtp) REVERT: A 697 MET cc_start: 0.7711 (ttt) cc_final: 0.7390 (ttt) REVERT: A 740 MET cc_start: 0.8944 (ttp) cc_final: 0.8576 (tpp) REVERT: A 765 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7916 (ttm110) REVERT: A 789 TYR cc_start: 0.7325 (m-80) cc_final: 0.7073 (m-10) REVERT: A 843 ASP cc_start: 0.5922 (OUTLIER) cc_final: 0.5522 (p0) REVERT: B 24 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7214 (tt) REVERT: B 220 PHE cc_start: 0.8793 (t80) cc_final: 0.8362 (t80) REVERT: B 741 TYR cc_start: 0.9064 (t80) cc_final: 0.8831 (t80) REVERT: B 814 LYS cc_start: 0.8104 (tppt) cc_final: 0.7554 (mptp) REVERT: B 817 PHE cc_start: 0.8292 (t80) cc_final: 0.7994 (t80) REVERT: B 823 PHE cc_start: 0.8233 (m-10) cc_final: 0.7854 (m-80) REVERT: B 841 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7280 (pt) REVERT: B 854 LYS cc_start: 0.7689 (tptt) cc_final: 0.7131 (mttp) REVERT: B 855 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: C 153 MET cc_start: 0.5799 (mtm) cc_final: 0.4951 (mtt) REVERT: C 258 TRP cc_start: 0.5891 (m100) cc_final: 0.5154 (t60) REVERT: C 740 MET cc_start: 0.9189 (mmm) cc_final: 0.8980 (tpp) REVERT: C 759 PHE cc_start: 0.8459 (t80) cc_final: 0.8174 (t80) REVERT: C 854 LYS cc_start: 0.7892 (tptt) cc_final: 0.7216 (mttp) REVERT: C 1072 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: H 53 ASP cc_start: 0.7818 (p0) cc_final: 0.7614 (p0) REVERT: H 82 MET cc_start: 0.7494 (ttp) cc_final: 0.6771 (tpp) REVERT: G 82 MET cc_start: 0.7199 (mmt) cc_final: 0.6907 (mmm) REVERT: G 94 LYS cc_start: 0.7609 (pttp) cc_final: 0.7022 (pptt) REVERT: J 49 TYR cc_start: 0.7412 (p90) cc_final: 0.7196 (p90) REVERT: I 58 HIS cc_start: 0.6417 (OUTLIER) cc_final: 0.5939 (m90) REVERT: I 71 ARG cc_start: 0.7394 (ptm160) cc_final: 0.7159 (ptm160) REVERT: I 79 TYR cc_start: 0.7073 (m-80) cc_final: 0.6775 (m-10) REVERT: K 35 TRP cc_start: 0.6800 (m100) cc_final: 0.6536 (m100) outliers start: 50 outliers final: 36 residues processed: 243 average time/residue: 0.5781 time to fit residues: 173.2020 Evaluate side-chains 247 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 360 optimal weight: 0.2980 chunk 179 optimal weight: 0.9990 chunk 240 optimal weight: 0.6980 chunk 282 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 183 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN H 39 GLN H 76 ASN L 31 GLN G 76 ASN J 31 GLN J 38 GLN I 82AASN K 31 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.143865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093084 restraints weight = 77394.922| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.50 r_work: 0.3070 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33530 Z= 0.115 Angle : 0.517 11.534 45823 Z= 0.263 Chirality : 0.043 0.179 5316 Planarity : 0.004 0.047 5797 Dihedral : 4.149 18.312 4385 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.40 % Allowed : 12.92 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.13), residues: 4030 helix: 1.33 (0.20), residues: 732 sheet: 0.19 (0.16), residues: 1044 loop : -0.62 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 646 TYR 0.032 0.001 TYR H 52A PHE 0.015 0.001 PHE B 759 TRP 0.043 0.002 TRP K 96 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (33401) covalent geometry : angle 0.51223 / 0.26 (45487) SS BOND : bond 0.00255 / 0.18 ( 51) SS BOND : angle 0.57205 / 0.40 ( 102) hydrogen bonds : bond 0.03411 / 2.26 ( 1190) hydrogen bonds : angle 5.07213 / 3.56 ( 3324) link_BETA1-4 : bond 0.00352 / 0.23 ( 24) link_BETA1-4 : angle 1.02471 / 0.68 ( 72) link_NAG-ASN : bond 0.00139 / 0.09 ( 54) link_NAG-ASN : angle 1.15006 / 0.80 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11077.91 seconds wall clock time: 189 minutes 30.61 seconds (11370.61 seconds total)