Starting phenix.real_space_refine on Sat Mar 7 05:44:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xdk_33150/03_2026/7xdk_33150.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xdk_33150/03_2026/7xdk_33150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xdk_33150/03_2026/7xdk_33150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xdk_33150/03_2026/7xdk_33150.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xdk_33150/03_2026/7xdk_33150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xdk_33150/03_2026/7xdk_33150.map" } resolution = 3.2 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= 0.089 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 168 5.16 5 C 24699 2.51 5 N 6477 2.21 5 O 7656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39000 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7857 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 7 Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1609 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "G" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 201} Chain: "D" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "E" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 7857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7857 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 7 Chain: "K" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1609 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "J" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 201} Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "I" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 7857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7857 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 7 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1609 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1640 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 201} Chain: "N" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "O" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.36, per 1000 atoms: 0.24 Number of scatterers: 39000 At special positions: 0 Unit cell: (183.312, 183.312, 241.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 7656 8.00 N 6477 7.00 C 24699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 344 " distance=2.04 Simple disulfide: pdb=" SG CYS A 362 " - pdb=" SG CYS A 415 " distance=2.04 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 508 " distance=2.05 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 471 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 573 " distance=2.04 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 632 " distance=2.03 Simple disulfide: pdb=" SG CYS A 645 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.03 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 141 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 362 " - pdb=" SG CYS B 415 " distance=2.04 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 508 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 632 " distance=2.03 Simple disulfide: pdb=" SG CYS B 645 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.03 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.04 Simple disulfide: pdb=" SG CYS K 141 " - pdb=" SG CYS K 197 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 274 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 319 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 362 " - pdb=" SG CYS C 415 " distance=2.04 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 508 " distance=2.04 Simple disulfide: pdb=" SG CYS C 463 " - pdb=" SG CYS C 471 " distance=2.03 Simple disulfide: pdb=" SG CYS C 521 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 600 " - pdb=" SG CYS C 632 " distance=2.03 Simple disulfide: pdb=" SG CYS C 645 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.03 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 141 " - pdb=" SG CYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 135 " - pdb=" SG CYS M 195 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 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 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-ASN " NAG A1201 " - " ASN A1117 " " NAG A1202 " - " ASN A 692 " " NAG A1203 " - " ASN A1057 " " NAG A1204 " - " ASN A 640 " " NAG B1201 " - " ASN B1117 " " NAG B1202 " - " ASN B 692 " " NAG B1203 " - " ASN B1057 " " NAG B1204 " - " ASN B 640 " " NAG C1201 " - " ASN C1117 " " NAG C1202 " - " ASN C 692 " " NAG C1203 " - " ASN C1057 " " NAG C1204 " - " ASN C 640 " " NAG P 1 " - " ASN A1081 " " NAG Q 1 " - " ASN A 700 " " NAG R 1 " - " ASN A 784 " " NAG S 1 " - " ASN A 314 " " NAG T 1 " - " ASN B1081 " " NAG U 1 " - " ASN B 700 " " NAG V 1 " - " ASN B 784 " " NAG W 1 " - " ASN B 314 " " NAG X 1 " - " ASN C1081 " " NAG Y 1 " - " ASN C 700 " " NAG Z 1 " - " ASN C 784 " " NAG a 1 " - " ASN C 314 " Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.8 seconds 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9270 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 94 sheets defined 16.9% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 277 through 287 Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 386 through 393 removed outlier: 3.607A pdb=" N GLU A 389 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG A 391 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 727 removed outlier: 3.619A pdb=" N TYR A 724 " --> pdb=" O ASP A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 737 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 743 through 766 removed outlier: 3.893A pdb=" N ASN A 747 " --> pdb=" O CYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 809 Processing helix chain 'A' and resid 849 through 867 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 880 through 891 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.252A pdb=" N LEU A 899 " --> pdb=" O THR A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 924 Processing helix chain 'A' and resid 928 through 950 removed outlier: 3.910A pdb=" N GLN A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 966 removed outlier: 3.871A pdb=" N ILE A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1016 Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.857A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.687A pdb=" N GLY F 191 " --> pdb=" O SER F 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 32 removed outlier: 3.668A pdb=" N SER G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 29 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.884A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 129 Processing helix chain 'G' and resid 184 through 190 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.503A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.597A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.664A pdb=" N TYR B 143 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 320 through 326 removed outlier: 3.534A pdb=" N VAL B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 388 through 393 removed outlier: 4.063A pdb=" N ARG B 391 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 729 through 737 removed outlier: 3.603A pdb=" N SER B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 742 through 766 removed outlier: 4.080A pdb=" N LEU B 746 " --> pdb=" O PHE B 742 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN B 747 " --> pdb=" O CYS B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 809 Processing helix chain 'B' and resid 849 through 868 Processing helix chain 'B' and resid 869 through 873 removed outlier: 3.706A pdb=" N GLY B 872 " --> pdb=" O TRP B 869 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 873 " --> pdb=" O THR B 870 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 869 through 873' Processing helix chain 'B' and resid 880 through 891 Processing helix chain 'B' and resid 895 through 901 removed outlier: 4.039A pdb=" N LEU B 899 " --> pdb=" O THR B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 924 Processing helix chain 'B' and resid 928 through 950 removed outlier: 4.090A pdb=" N SER B 950 " --> pdb=" O VAL B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 966 removed outlier: 4.097A pdb=" N ILE B 963 " --> pdb=" O VAL B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1015 Processing helix chain 'K' and resid 86 through 90 removed outlier: 3.823A pdb=" N THR K 90 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 159 No H-bonds generated for 'chain 'K' and resid 157 through 159' Processing helix chain 'K' and resid 186 through 193 Processing helix chain 'J' and resid 80 through 84 removed outlier: 4.022A pdb=" N PHE J 84 " --> pdb=" O PRO J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.519A pdb=" N TYR J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.991A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 144 removed outlier: 3.877A pdb=" N TYR C 143 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 144 " --> pdb=" O GLY C 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 140 through 144' Processing helix chain 'C' and resid 277 through 287 Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.908A pdb=" N VAL C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 354 Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.779A pdb=" N LEU C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 393 removed outlier: 4.668A pdb=" N ARG C 391 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 392 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 720 through 727 Processing helix chain 'C' and resid 729 through 738 removed outlier: 3.776A pdb=" N GLN C 738 " --> pdb=" O ASN C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 766 Processing helix chain 'C' and resid 799 through 809 Processing helix chain 'C' and resid 849 through 867 Processing helix chain 'C' and resid 869 through 873 Processing helix chain 'C' and resid 880 through 891 Processing helix chain 'C' and resid 895 through 901 removed outlier: 4.138A pdb=" N LEU C 899 " --> pdb=" O THR C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 924 Processing helix chain 'C' and resid 928 through 949 Processing helix chain 'C' and resid 959 through 966 removed outlier: 4.046A pdb=" N ILE C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 1015 Processing helix chain 'L' and resid 86 through 90 removed outlier: 3.889A pdb=" N THR L 90 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 159 Processing helix chain 'L' and resid 186 through 193 Processing helix chain 'M' and resid 29 through 32 Processing helix chain 'M' and resid 80 through 84 removed outlier: 4.029A pdb=" N PHE M 84 " --> pdb=" O PRO M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 129 removed outlier: 3.701A pdb=" N GLY M 129 " --> pdb=" O GLN M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 189 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.514A pdb=" N THR N 91 " --> pdb=" O ALA N 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.853A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 15 removed outlier: 3.624A pdb=" N ALA A 12 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ASN A 46 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR A 252 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 184 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP A 211 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE A 186 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.766A pdb=" N ALA B 558 " --> pdb=" O GLY B 549 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASP B 557 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 533 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.951A pdb=" N LYS A 261 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.652A pdb=" N GLY A 92 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY A 88 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA6, first strand: chain 'A' and resid 115 through 116 removed outlier: 7.048A pdb=" N VAL A 115 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 294 through 302 removed outlier: 6.756A pdb=" N VAL A 578 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN A 300 " --> pdb=" O GLY A 576 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY A 576 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY A 577 " --> pdb=" O GLN A 596 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.740A pdb=" N GLY A 533 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASP A 557 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 558 " --> pdb=" O GLY A 549 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE A 548 " --> pdb=" O PHE C 28 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 331 through 332 removed outlier: 7.091A pdb=" N ALA A 331 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 378 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 337 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 331 through 332 removed outlier: 7.091A pdb=" N ALA A 331 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 344 through 345 removed outlier: 6.461A pdb=" N CYS A 344 " --> pdb=" O CYS A 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AB4, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AB5, first strand: chain 'A' and resid 642 through 643 removed outlier: 3.979A pdb=" N TYR A 643 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 684 through 686 Processing sheet with id=AB7, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.549A pdb=" N SER A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR A1059 " --> pdb=" O SER A 694 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A1053 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR A1050 " --> pdb=" O HIS A1031 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N HIS A1031 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.630A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AC1, first strand: chain 'A' and resid 1103 through 1108 removed outlier: 3.535A pdb=" N SER A1106 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA A1070 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1077 through 1079 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 8 Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.558A pdb=" N TYR F 93 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP F 34 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN F 50 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 121 through 124 removed outlier: 3.606A pdb=" N LYS F 144 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 181 " --> pdb=" O CYS F 141 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 121 through 124 removed outlier: 3.606A pdb=" N LYS F 144 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR F 177 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.779A pdb=" N LEU G 11 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP G 106 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU G 13 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.779A pdb=" N LEU G 11 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP G 106 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU G 13 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR G 98 " --> pdb=" O GLN G 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 19 through 22 removed outlier: 4.031A pdb=" N ASP G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.740A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 154 through 155 removed outlier: 3.811A pdb=" N VAL G 151 " --> pdb=" O ALA G 154 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS G 195 " --> pdb=" O LYS G 208 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS G 208 " --> pdb=" O CYS G 195 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL G 197 " --> pdb=" O VAL G 206 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL G 206 " --> pdb=" O VAL G 197 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.511A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.870A pdb=" N TYR D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 69 through 73 Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.510A pdb=" N ASP E 105 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA E 13 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AD9, first strand: chain 'E' and resid 45 through 49 removed outlier: 5.699A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 87 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR E 85 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 13 through 15 removed outlier: 8.071A pdb=" N ASN B 46 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR B 252 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 250 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE B 184 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP B 211 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE B 186 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.568A pdb=" N ALA C 558 " --> pdb=" O GLY C 549 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASP C 557 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 533 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 33 through 40 removed outlier: 3.931A pdb=" N ASP B 270 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 69 through 70 removed outlier: 3.563A pdb=" N GLY B 92 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 115 through 116 removed outlier: 7.217A pdb=" N VAL B 115 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 294 through 302 removed outlier: 5.405A pdb=" N ILE B 295 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR B 582 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN B 297 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 580 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER B 299 " --> pdb=" O VAL B 578 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY B 577 " --> pdb=" O GLN B 596 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 337 through 341 removed outlier: 3.902A pdb=" N ASN B 337 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AE9, first strand: chain 'B' and resid 456 through 457 Processing sheet with id=AF1, first strand: chain 'B' and resid 642 through 643 removed outlier: 3.933A pdb=" N TYR B 643 " --> pdb=" O THR B 679 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.647A pdb=" N SER B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B1059 " --> pdb=" O SER B 694 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 704 " --> pdb=" O THR B1049 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 716 through 717 removed outlier: 4.568A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 770 through 772 removed outlier: 5.619A pdb=" N ILE B 771 " --> pdb=" O ASN C 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'B' and resid 1103 through 1108 removed outlier: 4.274A pdb=" N ALA B1070 " --> pdb=" O SER B1106 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1077 through 1079 Processing sheet with id=AF7, first strand: chain 'K' and resid 3 through 8 removed outlier: 5.924A pdb=" N GLU K 16 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.310A pdb=" N TRP K 34 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN K 50 " --> pdb=" O TRP K 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 122 through 124 removed outlier: 5.716A pdb=" N GLY K 140 " --> pdb=" O VAL K 183 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL K 183 " --> pdb=" O GLY K 140 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU K 142 " --> pdb=" O SER K 181 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER K 181 " --> pdb=" O LEU K 142 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS K 144 " --> pdb=" O LEU K 179 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU K 179 " --> pdb=" O LYS K 144 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 122 through 124 removed outlier: 5.716A pdb=" N GLY K 140 " --> pdb=" O VAL K 183 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL K 183 " --> pdb=" O GLY K 140 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU K 142 " --> pdb=" O SER K 181 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER K 181 " --> pdb=" O LEU K 142 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS K 144 " --> pdb=" O LEU K 179 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU K 179 " --> pdb=" O LYS K 144 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 153 through 155 removed outlier: 4.378A pdb=" N LYS K 210 " --> pdb=" O CYS K 197 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.547A pdb=" N LEU J 13 " --> pdb=" O ASP J 106 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.547A pdb=" N LEU J 13 " --> pdb=" O ASP J 106 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR J 98 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 19 through 22 removed outlier: 3.753A pdb=" N ASP J 71 " --> pdb=" O SER J 68 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 117 through 119 removed outlier: 4.164A pdb=" N VAL J 134 " --> pdb=" O PHE J 119 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA J 131 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N TYR J 174 " --> pdb=" O ASN J 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 146 through 151 removed outlier: 3.747A pdb=" N LYS J 146 " --> pdb=" O THR J 198 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR J 198 " --> pdb=" O LYS J 146 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR J 193 " --> pdb=" O PHE J 210 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.621A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.650A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.549A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE I 75 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N THR I 69 " --> pdb=" O ALA I 25 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.932A pdb=" N ALA I 13 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 45 through 48 removed outlier: 5.535A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 12 through 15 removed outlier: 3.649A pdb=" N ALA C 12 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ASN C 46 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR C 252 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE C 184 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP C 211 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE C 186 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS C 190 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N ALA C 205 " --> pdb=" O HIS C 190 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL C 21 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 35 through 40 removed outlier: 3.579A pdb=" N PHE C 40 " --> pdb=" O GLN C 254 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 254 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR C 257 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP C 273 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU C 259 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA C 271 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LYS C 261 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 69 through 70 removed outlier: 4.025A pdb=" N GLY C 88 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 101 through 103 removed outlier: 7.123A pdb=" N VAL C 115 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 294 through 302 removed outlier: 6.823A pdb=" N VAL C 578 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASN C 300 " --> pdb=" O GLY C 576 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY C 576 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 595 " --> pdb=" O CYS C 632 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS C 632 " --> pdb=" O TYR C 595 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY C 631 " --> pdb=" O THR C 628 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 337 through 341 removed outlier: 3.711A pdb=" N ASN C 337 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 378 " --> pdb=" O ILE C 341 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 435 through 437 Processing sheet with id=AI2, first strand: chain 'C' and resid 456 through 457 Processing sheet with id=AI3, first strand: chain 'C' and resid 642 through 643 removed outlier: 3.913A pdb=" N TYR C 643 " --> pdb=" O THR C 679 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER C 674 " --> pdb=" O GLN C 658 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 658 " --> pdb=" O SER C 674 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 694 through 710 removed outlier: 6.635A pdb=" N SER C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR C1059 " --> pdb=" O SER C 694 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C1053 " --> pdb=" O ASN C 700 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N TYR C1050 " --> pdb=" O HIS C1031 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N HIS C1031 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 717 through 719 Processing sheet with id=AI6, first strand: chain 'C' and resid 1103 through 1108 removed outlier: 4.387A pdb=" N ALA C1070 " --> pdb=" O SER C1106 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 1077 through 1079 Processing sheet with id=AI8, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AI9, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.710A pdb=" N GLY L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 121 through 124 removed outlier: 3.755A pdb=" N LYS L 144 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR L 177 " --> pdb=" O ASP L 145 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 165 through 166 Processing sheet with id=AJ3, first strand: chain 'L' and resid 199 through 201 Processing sheet with id=AJ4, first strand: chain 'M' and resid 10 through 12 removed outlier: 7.141A pdb=" N LEU M 11 " --> pdb=" O ASP M 106 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'M' and resid 10 through 12 removed outlier: 7.141A pdb=" N LEU M 11 " --> pdb=" O ASP M 106 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR M 98 " --> pdb=" O GLN M 91 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 19 through 22 removed outlier: 3.622A pdb=" N ASP M 71 " --> pdb=" O SER M 68 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'M' and resid 117 through 119 removed outlier: 3.933A pdb=" N VAL M 134 " --> pdb=" O PHE M 119 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR M 174 " --> pdb=" O ASN M 139 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'M' and resid 155 through 156 removed outlier: 4.611A pdb=" N TRP M 149 " --> pdb=" O GLN M 156 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS M 146 " --> pdb=" O THR M 198 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS M 195 " --> pdb=" O LYS M 208 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS M 208 " --> pdb=" O CYS M 195 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL M 197 " --> pdb=" O VAL M 206 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL M 206 " --> pdb=" O VAL M 197 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N HIS M 199 " --> pdb=" O SER M 204 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER M 204 " --> pdb=" O HIS M 199 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.686A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.798A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.642A pdb=" N THR O 74 " --> pdb=" O SER O 63 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'O' and resid 10 through 11 removed outlier: 3.608A pdb=" N VAL O 11 " --> pdb=" O LYS O 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK3 Processing sheet with id=AK4, first strand: chain 'O' and resid 45 through 48 removed outlier: 6.011A pdb=" N LEU O 46 " --> pdb=" O GLN O 37 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN O 37 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE O 48 " --> pdb=" O TRP O 35 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR O 87 " --> pdb=" O TYR O 36 " (cutoff:3.500A) 1390 hydrogen bonds defined for protein. 3690 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: 11.72 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11794 1.33 - 1.46: 10502 1.46 - 1.59: 17373 1.59 - 1.72: 0 1.72 - 1.85: 213 Bond restraints: 39882 Sorted by residual: bond pdb=" CA SER A 332 " pdb=" CB SER A 332 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.61e-02 3.86e+03 1.47e+01 bond pdb=" N VAL B 416 " pdb=" CA VAL B 416 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.11e+01 bond pdb=" N VAL B 598 " pdb=" CA VAL B 598 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.18e-02 7.18e+03 1.02e+01 bond pdb=" N ILE A 341 " pdb=" CA ILE A 341 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.06e+00 bond pdb=" N CYS B 415 " pdb=" CA CYS B 415 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.29e-02 6.01e+03 8.69e+00 ... (remaining 39877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 52895 1.55 - 3.11: 1120 3.11 - 4.66: 183 4.66 - 6.21: 41 6.21 - 7.76: 13 Bond angle restraints: 54252 Sorted by residual: angle pdb=" CA VAL B 603 " pdb=" C VAL B 603 " pdb=" N PRO B 604 " ideal model delta sigma weight residual 120.83 124.25 -3.42 6.10e-01 2.69e+00 3.14e+01 angle pdb=" N PHE A 321 " pdb=" CA PHE A 321 " pdb=" C PHE A 321 " ideal model delta sigma weight residual 113.28 107.06 6.22 1.22e+00 6.72e-01 2.60e+01 angle pdb=" CA SER A 332 " pdb=" C SER A 332 " pdb=" O SER A 332 " ideal model delta sigma weight residual 121.87 116.68 5.19 1.16e+00 7.43e-01 2.00e+01 angle pdb=" CA VAL A 333 " pdb=" C VAL A 333 " pdb=" O VAL A 333 " ideal model delta sigma weight residual 120.95 116.51 4.44 1.04e+00 9.25e-01 1.82e+01 angle pdb=" CA VAL B 603 " pdb=" C VAL B 603 " pdb=" O VAL B 603 " ideal model delta sigma weight residual 118.69 115.89 2.80 6.70e-01 2.23e+00 1.75e+01 ... (remaining 54247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 22077 17.97 - 35.94: 1737 35.94 - 53.92: 331 53.92 - 71.89: 69 71.89 - 89.86: 35 Dihedral angle restraints: 24249 sinusoidal: 9801 harmonic: 14448 Sorted by residual: dihedral pdb=" CB CYS C 600 " pdb=" SG CYS C 600 " pdb=" SG CYS C 632 " pdb=" CB CYS C 632 " ideal model delta sinusoidal sigma weight residual -86.00 -165.30 79.30 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS A 463 " pdb=" SG CYS A 463 " pdb=" SG CYS A 471 " pdb=" CB CYS A 471 " ideal model delta sinusoidal sigma weight residual 93.00 163.93 -70.93 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS C 319 " pdb=" SG CYS C 319 " pdb=" SG CYS C 344 " pdb=" CB CYS C 344 " ideal model delta sinusoidal sigma weight residual -86.00 -152.15 66.15 1 1.00e+01 1.00e-02 5.72e+01 ... (remaining 24246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 6210 0.154 - 0.308: 14 0.308 - 0.462: 1 0.462 - 0.616: 0 0.616 - 0.769: 3 Chirality restraints: 6228 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A1081 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C1081 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B1081 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 6225 not shown) Planarity restraints: 6987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 13 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO D 14 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER I 7 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO I 8 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO I 8 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 8 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 80 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO G 81 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO G 81 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 81 " 0.024 5.00e-02 4.00e+02 ... (remaining 6984 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2953 2.74 - 3.28: 37477 3.28 - 3.82: 62035 3.82 - 4.36: 73561 4.36 - 4.90: 131626 Nonbonded interactions: 307652 Sorted by model distance: nonbonded pdb=" OD1 ASP O 82 " pdb=" OH TYR O 86 " model vdw 2.200 3.040 nonbonded pdb=" OE1 GLN B 476 " pdb=" OG SER J 30 " model vdw 2.202 3.040 nonbonded pdb=" O GLY E 28 " pdb=" ND2 ASN E 92 " model vdw 2.206 3.120 nonbonded pdb=" OD2 ASP B 513 " pdb=" NE2 GLN B 563 " model vdw 2.209 3.120 nonbonded pdb=" OG1 THR F 152 " pdb=" OD1 ASN F 200 " model vdw 2.223 3.040 ... (remaining 307647 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 40.400 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 39975 Z= 0.178 Angle : 0.593 15.947 54474 Z= 0.312 Chirality : 0.047 0.769 6228 Planarity : 0.004 0.048 6963 Dihedral : 13.490 89.861 14808 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.00 % Favored : 95.98 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 4923 helix: 2.09 (0.21), residues: 687 sheet: -0.32 (0.13), residues: 1539 loop : -1.01 (0.12), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 87 TYR 0.019 0.001 TYR A 334 PHE 0.020 0.001 PHE B 889 TRP 0.014 0.001 TRP C 869 HIS 0.006 0.001 HIS G 199 Details of bonding type rmsd covalent geometry : bond 0.00354 (39882) covalent geometry : angle 0.57247 (54252) SS BOND : bond 0.00427 ( 57) SS BOND : angle 1.34168 ( 114) hydrogen bonds : bond 0.21688 ( 1375) hydrogen bonds : angle 8.71042 ( 3690) link_BETA1-4 : bond 0.00369 ( 12) link_BETA1-4 : angle 1.60158 ( 36) link_NAG-ASN : bond 0.00489 ( 24) link_NAG-ASN : angle 3.89254 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 463 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 764 VAL cc_start: 0.8992 (t) cc_final: 0.8748 (t) REVERT: B 1033 MET cc_start: 0.8918 (ptp) cc_final: 0.8716 (ptm) REVERT: K 142 LEU cc_start: 0.6407 (tt) cc_final: 0.6162 (tp) REVERT: J 150 LYS cc_start: 0.4670 (pttm) cc_final: 0.3522 (pttt) REVERT: I 90 GLN cc_start: 0.8464 (pp30) cc_final: 0.8240 (pp30) REVERT: C 413 THR cc_start: 0.8135 (t) cc_final: 0.7714 (m) outliers start: 5 outliers final: 2 residues processed: 466 average time/residue: 0.2575 time to fit residues: 193.3529 Evaluate side-chains 382 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 380 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 341 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 ASN A 975 GLN ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 596 GLN K 6 GLN ** K 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 139 ASN I 90 GLN C 589 ASN C 890 ASN C 985 GLN C1084 HIS O 92 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.149964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104090 restraints weight = 63120.771| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.00 r_work: 0.3190 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 39975 Z= 0.201 Angle : 0.634 17.010 54474 Z= 0.321 Chirality : 0.048 0.627 6228 Planarity : 0.004 0.048 6963 Dihedral : 5.291 56.121 6105 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.84 % Allowed : 6.82 % Favored : 92.34 % 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: -0.54 (0.12), residues: 4923 helix: 2.07 (0.21), residues: 686 sheet: -0.33 (0.13), residues: 1639 loop : -1.03 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 143 TYR 0.020 0.002 TYR C1050 PHE 0.027 0.002 PHE E 94 TRP 0.011 0.001 TRP B 869 HIS 0.004 0.001 HIS F 201 Details of bonding type rmsd covalent geometry : bond 0.00484 (39882) covalent geometry : angle 0.61145 (54252) SS BOND : bond 0.00483 ( 57) SS BOND : angle 1.74273 ( 114) hydrogen bonds : bond 0.05311 ( 1375) hydrogen bonds : angle 6.45511 ( 3690) link_BETA1-4 : bond 0.00374 ( 12) link_BETA1-4 : angle 1.02525 ( 36) link_NAG-ASN : bond 0.00354 ( 24) link_NAG-ASN : angle 4.14781 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 423 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8292 (ttp-110) REVERT: G 62 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8160 (ttp-110) REVERT: G 174 TYR cc_start: 0.7517 (m-10) cc_final: 0.7162 (m-10) REVERT: E 78 LEU cc_start: 0.7160 (mm) cc_final: 0.6837 (mm) REVERT: B 967 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6923 (tp) REVERT: K 176 LEU cc_start: 0.8681 (mt) cc_final: 0.8293 (mt) REVERT: J 4 MET cc_start: 0.8414 (mmt) cc_final: 0.7748 (mmt) REVERT: J 82 GLU cc_start: 0.8727 (pm20) cc_final: 0.8517 (pm20) REVERT: I 35 TRP cc_start: 0.7868 (m100) cc_final: 0.7398 (m-10) REVERT: I 90 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8590 (pp30) REVERT: C 413 THR cc_start: 0.8619 (t) cc_final: 0.8194 (m) REVERT: M 143 ARG cc_start: 0.7626 (tpt90) cc_final: 0.7281 (tpt90) REVERT: O 4 MET cc_start: 0.7784 (mmm) cc_final: 0.6905 (mmm) REVERT: O 37 GLN cc_start: 0.7800 (tt0) cc_final: 0.7445 (tm-30) outliers start: 36 outliers final: 22 residues processed: 436 average time/residue: 0.2534 time to fit residues: 177.0561 Evaluate side-chains 420 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 395 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 198 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain O residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 184 optimal weight: 2.9990 chunk 346 optimal weight: 9.9990 chunk 321 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 148 optimal weight: 3.9990 chunk 356 optimal weight: 5.9990 chunk 355 optimal weight: 1.9990 chunk 391 optimal weight: 0.9990 chunk 283 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 overall best weight: 1.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 890 ASN C1084 HIS L 6 GLN N 3 GLN O 89 GLN O 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.151242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105717 restraints weight = 62980.576| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.00 r_work: 0.3224 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39975 Z= 0.127 Angle : 0.567 16.285 54474 Z= 0.286 Chirality : 0.046 0.610 6228 Planarity : 0.004 0.047 6963 Dihedral : 4.936 56.888 6102 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.02 % Allowed : 9.54 % Favored : 89.44 % 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: -0.47 (0.12), residues: 4923 helix: 2.29 (0.21), residues: 682 sheet: -0.31 (0.13), residues: 1643 loop : -1.02 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 24 TYR 0.019 0.001 TYR C1050 PHE 0.017 0.001 PHE N 27 TRP 0.009 0.001 TRP B 869 HIS 0.005 0.000 HIS F 201 Details of bonding type rmsd covalent geometry : bond 0.00296 (39882) covalent geometry : angle 0.54498 (54252) SS BOND : bond 0.00553 ( 57) SS BOND : angle 1.30183 ( 114) hydrogen bonds : bond 0.04455 ( 1375) hydrogen bonds : angle 5.93899 ( 3690) link_BETA1-4 : bond 0.00319 ( 12) link_BETA1-4 : angle 1.07566 ( 36) link_NAG-ASN : bond 0.00402 ( 24) link_NAG-ASN : angle 4.05021 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 425 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 764 VAL cc_start: 0.9152 (t) cc_final: 0.8883 (t) REVERT: A 1125 GLN cc_start: 0.7524 (tp40) cc_final: 0.7263 (pp30) REVERT: G 62 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8098 (ttp-110) REVERT: D 6 GLU cc_start: 0.7425 (pm20) cc_final: 0.7194 (pm20) REVERT: E 78 LEU cc_start: 0.7135 (mm) cc_final: 0.6827 (mm) REVERT: B 967 LEU cc_start: 0.7372 (tp) cc_final: 0.6964 (tp) REVERT: K 156 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6659 (p0) REVERT: K 176 LEU cc_start: 0.8697 (mt) cc_final: 0.8288 (mt) REVERT: I 35 TRP cc_start: 0.7965 (m100) cc_final: 0.7412 (m-10) REVERT: C 413 THR cc_start: 0.8651 (t) cc_final: 0.8236 (m) REVERT: C 1033 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8777 (ptp) REVERT: M 143 ARG cc_start: 0.7685 (tpt90) cc_final: 0.7163 (tpt90) REVERT: M 162 GLU cc_start: 0.8668 (pp20) cc_final: 0.8115 (pp20) REVERT: O 4 MET cc_start: 0.7841 (mmm) cc_final: 0.7025 (mmm) REVERT: O 37 GLN cc_start: 0.7766 (tt0) cc_final: 0.7450 (tm-30) outliers start: 44 outliers final: 26 residues processed: 447 average time/residue: 0.2578 time to fit residues: 184.9805 Evaluate side-chains 421 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 392 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1033 MET Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 198 ASN Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain O residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 435 optimal weight: 7.9990 chunk 386 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 214 optimal weight: 0.8980 chunk 395 optimal weight: 0.8980 chunk 404 optimal weight: 2.9990 chunk 371 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 483 optimal weight: 10.0000 chunk 335 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 GLN G 190 HIS E 27 GLN B 624 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN C 890 ASN ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 HIS L 6 GLN O 92 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.148879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.102657 restraints weight = 62886.197| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.05 r_work: 0.3174 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 39975 Z= 0.212 Angle : 0.615 16.842 54474 Z= 0.309 Chirality : 0.047 0.631 6228 Planarity : 0.004 0.048 6963 Dihedral : 4.944 54.064 6102 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.37 % Allowed : 11.72 % Favored : 86.91 % 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: -0.60 (0.12), residues: 4923 helix: 2.09 (0.20), residues: 685 sheet: -0.34 (0.13), residues: 1663 loop : -1.12 (0.12), residues: 2575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 87 TYR 0.021 0.002 TYR M 92 PHE 0.024 0.002 PHE B 889 TRP 0.010 0.001 TRP K 155 HIS 0.006 0.001 HIS F 201 Details of bonding type rmsd covalent geometry : bond 0.00518 (39882) covalent geometry : angle 0.59212 (54252) SS BOND : bond 0.00433 ( 57) SS BOND : angle 1.55508 ( 114) hydrogen bonds : bond 0.04960 ( 1375) hydrogen bonds : angle 5.79893 ( 3690) link_BETA1-4 : bond 0.00309 ( 12) link_BETA1-4 : angle 1.12255 ( 36) link_NAG-ASN : bond 0.00402 ( 24) link_NAG-ASN : angle 4.15644 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 407 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8799 (tt) REVERT: A 569 ASP cc_start: 0.8437 (m-30) cc_final: 0.8109 (m-30) REVERT: A 1125 GLN cc_start: 0.7594 (tp40) cc_final: 0.7226 (pp30) REVERT: G 62 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8403 (ttp-110) REVERT: D 58 LYS cc_start: 0.8555 (mttp) cc_final: 0.8322 (mtmm) REVERT: E 78 LEU cc_start: 0.7161 (mm) cc_final: 0.6784 (mm) REVERT: B 453 THR cc_start: 0.8782 (p) cc_final: 0.8547 (p) REVERT: B 967 LEU cc_start: 0.7358 (tp) cc_final: 0.7109 (tp) REVERT: K 156 ASN cc_start: 0.7266 (OUTLIER) cc_final: 0.6697 (p0) REVERT: K 176 LEU cc_start: 0.8765 (mt) cc_final: 0.8400 (mt) REVERT: H 76 LYS cc_start: 0.8583 (mptt) cc_final: 0.8340 (mmtp) REVERT: I 35 TRP cc_start: 0.8074 (m100) cc_final: 0.7481 (m-10) REVERT: I 90 GLN cc_start: 0.8948 (pp30) cc_final: 0.8406 (pp30) REVERT: C 451 ILE cc_start: 0.8769 (mm) cc_final: 0.8560 (mm) REVERT: O 4 MET cc_start: 0.7895 (mmm) cc_final: 0.6982 (mmm) REVERT: O 37 GLN cc_start: 0.7817 (tt0) cc_final: 0.7437 (tm-30) outliers start: 59 outliers final: 40 residues processed: 447 average time/residue: 0.2567 time to fit residues: 183.7518 Evaluate side-chains 436 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 393 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 198 ASN Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 104 optimal weight: 9.9990 chunk 344 optimal weight: 40.0000 chunk 469 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 429 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 142 optimal weight: 30.0000 chunk 304 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 416 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN G 125 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN C 884 GLN ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 HIS L 6 GLN N 3 GLN O 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.147240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102166 restraints weight = 62730.610| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.98 r_work: 0.3145 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 39975 Z= 0.270 Angle : 0.658 17.158 54474 Z= 0.331 Chirality : 0.049 0.657 6228 Planarity : 0.004 0.049 6963 Dihedral : 5.064 46.427 6102 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.09 % Allowed : 12.60 % Favored : 85.31 % 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: -0.79 (0.12), residues: 4923 helix: 1.86 (0.20), residues: 688 sheet: -0.43 (0.13), residues: 1666 loop : -1.24 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 966 TYR 0.021 0.002 TYR B1050 PHE 0.030 0.002 PHE E 94 TRP 0.012 0.002 TRP B 869 HIS 0.006 0.001 HIS A1031 Details of bonding type rmsd covalent geometry : bond 0.00658 (39882) covalent geometry : angle 0.63518 (54252) SS BOND : bond 0.00501 ( 57) SS BOND : angle 1.71229 ( 114) hydrogen bonds : bond 0.05339 ( 1375) hydrogen bonds : angle 5.81201 ( 3690) link_BETA1-4 : bond 0.00296 ( 12) link_BETA1-4 : angle 1.16947 ( 36) link_NAG-ASN : bond 0.00400 ( 24) link_NAG-ASN : angle 4.27046 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 410 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8734 (tt) REVERT: G 62 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8270 (ttp-110) REVERT: G 168 ASP cc_start: 0.7662 (t70) cc_final: 0.7322 (t70) REVERT: D 6 GLU cc_start: 0.7201 (pm20) cc_final: 0.6979 (pm20) REVERT: D 32 TYR cc_start: 0.7685 (m-10) cc_final: 0.7482 (m-10) REVERT: E 78 LEU cc_start: 0.7231 (mm) cc_final: 0.6794 (mm) REVERT: B 453 THR cc_start: 0.8956 (p) cc_final: 0.8663 (p) REVERT: B 967 LEU cc_start: 0.7474 (tp) cc_final: 0.7216 (tp) REVERT: K 98 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7820 (mt-10) REVERT: K 156 ASN cc_start: 0.7546 (OUTLIER) cc_final: 0.6958 (p0) REVERT: K 176 LEU cc_start: 0.8757 (mt) cc_final: 0.8412 (mt) REVERT: J 4 MET cc_start: 0.8604 (mmt) cc_final: 0.8125 (mmt) REVERT: J 82 GLU cc_start: 0.8599 (pm20) cc_final: 0.8355 (pm20) REVERT: J 166 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8380 (tm-30) REVERT: H 76 LYS cc_start: 0.8619 (mptt) cc_final: 0.8405 (mmtp) REVERT: I 35 TRP cc_start: 0.8181 (m100) cc_final: 0.7565 (m-10) REVERT: I 90 GLN cc_start: 0.9022 (pp30) cc_final: 0.8364 (pp30) REVERT: C 451 ILE cc_start: 0.8895 (mm) cc_final: 0.8645 (mm) REVERT: C 478 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: C 748 ARG cc_start: 0.8331 (ttm170) cc_final: 0.7523 (ttp-170) REVERT: C 1033 MET cc_start: 0.9054 (ptp) cc_final: 0.8767 (ptm) REVERT: M 143 ARG cc_start: 0.7852 (tpt90) cc_final: 0.7345 (tpt90) REVERT: O 4 MET cc_start: 0.7865 (mmm) cc_final: 0.6847 (mmm) REVERT: O 37 GLN cc_start: 0.7914 (tt0) cc_final: 0.7458 (tm-30) outliers start: 90 outliers final: 70 residues processed: 468 average time/residue: 0.2563 time to fit residues: 194.3642 Evaluate side-chains 468 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 394 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 146 LYS Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 198 ASN Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 105 ASP Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 286 optimal weight: 0.0670 chunk 229 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 405 optimal weight: 0.6980 chunk 308 optimal weight: 0.9990 chunk 451 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 890 ASN G 125 GLN E 27 GLN B1089 GLN I 90 GLN ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN O 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.150589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104742 restraints weight = 62802.997| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.91 r_work: 0.3221 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39975 Z= 0.111 Angle : 0.563 16.142 54474 Z= 0.283 Chirality : 0.045 0.618 6228 Planarity : 0.004 0.050 6963 Dihedral : 4.663 42.531 6102 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.69 % Allowed : 13.97 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.12), residues: 4923 helix: 2.34 (0.21), residues: 678 sheet: -0.28 (0.13), residues: 1613 loop : -1.13 (0.12), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 87 TYR 0.028 0.001 TYR A1121 PHE 0.024 0.001 PHE E 94 TRP 0.011 0.001 TRP K 47 HIS 0.005 0.000 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00252 (39882) covalent geometry : angle 0.54121 (54252) SS BOND : bond 0.00447 ( 57) SS BOND : angle 1.21622 ( 114) hydrogen bonds : bond 0.04038 ( 1375) hydrogen bonds : angle 5.50472 ( 3690) link_BETA1-4 : bond 0.00319 ( 12) link_BETA1-4 : angle 1.16885 ( 36) link_NAG-ASN : bond 0.00404 ( 24) link_NAG-ASN : angle 4.05468 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 407 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 ASP cc_start: 0.8735 (m-30) cc_final: 0.8048 (t0) REVERT: A 764 VAL cc_start: 0.9049 (t) cc_final: 0.8763 (t) REVERT: A 1125 GLN cc_start: 0.7528 (tp40) cc_final: 0.7263 (pp30) REVERT: G 55 ARG cc_start: 0.7905 (ptp-110) cc_final: 0.7214 (mtm-85) REVERT: G 62 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8396 (ttp-110) REVERT: G 109 ARG cc_start: 0.8266 (ptm160) cc_final: 0.8031 (ptm160) REVERT: G 168 ASP cc_start: 0.7573 (t70) cc_final: 0.7225 (t70) REVERT: G 171 ASP cc_start: 0.8235 (p0) cc_final: 0.7975 (p0) REVERT: D 32 TYR cc_start: 0.7510 (m-10) cc_final: 0.7274 (m-10) REVERT: E 4 MET cc_start: 0.6947 (mmm) cc_final: 0.6651 (mmm) REVERT: E 78 LEU cc_start: 0.7225 (mm) cc_final: 0.6781 (mm) REVERT: B 323 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 453 THR cc_start: 0.8726 (p) cc_final: 0.8497 (p) REVERT: B 600 CYS cc_start: 0.5227 (OUTLIER) cc_final: 0.4074 (m) REVERT: B 742 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7819 (t80) REVERT: B 967 LEU cc_start: 0.7282 (tp) cc_final: 0.7011 (tp) REVERT: K 98 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7746 (mt-10) REVERT: K 156 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.6958 (m110) REVERT: K 176 LEU cc_start: 0.8766 (mt) cc_final: 0.8400 (mt) REVERT: J 4 MET cc_start: 0.8552 (mmt) cc_final: 0.8059 (mmt) REVERT: J 166 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8441 (tm-30) REVERT: H 76 LYS cc_start: 0.8636 (mptt) cc_final: 0.8395 (mmtp) REVERT: H 80 TYR cc_start: 0.6757 (m-10) cc_final: 0.6405 (m-10) REVERT: I 35 TRP cc_start: 0.8151 (m100) cc_final: 0.7509 (m-10) REVERT: I 90 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8361 (pp30) REVERT: C 77 PHE cc_start: 0.7668 (t80) cc_final: 0.7412 (t80) REVERT: C 451 ILE cc_start: 0.8783 (mm) cc_final: 0.8547 (mm) REVERT: C 478 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: M 143 ARG cc_start: 0.7787 (tpt90) cc_final: 0.7346 (tpt90) REVERT: O 4 MET cc_start: 0.7837 (mmm) cc_final: 0.6977 (mmm) REVERT: O 37 GLN cc_start: 0.7899 (tt0) cc_final: 0.7413 (tm-30) outliers start: 73 outliers final: 43 residues processed: 453 average time/residue: 0.2482 time to fit residues: 181.0167 Evaluate side-chains 436 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 387 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 146 LYS Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 98 GLU Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 105 ASP Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 359 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 228 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 197 optimal weight: 0.6980 chunk 318 optimal weight: 10.0000 chunk 454 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 chunk 302 optimal weight: 20.0000 chunk 277 optimal weight: 50.0000 chunk 276 optimal weight: 6.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 890 ASN G 125 GLN ** G 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 HIS O 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.147908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.099491 restraints weight = 62759.964| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.86 r_work: 0.3175 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 39975 Z= 0.219 Angle : 0.624 16.517 54474 Z= 0.313 Chirality : 0.048 0.637 6228 Planarity : 0.004 0.052 6963 Dihedral : 4.790 42.206 6102 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.86 % Allowed : 14.48 % Favored : 83.66 % 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: -0.62 (0.12), residues: 4923 helix: 2.09 (0.21), residues: 688 sheet: -0.34 (0.13), residues: 1651 loop : -1.15 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 966 TYR 0.025 0.002 TYR A1121 PHE 0.028 0.002 PHE E 94 TRP 0.010 0.001 TRP B 869 HIS 0.005 0.001 HIS F 201 Details of bonding type rmsd covalent geometry : bond 0.00535 (39882) covalent geometry : angle 0.60150 (54252) SS BOND : bond 0.00454 ( 57) SS BOND : angle 1.55867 ( 114) hydrogen bonds : bond 0.04864 ( 1375) hydrogen bonds : angle 5.55755 ( 3690) link_BETA1-4 : bond 0.00289 ( 12) link_BETA1-4 : angle 1.19047 ( 36) link_NAG-ASN : bond 0.00400 ( 24) link_NAG-ASN : angle 4.16062 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 409 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8743 (tt) REVERT: A 554 ASP cc_start: 0.8736 (m-30) cc_final: 0.8119 (t0) REVERT: G 109 ARG cc_start: 0.8335 (ptm160) cc_final: 0.8069 (ptm160) REVERT: G 168 ASP cc_start: 0.7731 (t70) cc_final: 0.7414 (t70) REVERT: G 171 ASP cc_start: 0.8240 (p0) cc_final: 0.7972 (p0) REVERT: E 78 LEU cc_start: 0.7299 (mm) cc_final: 0.6833 (mm) REVERT: B 453 THR cc_start: 0.8920 (p) cc_final: 0.8654 (p) REVERT: B 967 LEU cc_start: 0.7272 (tp) cc_final: 0.6979 (tp) REVERT: K 156 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.6991 (m110) REVERT: K 176 LEU cc_start: 0.8744 (mt) cc_final: 0.8456 (mt) REVERT: J 4 MET cc_start: 0.8593 (mmt) cc_final: 0.8171 (mmt) REVERT: J 144 GLU cc_start: 0.6710 (tm-30) cc_final: 0.6441 (tm-30) REVERT: J 166 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8099 (tm-30) REVERT: H 76 LYS cc_start: 0.8695 (mptt) cc_final: 0.8441 (mmtp) REVERT: H 80 TYR cc_start: 0.6589 (m-10) cc_final: 0.6255 (m-10) REVERT: I 35 TRP cc_start: 0.8230 (m100) cc_final: 0.7541 (m-10) REVERT: C 270 ASP cc_start: 0.8505 (t0) cc_final: 0.8294 (t0) REVERT: C 451 ILE cc_start: 0.8889 (mm) cc_final: 0.8589 (mm) REVERT: C 478 TYR cc_start: 0.9248 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: C 850 ASP cc_start: 0.8330 (m-30) cc_final: 0.8037 (t0) REVERT: M 143 ARG cc_start: 0.7938 (tpt90) cc_final: 0.7481 (tpt90) REVERT: O 4 MET cc_start: 0.7853 (mmm) cc_final: 0.6951 (mmm) REVERT: O 37 GLN cc_start: 0.7926 (tt0) cc_final: 0.7453 (tm-30) outliers start: 80 outliers final: 66 residues processed: 457 average time/residue: 0.2448 time to fit residues: 180.8936 Evaluate side-chains 464 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 395 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 632 CYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 146 LYS Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 16 GLU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 105 ASP Chi-restraints excluded: chain O residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 210 optimal weight: 0.8980 chunk 219 optimal weight: 0.7980 chunk 274 optimal weight: 2.9990 chunk 337 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 201 optimal weight: 0.8980 chunk 451 optimal weight: 0.9980 chunk 433 optimal weight: 0.8980 chunk 260 optimal weight: 0.7980 chunk 363 optimal weight: 1.9990 chunk 444 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 GLN ** G 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN K 198 ASN ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.150616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.104157 restraints weight = 62759.512| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.07 r_work: 0.3161 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39975 Z= 0.114 Angle : 0.569 15.956 54474 Z= 0.285 Chirality : 0.045 0.615 6228 Planarity : 0.004 0.051 6963 Dihedral : 4.562 42.049 6102 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.67 % Allowed : 15.00 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.12), residues: 4923 helix: 2.36 (0.21), residues: 683 sheet: -0.23 (0.13), residues: 1628 loop : -1.07 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 87 TYR 0.024 0.001 TYR A1121 PHE 0.029 0.001 PHE J 210 TRP 0.011 0.001 TRP K 47 HIS 0.004 0.000 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00261 (39882) covalent geometry : angle 0.54712 (54252) SS BOND : bond 0.00413 ( 57) SS BOND : angle 1.27423 ( 114) hydrogen bonds : bond 0.03928 ( 1375) hydrogen bonds : angle 5.34410 ( 3690) link_BETA1-4 : bond 0.00325 ( 12) link_BETA1-4 : angle 1.21750 ( 36) link_NAG-ASN : bond 0.00416 ( 24) link_NAG-ASN : angle 3.99754 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 404 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.7750 (m) cc_final: 0.7457 (p) REVERT: A 554 ASP cc_start: 0.8814 (m-30) cc_final: 0.8182 (t0) REVERT: A 764 VAL cc_start: 0.9051 (t) cc_final: 0.8762 (t) REVERT: A 1125 GLN cc_start: 0.7578 (tp40) cc_final: 0.7334 (pp30) REVERT: G 55 ARG cc_start: 0.7909 (ptp-110) cc_final: 0.7251 (mtm-85) REVERT: D 39 GLN cc_start: 0.5002 (tt0) cc_final: 0.4732 (tt0) REVERT: D 87 ARG cc_start: 0.6875 (mtt90) cc_final: 0.6574 (mtt90) REVERT: E 55 GLN cc_start: 0.8487 (tp40) cc_final: 0.8130 (tp40) REVERT: E 78 LEU cc_start: 0.7247 (mm) cc_final: 0.6787 (mm) REVERT: B 401 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8561 (tp) REVERT: B 453 THR cc_start: 0.8781 (p) cc_final: 0.8543 (p) REVERT: B 600 CYS cc_start: 0.5059 (OUTLIER) cc_final: 0.3767 (m) REVERT: B 742 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.7970 (t80) REVERT: K 156 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7131 (m110) REVERT: K 176 LEU cc_start: 0.8713 (mt) cc_final: 0.8397 (mt) REVERT: J 4 MET cc_start: 0.8579 (mmt) cc_final: 0.8177 (mmt) REVERT: J 144 GLU cc_start: 0.6675 (tm-30) cc_final: 0.6407 (tm-30) REVERT: J 166 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8055 (tm-30) REVERT: H 38 ARG cc_start: 0.8299 (ptt180) cc_final: 0.7987 (ptt180) REVERT: H 76 LYS cc_start: 0.8690 (mptt) cc_final: 0.8431 (mmtp) REVERT: H 80 TYR cc_start: 0.6589 (m-10) cc_final: 0.6274 (m-10) REVERT: I 35 TRP cc_start: 0.8254 (m100) cc_final: 0.7461 (m-10) REVERT: I 90 GLN cc_start: 0.8886 (pp30) cc_final: 0.8098 (pp30) REVERT: C 77 PHE cc_start: 0.7703 (t80) cc_final: 0.7395 (t80) REVERT: C 270 ASP cc_start: 0.8516 (t0) cc_final: 0.8287 (t0) REVERT: C 451 ILE cc_start: 0.8823 (mm) cc_final: 0.8584 (mm) REVERT: C 478 TYR cc_start: 0.9246 (OUTLIER) cc_final: 0.8615 (m-10) REVERT: M 143 ARG cc_start: 0.7887 (tpt90) cc_final: 0.7453 (tpt90) REVERT: N 73 ASP cc_start: 0.6743 (t0) cc_final: 0.6458 (t0) REVERT: N 111 TRP cc_start: 0.8338 (m100) cc_final: 0.8127 (m100) REVERT: O 4 MET cc_start: 0.7848 (mmm) cc_final: 0.6955 (mmm) REVERT: O 37 GLN cc_start: 0.7954 (tt0) cc_final: 0.7429 (tm-30) outliers start: 72 outliers final: 57 residues processed: 448 average time/residue: 0.2541 time to fit residues: 184.0714 Evaluate side-chains 450 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 388 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 146 LYS Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain L residue 16 GLU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 105 ASP Chi-restraints excluded: chain O residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 7 optimal weight: 0.0980 chunk 75 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 455 optimal weight: 5.9990 chunk 443 optimal weight: 4.9990 chunk 378 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 402 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 101 optimal weight: 0.0000 overall best weight: 2.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN B1066 HIS ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.147727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101360 restraints weight = 62839.888| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.83 r_work: 0.3174 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 39975 Z= 0.233 Angle : 0.644 16.460 54474 Z= 0.322 Chirality : 0.048 0.639 6228 Planarity : 0.004 0.052 6963 Dihedral : 4.796 42.032 6102 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.07 % Allowed : 14.74 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.12), residues: 4923 helix: 2.09 (0.21), residues: 689 sheet: -0.32 (0.13), residues: 1661 loop : -1.17 (0.12), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 966 TYR 0.024 0.002 TYR A1121 PHE 0.047 0.002 PHE J 210 TRP 0.016 0.002 TRP C 49 HIS 0.006 0.001 HIS A1031 Details of bonding type rmsd covalent geometry : bond 0.00568 (39882) covalent geometry : angle 0.62170 (54252) SS BOND : bond 0.00510 ( 57) SS BOND : angle 1.59740 ( 114) hydrogen bonds : bond 0.04954 ( 1375) hydrogen bonds : angle 5.48502 ( 3690) link_BETA1-4 : bond 0.00302 ( 12) link_BETA1-4 : angle 1.23214 ( 36) link_NAG-ASN : bond 0.00397 ( 24) link_NAG-ASN : angle 4.15742 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 400 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 ASP cc_start: 0.8765 (m-30) cc_final: 0.8180 (t0) REVERT: E 4 MET cc_start: 0.7408 (mmm) cc_final: 0.7199 (mmm) REVERT: E 55 GLN cc_start: 0.8579 (tp40) cc_final: 0.8217 (tp40) REVERT: E 78 LEU cc_start: 0.7396 (mm) cc_final: 0.6913 (mm) REVERT: B 401 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8702 (tp) REVERT: B 453 THR cc_start: 0.8964 (p) cc_final: 0.8694 (p) REVERT: B 742 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7978 (t80) REVERT: B 967 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7070 (tp) REVERT: K 156 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.6957 (m110) REVERT: K 176 LEU cc_start: 0.8745 (mt) cc_final: 0.8379 (mt) REVERT: J 144 GLU cc_start: 0.6760 (tm-30) cc_final: 0.6482 (tm-30) REVERT: H 76 LYS cc_start: 0.8727 (mptt) cc_final: 0.8486 (mmtp) REVERT: H 80 TYR cc_start: 0.6576 (m-10) cc_final: 0.6243 (m-10) REVERT: I 90 GLN cc_start: 0.8924 (pp30) cc_final: 0.8312 (pp30) REVERT: C 77 PHE cc_start: 0.7673 (t80) cc_final: 0.7344 (t80) REVERT: C 451 ILE cc_start: 0.8903 (mm) cc_final: 0.8599 (mm) REVERT: C 478 TYR cc_start: 0.9265 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: C 850 ASP cc_start: 0.8351 (m-30) cc_final: 0.8037 (t0) REVERT: M 143 ARG cc_start: 0.7991 (tpt90) cc_final: 0.7567 (tpt90) REVERT: N 73 ASP cc_start: 0.6700 (t0) cc_final: 0.6468 (t0) REVERT: O 4 MET cc_start: 0.7838 (mmm) cc_final: 0.6843 (mmm) REVERT: O 37 GLN cc_start: 0.7913 (tt0) cc_final: 0.7426 (tm-30) outliers start: 89 outliers final: 70 residues processed: 459 average time/residue: 0.2439 time to fit residues: 181.9337 Evaluate side-chains 470 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 395 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 632 CYS Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 146 LYS Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain L residue 16 GLU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 105 ASP Chi-restraints excluded: chain O residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 220 optimal weight: 5.9990 chunk 259 optimal weight: 0.6980 chunk 393 optimal weight: 4.9990 chunk 345 optimal weight: 20.0000 chunk 207 optimal weight: 0.9980 chunk 293 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 328 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS G 125 GLN ** G 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN E 27 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.150014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103181 restraints weight = 62553.895| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.04 r_work: 0.3203 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39975 Z= 0.119 Angle : 0.578 15.877 54474 Z= 0.289 Chirality : 0.046 0.621 6228 Planarity : 0.004 0.051 6963 Dihedral : 4.598 41.954 6102 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.74 % Allowed : 15.00 % Favored : 83.26 % 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: -0.45 (0.12), residues: 4923 helix: 2.33 (0.21), residues: 687 sheet: -0.21 (0.13), residues: 1638 loop : -1.08 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 87 TYR 0.030 0.001 TYR I 49 PHE 0.025 0.001 PHE J 210 TRP 0.015 0.001 TRP N 111 HIS 0.005 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00276 (39882) covalent geometry : angle 0.55598 (54252) SS BOND : bond 0.00427 ( 57) SS BOND : angle 1.34471 ( 114) hydrogen bonds : bond 0.04003 ( 1375) hydrogen bonds : angle 5.30063 ( 3690) link_BETA1-4 : bond 0.00334 ( 12) link_BETA1-4 : angle 1.24574 ( 36) link_NAG-ASN : bond 0.00414 ( 24) link_NAG-ASN : angle 4.00175 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9846 Ramachandran restraints generated. 4923 Oldfield, 0 Emsley, 4923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 397 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.7633 (m) cc_final: 0.7341 (p) REVERT: A 451 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8325 (tp) REVERT: A 554 ASP cc_start: 0.8772 (m-30) cc_final: 0.8178 (t0) REVERT: A 764 VAL cc_start: 0.9081 (t) cc_final: 0.8806 (t) REVERT: A 1125 GLN cc_start: 0.7585 (tp40) cc_final: 0.7315 (pp30) REVERT: G 55 ARG cc_start: 0.7885 (ptp-110) cc_final: 0.7324 (mtm-85) REVERT: D 39 GLN cc_start: 0.5297 (tt0) cc_final: 0.5053 (tt0) REVERT: E 4 MET cc_start: 0.7413 (mmm) cc_final: 0.7189 (mmm) REVERT: E 55 GLN cc_start: 0.8489 (tp40) cc_final: 0.8151 (tp40) REVERT: E 78 LEU cc_start: 0.7309 (mm) cc_final: 0.6837 (mm) REVERT: B 401 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8558 (tp) REVERT: B 453 THR cc_start: 0.8826 (p) cc_final: 0.8571 (p) REVERT: B 742 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7763 (t80) REVERT: B 967 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6839 (tp) REVERT: K 156 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7112 (m110) REVERT: K 176 LEU cc_start: 0.8736 (mt) cc_final: 0.8351 (mt) REVERT: J 4 MET cc_start: 0.8465 (mmt) cc_final: 0.7854 (mmt) REVERT: J 144 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6554 (tm-30) REVERT: J 150 LYS cc_start: 0.6251 (pttm) cc_final: 0.5688 (pttt) REVERT: J 166 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8320 (tm-30) REVERT: H 38 ARG cc_start: 0.8377 (ptt180) cc_final: 0.8076 (ptt180) REVERT: H 76 LYS cc_start: 0.8698 (mptt) cc_final: 0.8457 (mmtp) REVERT: H 80 TYR cc_start: 0.6586 (m-10) cc_final: 0.6269 (m-10) REVERT: I 35 TRP cc_start: 0.8280 (m100) cc_final: 0.7648 (m100) REVERT: C 77 PHE cc_start: 0.7683 (t80) cc_final: 0.7349 (t80) REVERT: C 451 ILE cc_start: 0.8839 (mm) cc_final: 0.8540 (mm) REVERT: C 478 TYR cc_start: 0.9239 (OUTLIER) cc_final: 0.8635 (m-10) REVERT: M 143 ARG cc_start: 0.7894 (tpt90) cc_final: 0.7483 (tpt90) REVERT: N 73 ASP cc_start: 0.6712 (t0) cc_final: 0.6450 (t0) REVERT: O 4 MET cc_start: 0.7844 (mmm) cc_final: 0.6894 (mmm) REVERT: O 37 GLN cc_start: 0.7919 (tt0) cc_final: 0.7438 (tm-30) outliers start: 75 outliers final: 63 residues processed: 444 average time/residue: 0.2475 time to fit residues: 177.7843 Evaluate side-chains 461 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 392 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 573 CYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 600 CYS Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 632 CYS Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 146 LYS Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain L residue 16 GLU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 105 ASP Chi-restraints excluded: chain O residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 330 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 chunk 301 optimal weight: 20.0000 chunk 163 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 446 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 438 optimal weight: 5.9990 chunk 327 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 HIS G 125 GLN ** G 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.146753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.101140 restraints weight = 63046.710| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.96 r_work: 0.3143 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 39975 Z= 0.284 Angle : 0.683 16.938 54474 Z= 0.343 Chirality : 0.050 0.656 6228 Planarity : 0.005 0.053 6963 Dihedral : 4.987 42.095 6102 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.95 % Allowed : 15.00 % Favored : 83.05 % 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: -0.72 (0.12), residues: 4923 helix: 1.92 (0.20), residues: 690 sheet: -0.33 (0.13), residues: 1662 loop : -1.24 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 87 TYR 0.026 0.002 TYR I 49 PHE 0.032 0.002 PHE J 210 TRP 0.019 0.002 TRP C 49 HIS 0.007 0.001 HIS A1031 Details of bonding type rmsd covalent geometry : bond 0.00692 (39882) covalent geometry : angle 0.66042 (54252) SS BOND : bond 0.00552 ( 57) SS BOND : angle 1.83878 ( 114) hydrogen bonds : bond 0.05374 ( 1375) hydrogen bonds : angle 5.56201 ( 3690) link_BETA1-4 : bond 0.00294 ( 12) link_BETA1-4 : angle 1.27130 ( 36) link_NAG-ASN : bond 0.00414 ( 24) link_NAG-ASN : angle 4.26316 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14763.59 seconds wall clock time: 251 minutes 57.02 seconds (15117.02 seconds total)