Starting phenix.real_space_refine on Mon Jul 6 02:10:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mjj_23875/07_2026/7mjj_23875.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjj_23875/07_2026/7mjj_23875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mjj_23875/07_2026/7mjj_23875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjj_23875/07_2026/7mjj_23875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mjj_23875/07_2026/7mjj_23875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjj_23875/07_2026/7mjj_23875.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mjj_23875/07_2026/7mjj_23875.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mjj_23875/07_2026/7mjj_23875.cif" } resolution = 3.32 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= 0.029 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 133 5.16 5 C 20126 2.51 5 N 5191 2.21 5 O 6230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31680 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1585 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain breaks: 1 Chain: "E" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "F" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1585 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain breaks: 1 Chain: "G" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.26, per 1000 atoms: 0.17 Number of scatterers: 31680 At special positions: 0 Unit cell: (138, 147, 247, 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 133 16.00 O 6230 8.00 N 5191 7.00 C 20126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 200 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.04 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG H 1 " - " ASN A 17 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 17 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 17 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C1134 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7402 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 73 sheets defined 21.1% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.837A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.626A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.098A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.158A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.668A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.936A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.520A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.005A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.858A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.833A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.623A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.074A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.519A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.574A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.656A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.915A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.544A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.107A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.152A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.814A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.825A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.555A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.945A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.651A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.972A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.595A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.250A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.030A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.604A pdb=" N ASN D 32 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.530A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 90' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.633A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'E' and resid 121 through 126 removed outlier: 3.665A pdb=" N LYS E 126 " --> pdb=" O ASP E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 187 removed outlier: 3.613A pdb=" N GLU E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 183 through 187' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.609A pdb=" N ASN F 32 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.524A pdb=" N ASP F 89 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 90' Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.645A pdb=" N ASP G 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.618A pdb=" N LYS G 126 " --> pdb=" O ASP G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.988A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.031A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.587A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.587A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.659A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.042A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.150A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.997A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.760A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.579A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.579A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.373A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.776A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.335A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.130A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.759A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 154 through 163 removed outlier: 5.169A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 13.117A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.348A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.914A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.450A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.590A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.709A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.204A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.986A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.267A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.580A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.580A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.402A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.249A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.196A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.915A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.440A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.703A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.393A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.920A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.920A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.205A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.518A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.518A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.368A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.545A pdb=" N THR D 77 " --> pdb=" O HIS D 72 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.401A pdb=" N TYR D 33 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.940A pdb=" N TYR D 106 " --> pdb=" O ARG D 97 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 124 through 128 removed outlier: 4.090A pdb=" N GLY D 143 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR D 180 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 124 through 128 removed outlier: 4.090A pdb=" N GLY D 143 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR D 180 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 155 through 158 removed outlier: 3.812A pdb=" N TYR D 198 " --> pdb=" O VAL D 215 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.693A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.357A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.357A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.529A pdb=" N SER E 131 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU E 181 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL E 133 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU E 179 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU E 135 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER E 177 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASN E 137 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU E 175 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 144 through 150 Processing sheet with id=AG9, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.544A pdb=" N THR F 77 " --> pdb=" O HIS F 72 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.386A pdb=" N TYR F 33 " --> pdb=" O GLY F 98 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.926A pdb=" N TYR F 106 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 124 through 128 removed outlier: 4.119A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 124 through 128 removed outlier: 4.119A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 155 through 158 removed outlier: 4.134A pdb=" N TYR F 198 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.689A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.366A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.366A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 114 through 118 removed outlier: 5.570A pdb=" N SER G 131 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU G 181 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL G 133 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU G 179 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU G 135 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N SER G 177 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN G 137 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU G 175 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 144 through 150 1389 hydrogen bonds defined for protein. 3750 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: 10.43 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9231 1.34 - 1.46: 7285 1.46 - 1.58: 15720 1.58 - 1.70: 0 1.70 - 1.82: 166 Bond restraints: 32402 Sorted by residual: bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 1.335 1.370 -0.035 1.38e-02 5.25e+03 6.33e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.23e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.46e+00 ... (remaining 32397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 42950 2.15 - 4.29: 1056 4.29 - 6.44: 73 6.44 - 8.58: 27 8.58 - 10.73: 3 Bond angle restraints: 44109 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.41 -5.71 1.22e+00 6.72e-01 2.19e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.30 -5.60 1.22e+00 6.72e-01 2.10e+01 angle pdb=" C GLY D 100 " pdb=" N ASP D 101 " pdb=" CA ASP D 101 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" C GLY F 100 " pdb=" N ASP F 101 " pdb=" CA ASP F 101 " ideal model delta sigma weight residual 121.54 129.70 -8.16 1.91e+00 2.74e-01 1.82e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.85 -5.15 1.22e+00 6.72e-01 1.78e+01 ... (remaining 44104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 17459 17.98 - 35.96: 1091 35.96 - 53.94: 190 53.94 - 71.92: 59 71.92 - 89.91: 34 Dihedral angle restraints: 18833 sinusoidal: 7304 harmonic: 11529 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.73 -59.73 1 1.00e+01 1.00e-02 4.76e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.24 -59.24 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CA CYS B 590 " pdb=" C CYS B 590 " pdb=" N SER B 591 " pdb=" CA SER B 591 " ideal model delta harmonic sigma weight residual -180.00 -150.91 -29.09 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 18830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4111 0.063 - 0.125: 924 0.125 - 0.188: 107 0.188 - 0.250: 18 0.250 - 0.313: 5 Chirality restraints: 5165 Sorted by residual: chirality pdb=" CB ILE B 332 " pdb=" CA ILE B 332 " pdb=" CG1 ILE B 332 " pdb=" CG2 ILE B 332 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 5162 not shown) Planarity restraints: 5663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C MET C 902 " 0.057 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C GLN C 920 " 0.049 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 213 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.35e+00 pdb=" C LYS D 213 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS D 213 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS D 214 " 0.016 2.00e-02 2.50e+03 ... (remaining 5660 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7849 2.80 - 3.33: 26184 3.33 - 3.85: 53540 3.85 - 4.38: 62353 4.38 - 4.90: 107387 Nonbonded interactions: 257313 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.278 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.319 3.040 ... (remaining 257308 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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: 6.000 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 30.040 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 0.059 32512 Z= 0.209 Angle : 0.779 15.241 44389 Z= 0.410 Chirality : 0.053 0.313 5165 Planarity : 0.007 0.066 5621 Dihedral : 12.962 89.905 11281 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.12), residues: 3908 helix: 0.15 (0.18), residues: 673 sheet: 0.05 (0.15), residues: 1105 loop : -0.91 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 983 TYR 0.037 0.002 TYR A 200 PHE 0.039 0.002 PHE B 135 TRP 0.018 0.002 TRP G 148 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (32402) covalent geometry : angle 0.75680 / 0.41 (44109) SS BOND : bond 0.00240 / 0.15 ( 50) SS BOND : angle 1.19741 / 0.80 ( 100) hydrogen bonds : bond 0.12018 / 8.00 ( 1278) hydrogen bonds : angle 7.39431 / 5.24 ( 3750) link_BETA1-4 : bond 0.00636 / 0.40 ( 18) link_BETA1-4 : angle 1.42608 / 0.97 ( 54) link_NAG-ASN : bond 0.00687 / 0.34 ( 42) link_NAG-ASN : angle 3.32344 / 2.81 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7715 (m-80) cc_final: 0.6755 (m-80) REVERT: A 168 PHE cc_start: 0.8845 (t80) cc_final: 0.8349 (t80) REVERT: A 365 TYR cc_start: 0.8958 (m-80) cc_final: 0.8442 (m-80) REVERT: A 390 LEU cc_start: 0.8420 (mt) cc_final: 0.7966 (mt) REVERT: A 508 TYR cc_start: 0.8404 (m-80) cc_final: 0.8143 (m-10) REVERT: A 751 ASN cc_start: 0.9312 (m-40) cc_final: 0.9094 (m-40) REVERT: A 936 ASP cc_start: 0.8803 (m-30) cc_final: 0.8471 (m-30) REVERT: B 271 GLN cc_start: 0.9069 (mt0) cc_final: 0.8682 (mp10) REVERT: B 458 LYS cc_start: 0.8445 (mmtm) cc_final: 0.8219 (mptt) REVERT: B 571 ASP cc_start: 0.8647 (m-30) cc_final: 0.7759 (t0) REVERT: B 574 ASP cc_start: 0.9002 (p0) cc_final: 0.8723 (p0) REVERT: B 858 LEU cc_start: 0.8845 (mt) cc_final: 0.8363 (pt) REVERT: B 950 ASP cc_start: 0.8774 (m-30) cc_final: 0.8464 (m-30) REVERT: B 964 LYS cc_start: 0.9084 (mmtp) cc_final: 0.8843 (mmtt) REVERT: C 191 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8036 (mp0) REVERT: C 217 PRO cc_start: 0.8272 (Cg_endo) cc_final: 0.8025 (Cg_exo) REVERT: C 398 ASP cc_start: 0.8693 (m-30) cc_final: 0.8127 (m-30) REVERT: C 858 LEU cc_start: 0.8759 (mp) cc_final: 0.8474 (pp) REVERT: D 34 MET cc_start: 0.3217 (mmm) cc_final: 0.2810 (mmm) REVERT: D 81 GLN cc_start: 0.8657 (tp40) cc_final: 0.8449 (tm-30) REVERT: E 18 LYS cc_start: 0.2029 (tmmt) cc_final: 0.1051 (mttp) REVERT: G 54 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7445 (ttm110) REVERT: G 192 TYR cc_start: 0.1966 (m-80) cc_final: 0.1039 (m-80) outliers start: 0 outliers final: 0 residues processed: 472 average time/residue: 0.2015 time to fit residues: 146.8217 Evaluate side-chains 214 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 519 HIS A 907 ASN A1142 GLN B 137 ASN B 314 GLN B 360 ASN B 613 GLN B 926 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.096565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.059810 restraints weight = 122480.223| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.61 r_work: 0.3048 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32512 Z= 0.143 Angle : 0.598 10.416 44389 Z= 0.307 Chirality : 0.045 0.242 5165 Planarity : 0.005 0.056 5621 Dihedral : 4.596 22.135 4259 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.87 % Allowed : 6.56 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.13), residues: 3908 helix: 1.67 (0.20), residues: 668 sheet: 0.39 (0.15), residues: 1117 loop : -0.60 (0.12), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 995 TYR 0.026 0.001 TYR D 59 PHE 0.017 0.001 PHE C 168 TRP 0.008 0.001 TRP B 886 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (32402) covalent geometry : angle 0.58183 / 0.30 (44109) SS BOND : bond 0.00199 / 0.13 ( 50) SS BOND : angle 0.78510 / 0.54 ( 100) hydrogen bonds : bond 0.03846 / 2.59 ( 1278) hydrogen bonds : angle 5.92687 / 4.19 ( 3750) link_BETA1-4 : bond 0.00148 / 0.09 ( 18) link_BETA1-4 : angle 1.06353 / 0.73 ( 54) link_NAG-ASN : bond 0.00539 / 0.29 ( 42) link_NAG-ASN : angle 2.52941 / 2.04 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7822 (m-80) cc_final: 0.6992 (m-80) REVERT: A 153 MET cc_start: 0.5144 (pmm) cc_final: 0.4766 (pmm) REVERT: A 204 TYR cc_start: 0.6971 (m-80) cc_final: 0.6203 (m-80) REVERT: A 238 PHE cc_start: 0.6484 (p90) cc_final: 0.5736 (p90) REVERT: A 299 THR cc_start: 0.9523 (m) cc_final: 0.9310 (p) REVERT: A 508 TYR cc_start: 0.8444 (m-80) cc_final: 0.8174 (m-10) REVERT: A 762 GLN cc_start: 0.8968 (mt0) cc_final: 0.8577 (mt0) REVERT: A 904 TYR cc_start: 0.8943 (m-10) cc_final: 0.8741 (m-10) REVERT: A 936 ASP cc_start: 0.9207 (m-30) cc_final: 0.8897 (m-30) REVERT: A 1019 ARG cc_start: 0.9194 (ttp80) cc_final: 0.8859 (ttm110) REVERT: B 201 PHE cc_start: 0.8719 (t80) cc_final: 0.8440 (t80) REVERT: B 271 GLN cc_start: 0.9140 (mt0) cc_final: 0.8728 (mp10) REVERT: B 458 LYS cc_start: 0.8403 (mmtm) cc_final: 0.8153 (mptt) REVERT: B 574 ASP cc_start: 0.9131 (p0) cc_final: 0.8815 (p0) REVERT: B 858 LEU cc_start: 0.9041 (mt) cc_final: 0.8545 (pt) REVERT: B 964 LYS cc_start: 0.9418 (mmtp) cc_final: 0.9160 (mmtt) REVERT: B 1002 GLN cc_start: 0.9186 (tt0) cc_final: 0.8976 (tt0) REVERT: C 191 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8158 (mp0) REVERT: C 378 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8048 (mppt) REVERT: C 398 ASP cc_start: 0.9042 (m-30) cc_final: 0.8295 (m-30) REVERT: D 46 GLU cc_start: 0.4532 (OUTLIER) cc_final: 0.4236 (pm20) REVERT: D 61 ASP cc_start: 0.7098 (p0) cc_final: 0.6730 (t0) REVERT: D 197 THR cc_start: 0.5249 (p) cc_final: 0.5023 (t) REVERT: F 72 HIS cc_start: 0.7854 (t-90) cc_final: 0.7631 (t70) REVERT: G 24 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7830 (ptp90) REVERT: G 54 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7437 (ttp-110) REVERT: G 82 ASP cc_start: 0.5619 (m-30) cc_final: 0.4103 (p0) outliers start: 30 outliers final: 18 residues processed: 259 average time/residue: 0.2048 time to fit residues: 85.0626 Evaluate side-chains 203 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 152 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 360 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 245 optimal weight: 0.9990 chunk 328 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN A 907 ASN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C1011 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.096164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.059526 restraints weight = 124404.654| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 4.71 r_work: 0.3033 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32512 Z= 0.134 Angle : 0.551 10.077 44389 Z= 0.283 Chirality : 0.044 0.261 5165 Planarity : 0.004 0.059 5621 Dihedral : 4.352 21.664 4259 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.90 % Allowed : 7.84 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 0.31 (0.13), residues: 3908 helix: 2.05 (0.20), residues: 675 sheet: 0.43 (0.15), residues: 1129 loop : -0.52 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 983 TYR 0.025 0.001 TYR A 369 PHE 0.020 0.001 PHE C 392 TRP 0.010 0.001 TRP D 107 HIS 0.017 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (32402) covalent geometry : angle 0.53591 / 0.28 (44109) SS BOND : bond 0.00184 / 0.13 ( 50) SS BOND : angle 0.65932 / 0.50 ( 100) hydrogen bonds : bond 0.03683 / 2.48 ( 1278) hydrogen bonds : angle 5.59764 / 3.96 ( 3750) link_BETA1-4 : bond 0.00278 / 0.17 ( 18) link_BETA1-4 : angle 1.00113 / 0.70 ( 54) link_NAG-ASN : bond 0.00530 / 0.27 ( 42) link_NAG-ASN : angle 2.37898 / 1.99 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7574 (m-80) cc_final: 0.7304 (m-80) REVERT: A 168 PHE cc_start: 0.8707 (t80) cc_final: 0.8290 (t80) REVERT: A 299 THR cc_start: 0.9550 (m) cc_final: 0.9336 (p) REVERT: A 508 TYR cc_start: 0.8484 (m-80) cc_final: 0.8196 (m-10) REVERT: A 762 GLN cc_start: 0.8994 (mt0) cc_final: 0.8628 (mt0) REVERT: A 904 TYR cc_start: 0.8949 (m-10) cc_final: 0.8745 (m-10) REVERT: A 936 ASP cc_start: 0.9187 (m-30) cc_final: 0.8868 (m-30) REVERT: B 201 PHE cc_start: 0.8860 (t80) cc_final: 0.8502 (t80) REVERT: B 271 GLN cc_start: 0.9187 (mt0) cc_final: 0.8775 (mp10) REVERT: B 458 LYS cc_start: 0.8395 (mmtm) cc_final: 0.8120 (mptt) REVERT: B 574 ASP cc_start: 0.9134 (p0) cc_final: 0.8775 (p0) REVERT: B 773 GLU cc_start: 0.9006 (tp30) cc_final: 0.8641 (tt0) REVERT: B 858 LEU cc_start: 0.9081 (mt) cc_final: 0.8579 (pt) REVERT: B 964 LYS cc_start: 0.9392 (mmtp) cc_final: 0.9142 (mmtt) REVERT: C 191 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8212 (mp0) REVERT: C 378 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8021 (mppt) REVERT: C 398 ASP cc_start: 0.9007 (m-30) cc_final: 0.8298 (m-30) REVERT: C 462 LYS cc_start: 0.9186 (mmmt) cc_final: 0.8840 (mppt) REVERT: C 923 ILE cc_start: 0.9738 (OUTLIER) cc_final: 0.9518 (mp) REVERT: C 1002 GLN cc_start: 0.9282 (tt0) cc_final: 0.8817 (tp40) REVERT: D 61 ASP cc_start: 0.6968 (p0) cc_final: 0.6619 (t0) REVERT: D 82 MET cc_start: 0.3322 (mpp) cc_final: 0.2951 (mpp) REVERT: E 32 TYR cc_start: 0.8528 (m-80) cc_final: 0.8202 (m-80) REVERT: E 195 GLU cc_start: 0.4466 (tt0) cc_final: 0.4166 (pt0) REVERT: G 24 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7859 (ptp90) REVERT: G 32 TYR cc_start: 0.8484 (m-80) cc_final: 0.8262 (m-80) REVERT: G 82 ASP cc_start: 0.5611 (m-30) cc_final: 0.4126 (p0) outliers start: 31 outliers final: 15 residues processed: 219 average time/residue: 0.2027 time to fit residues: 72.2501 Evaluate side-chains 191 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 188 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 209 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 378 optimal weight: 20.0000 chunk 153 optimal weight: 0.5980 chunk 246 optimal weight: 2.9990 chunk 387 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN A 755 GLN C 218 GLN C 955 ASN C 957 GLN C1011 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.094663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.057973 restraints weight = 123293.048| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 4.50 r_work: 0.2991 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32512 Z= 0.166 Angle : 0.552 9.755 44389 Z= 0.282 Chirality : 0.044 0.277 5165 Planarity : 0.004 0.056 5621 Dihedral : 4.263 21.759 4259 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.27 % Allowed : 8.42 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.13), residues: 3908 helix: 1.98 (0.20), residues: 681 sheet: 0.51 (0.15), residues: 1101 loop : -0.41 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 66 TYR 0.020 0.001 TYR C1067 PHE 0.019 0.001 PHE C 515 TRP 0.009 0.001 TRP D 158 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (32402) covalent geometry : angle 0.53782 / 0.28 (44109) SS BOND : bond 0.00134 / 0.09 ( 50) SS BOND : angle 0.63960 / 0.47 ( 100) hydrogen bonds : bond 0.03731 / 2.50 ( 1278) hydrogen bonds : angle 5.35910 / 3.77 ( 3750) link_BETA1-4 : bond 0.00282 / 0.16 ( 18) link_BETA1-4 : angle 1.13013 / 0.79 ( 54) link_NAG-ASN : bond 0.00526 / 0.28 ( 42) link_NAG-ASN : angle 2.30007 / 1.92 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7751 (m-80) cc_final: 0.7473 (m-80) REVERT: A 153 MET cc_start: 0.5260 (pmm) cc_final: 0.4889 (pmm) REVERT: A 762 GLN cc_start: 0.8971 (mt0) cc_final: 0.8648 (mt0) REVERT: A 936 ASP cc_start: 0.9212 (m-30) cc_final: 0.8914 (m-30) REVERT: B 226 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8749 (mm) REVERT: B 271 GLN cc_start: 0.9255 (mt0) cc_final: 0.8814 (mp10) REVERT: B 458 LYS cc_start: 0.8476 (mmtm) cc_final: 0.8149 (mptt) REVERT: B 574 ASP cc_start: 0.9150 (p0) cc_final: 0.8787 (p0) REVERT: B 773 GLU cc_start: 0.9033 (tp30) cc_final: 0.8686 (tt0) REVERT: B 858 LEU cc_start: 0.9151 (mt) cc_final: 0.8625 (pt) REVERT: B 964 LYS cc_start: 0.9402 (mmtp) cc_final: 0.9166 (mmtt) REVERT: C 191 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8652 (mt-10) REVERT: C 360 ASN cc_start: 0.9343 (t0) cc_final: 0.9101 (t0) REVERT: C 378 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8148 (mtmm) REVERT: C 398 ASP cc_start: 0.9055 (m-30) cc_final: 0.8342 (m-30) REVERT: C 462 LYS cc_start: 0.9215 (mmmt) cc_final: 0.8875 (mppt) REVERT: C 900 MET cc_start: 0.9362 (mtp) cc_final: 0.9147 (mtt) REVERT: C 923 ILE cc_start: 0.9758 (OUTLIER) cc_final: 0.9551 (mp) REVERT: C 1002 GLN cc_start: 0.9272 (tt0) cc_final: 0.8898 (tp40) REVERT: D 78 LEU cc_start: 0.1638 (OUTLIER) cc_final: 0.1399 (mm) REVERT: D 82 MET cc_start: 0.2738 (mpp) cc_final: 0.2318 (mpp) REVERT: E 32 TYR cc_start: 0.8638 (m-80) cc_final: 0.8289 (m-80) REVERT: E 195 GLU cc_start: 0.4444 (tt0) cc_final: 0.4184 (pt0) REVERT: F 158 TRP cc_start: 0.3776 (m100) cc_final: 0.3026 (m100) REVERT: G 117 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.6225 (mm) outliers start: 44 outliers final: 23 residues processed: 229 average time/residue: 0.2042 time to fit residues: 74.8579 Evaluate side-chains 194 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 117 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 0.9980 chunk 109 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 275 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 260 optimal weight: 10.0000 chunk 370 optimal weight: 6.9990 chunk 374 optimal weight: 20.0000 chunk 286 optimal weight: 2.9990 chunk 242 optimal weight: 0.6980 chunk 154 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN C 388 ASN C 613 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.093678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.057905 restraints weight = 123317.197| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.51 r_work: 0.2960 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32512 Z= 0.193 Angle : 0.562 9.512 44389 Z= 0.286 Chirality : 0.044 0.284 5165 Planarity : 0.004 0.056 5621 Dihedral : 4.284 20.918 4259 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.39 % Allowed : 8.99 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 0.37 (0.13), residues: 3908 helix: 1.92 (0.20), residues: 695 sheet: 0.46 (0.16), residues: 1082 loop : -0.39 (0.13), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1107 TYR 0.018 0.001 TYR A1067 PHE 0.026 0.001 PHE A 201 TRP 0.009 0.001 TRP A 104 HIS 0.004 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (32402) covalent geometry : angle 0.54856 / 0.28 (44109) SS BOND : bond 0.00132 / 0.09 ( 50) SS BOND : angle 0.65671 / 0.46 ( 100) hydrogen bonds : bond 0.03819 / 2.56 ( 1278) hydrogen bonds : angle 5.32960 / 3.75 ( 3750) link_BETA1-4 : bond 0.00226 / 0.13 ( 18) link_BETA1-4 : angle 1.04371 / 0.73 ( 54) link_NAG-ASN : bond 0.00535 / 0.30 ( 42) link_NAG-ASN : angle 2.26845 / 1.90 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7914 (m-80) cc_final: 0.7570 (m-80) REVERT: A 762 GLN cc_start: 0.9010 (mt0) cc_final: 0.8687 (mt0) REVERT: A 936 ASP cc_start: 0.9285 (m-30) cc_final: 0.8986 (m-30) REVERT: B 271 GLN cc_start: 0.9286 (mt0) cc_final: 0.9061 (mt0) REVERT: B 458 LYS cc_start: 0.8490 (mmtm) cc_final: 0.8185 (tppt) REVERT: B 574 ASP cc_start: 0.9206 (p0) cc_final: 0.8885 (p0) REVERT: B 773 GLU cc_start: 0.9107 (tp30) cc_final: 0.8741 (tt0) REVERT: B 858 LEU cc_start: 0.9330 (mt) cc_final: 0.8715 (pt) REVERT: B 964 LYS cc_start: 0.9409 (mmtp) cc_final: 0.9189 (mmtt) REVERT: C 170 TYR cc_start: 0.8606 (t80) cc_final: 0.8203 (t80) REVERT: C 378 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8145 (mtmm) REVERT: C 398 ASP cc_start: 0.9072 (m-30) cc_final: 0.8397 (m-30) REVERT: C 462 LYS cc_start: 0.9239 (mmmt) cc_final: 0.8864 (mppt) REVERT: C 923 ILE cc_start: 0.9773 (OUTLIER) cc_final: 0.9553 (mp) REVERT: C 1002 GLN cc_start: 0.9293 (tt0) cc_final: 0.9053 (tp40) REVERT: D 78 LEU cc_start: 0.1545 (OUTLIER) cc_final: 0.1225 (mt) REVERT: D 82 MET cc_start: 0.2770 (mpp) cc_final: 0.2392 (mpp) REVERT: E 32 TYR cc_start: 0.8666 (m-80) cc_final: 0.8296 (m-80) REVERT: E 195 GLU cc_start: 0.4460 (tt0) cc_final: 0.4190 (pt0) REVERT: F 158 TRP cc_start: 0.4148 (m100) cc_final: 0.3415 (m100) REVERT: G 117 ILE cc_start: 0.6666 (OUTLIER) cc_final: 0.6241 (mm) outliers start: 48 outliers final: 31 residues processed: 204 average time/residue: 0.2029 time to fit residues: 67.9038 Evaluate side-chains 186 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 117 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 228 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 211 optimal weight: 8.9990 chunk 194 optimal weight: 0.7980 chunk 362 optimal weight: 5.9990 chunk 343 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1036 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.094123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.057544 restraints weight = 122982.213| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 4.50 r_work: 0.2979 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32512 Z= 0.137 Angle : 0.529 9.380 44389 Z= 0.271 Chirality : 0.044 0.281 5165 Planarity : 0.004 0.055 5621 Dihedral : 4.186 21.519 4259 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.33 % Allowed : 10.15 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 0.40 (0.13), residues: 3908 helix: 1.95 (0.20), residues: 695 sheet: 0.43 (0.16), residues: 1094 loop : -0.35 (0.13), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 214 TYR 0.018 0.001 TYR A 904 PHE 0.018 0.001 PHE A 133 TRP 0.010 0.001 TRP B 104 HIS 0.002 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (32402) covalent geometry : angle 0.51198 / 0.27 (44109) SS BOND : bond 0.00209 / 0.15 ( 50) SS BOND : angle 1.42693 / 1.04 ( 100) hydrogen bonds : bond 0.03609 / 2.40 ( 1278) hydrogen bonds : angle 5.20544 / 3.66 ( 3750) link_BETA1-4 : bond 0.00219 / 0.14 ( 18) link_BETA1-4 : angle 0.89097 / 0.62 ( 54) link_NAG-ASN : bond 0.00491 / 0.25 ( 42) link_NAG-ASN : angle 2.17654 / 1.86 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7855 (m-80) cc_final: 0.7415 (m-80) REVERT: A 133 PHE cc_start: 0.7918 (m-80) cc_final: 0.7582 (m-80) REVERT: A 153 MET cc_start: 0.5381 (pmm) cc_final: 0.5022 (pmm) REVERT: A 762 GLN cc_start: 0.9096 (mt0) cc_final: 0.8866 (mt0) REVERT: A 904 TYR cc_start: 0.9002 (m-10) cc_final: 0.8703 (m-80) REVERT: A 936 ASP cc_start: 0.9269 (m-30) cc_final: 0.8964 (m-30) REVERT: B 226 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8676 (mm) REVERT: B 271 GLN cc_start: 0.9285 (mt0) cc_final: 0.9052 (mt0) REVERT: B 458 LYS cc_start: 0.8524 (mmtm) cc_final: 0.8204 (tppt) REVERT: B 574 ASP cc_start: 0.9205 (p0) cc_final: 0.8874 (p0) REVERT: B 773 GLU cc_start: 0.9046 (tp30) cc_final: 0.8645 (tt0) REVERT: B 858 LEU cc_start: 0.9320 (mt) cc_final: 0.8724 (pt) REVERT: C 170 TYR cc_start: 0.8685 (t80) cc_final: 0.8432 (t80) REVERT: C 378 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8171 (mtmm) REVERT: C 398 ASP cc_start: 0.9037 (m-30) cc_final: 0.8397 (m-30) REVERT: C 460 ASN cc_start: 0.9069 (m-40) cc_final: 0.8594 (t0) REVERT: C 462 LYS cc_start: 0.9242 (mmmt) cc_final: 0.8872 (mppt) REVERT: C 923 ILE cc_start: 0.9770 (OUTLIER) cc_final: 0.9546 (mp) REVERT: C 1002 GLN cc_start: 0.9261 (tt0) cc_final: 0.9018 (tp40) REVERT: D 11 LEU cc_start: 0.5757 (tp) cc_final: 0.5527 (tp) REVERT: D 34 MET cc_start: 0.3150 (mpt) cc_final: 0.2596 (mmt) REVERT: D 78 LEU cc_start: 0.1588 (OUTLIER) cc_final: 0.0575 (mm) REVERT: D 82 MET cc_start: 0.2533 (mpp) cc_final: 0.2189 (mpp) REVERT: E 32 TYR cc_start: 0.8702 (m-80) cc_final: 0.8312 (m-80) REVERT: E 195 GLU cc_start: 0.4449 (tt0) cc_final: 0.4190 (pt0) REVERT: F 158 TRP cc_start: 0.3836 (m100) cc_final: 0.3262 (m100) REVERT: G 54 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.7305 (ttm110) REVERT: G 117 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6280 (mm) outliers start: 46 outliers final: 32 residues processed: 203 average time/residue: 0.1989 time to fit residues: 65.9444 Evaluate side-chains 192 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 117 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 258 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 348 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 178 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 121 ASN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.094119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.057613 restraints weight = 123151.993| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 4.47 r_work: 0.2984 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32512 Z= 0.126 Angle : 0.521 9.615 44389 Z= 0.266 Chirality : 0.043 0.277 5165 Planarity : 0.004 0.097 5621 Dihedral : 4.108 22.284 4259 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.42 % Allowed : 10.53 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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 (0.13), residues: 3908 helix: 2.10 (0.20), residues: 683 sheet: 0.40 (0.16), residues: 1119 loop : -0.30 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.031 0.001 TYR D 79 PHE 0.027 0.001 PHE A 201 TRP 0.010 0.001 TRP B 104 HIS 0.003 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (32402) covalent geometry : angle 0.50574 / 0.26 (44109) SS BOND : bond 0.00150 / 0.11 ( 50) SS BOND : angle 1.27137 / 0.93 ( 100) hydrogen bonds : bond 0.03519 / 2.34 ( 1278) hydrogen bonds : angle 5.09871 / 3.59 ( 3750) link_BETA1-4 : bond 0.00263 / 0.16 ( 18) link_BETA1-4 : angle 0.90816 / 0.63 ( 54) link_NAG-ASN : bond 0.00472 / 0.24 ( 42) link_NAG-ASN : angle 2.14180 / 1.83 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7918 (m-80) cc_final: 0.7502 (m-80) REVERT: A 153 MET cc_start: 0.5347 (pmm) cc_final: 0.5012 (pmm) REVERT: A 904 TYR cc_start: 0.9008 (m-10) cc_final: 0.8772 (m-10) REVERT: A 936 ASP cc_start: 0.9263 (m-30) cc_final: 0.8956 (m-30) REVERT: B 226 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8673 (mm) REVERT: B 271 GLN cc_start: 0.9302 (mt0) cc_final: 0.8780 (mp10) REVERT: B 458 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8225 (tppt) REVERT: B 574 ASP cc_start: 0.9227 (p0) cc_final: 0.8935 (p0) REVERT: B 773 GLU cc_start: 0.9025 (tp30) cc_final: 0.8703 (tt0) REVERT: B 858 LEU cc_start: 0.9309 (mt) cc_final: 0.8686 (pt) REVERT: C 170 TYR cc_start: 0.8735 (t80) cc_final: 0.8507 (t80) REVERT: C 378 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8230 (mtmm) REVERT: C 398 ASP cc_start: 0.9059 (m-30) cc_final: 0.8431 (m-30) REVERT: C 460 ASN cc_start: 0.9035 (m-40) cc_final: 0.8593 (t0) REVERT: C 462 LYS cc_start: 0.9249 (mmmt) cc_final: 0.8871 (mppt) REVERT: C 776 LYS cc_start: 0.9437 (tppt) cc_final: 0.9226 (tptp) REVERT: C 923 ILE cc_start: 0.9773 (OUTLIER) cc_final: 0.9548 (mp) REVERT: C 1002 GLN cc_start: 0.9260 (tt0) cc_final: 0.8991 (tp40) REVERT: D 11 LEU cc_start: 0.5718 (tp) cc_final: 0.5513 (tp) REVERT: D 34 MET cc_start: 0.3026 (mpp) cc_final: 0.1853 (mmt) REVERT: D 82 MET cc_start: 0.2671 (mpp) cc_final: 0.2392 (mpp) REVERT: E 32 TYR cc_start: 0.8722 (m-80) cc_final: 0.8291 (m-80) REVERT: E 195 GLU cc_start: 0.4459 (tt0) cc_final: 0.4184 (pt0) REVERT: F 158 TRP cc_start: 0.3747 (m100) cc_final: 0.3193 (m100) REVERT: G 54 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7287 (ttm110) REVERT: G 117 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6433 (mm) outliers start: 49 outliers final: 35 residues processed: 207 average time/residue: 0.1881 time to fit residues: 63.5933 Evaluate side-chains 194 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 117 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 278 optimal weight: 1.9990 chunk 348 optimal weight: 30.0000 chunk 86 optimal weight: 5.9990 chunk 183 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 366 optimal weight: 0.3980 chunk 203 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.094287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.057905 restraints weight = 122931.649| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.60 r_work: 0.2987 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32512 Z= 0.121 Angle : 0.522 9.273 44389 Z= 0.266 Chirality : 0.043 0.276 5165 Planarity : 0.004 0.087 5621 Dihedral : 4.057 22.652 4259 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.30 % Allowed : 11.02 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 0.50 (0.13), residues: 3908 helix: 2.18 (0.20), residues: 669 sheet: 0.40 (0.16), residues: 1126 loop : -0.27 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.017 0.001 TYR D 79 PHE 0.015 0.001 PHE C 392 TRP 0.010 0.001 TRP B 104 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (32402) covalent geometry : angle 0.50761 / 0.26 (44109) SS BOND : bond 0.00204 / 0.16 ( 50) SS BOND : angle 1.08408 / 0.79 ( 100) hydrogen bonds : bond 0.03467 / 2.31 ( 1278) hydrogen bonds : angle 5.02085 / 3.53 ( 3750) link_BETA1-4 : bond 0.00265 / 0.15 ( 18) link_BETA1-4 : angle 0.88827 / 0.62 ( 54) link_NAG-ASN : bond 0.00463 / 0.23 ( 42) link_NAG-ASN : angle 2.10838 / 1.82 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7963 (m-80) cc_final: 0.7570 (m-80) REVERT: A 133 PHE cc_start: 0.7602 (m-80) cc_final: 0.7052 (t80) REVERT: A 153 MET cc_start: 0.5301 (pmm) cc_final: 0.4986 (pmm) REVERT: A 762 GLN cc_start: 0.9137 (mt0) cc_final: 0.8908 (mt0) REVERT: A 936 ASP cc_start: 0.9255 (m-30) cc_final: 0.8943 (m-30) REVERT: A 954 GLN cc_start: 0.9108 (mt0) cc_final: 0.8893 (tm-30) REVERT: B 226 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8742 (mm) REVERT: B 271 GLN cc_start: 0.9305 (mt0) cc_final: 0.8788 (mp10) REVERT: B 458 LYS cc_start: 0.8531 (mmtm) cc_final: 0.8222 (tppt) REVERT: B 574 ASP cc_start: 0.9208 (p0) cc_final: 0.8916 (p0) REVERT: B 773 GLU cc_start: 0.9023 (tp30) cc_final: 0.8706 (tt0) REVERT: B 858 LEU cc_start: 0.9294 (mt) cc_final: 0.8657 (pt) REVERT: B 1002 GLN cc_start: 0.9216 (tt0) cc_final: 0.8834 (tm-30) REVERT: C 170 TYR cc_start: 0.8684 (t80) cc_final: 0.8482 (t80) REVERT: C 378 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8327 (mtmm) REVERT: C 398 ASP cc_start: 0.9057 (m-30) cc_final: 0.8421 (m-30) REVERT: C 460 ASN cc_start: 0.8961 (m-40) cc_final: 0.8527 (t0) REVERT: C 462 LYS cc_start: 0.9235 (mmmt) cc_final: 0.8868 (mppt) REVERT: C 923 ILE cc_start: 0.9774 (OUTLIER) cc_final: 0.9552 (mp) REVERT: C 1002 GLN cc_start: 0.9251 (tt0) cc_final: 0.8965 (tp40) REVERT: D 11 LEU cc_start: 0.5309 (tp) cc_final: 0.5104 (tp) REVERT: D 34 MET cc_start: 0.3019 (mpp) cc_final: 0.1850 (mmt) REVERT: D 82 MET cc_start: 0.2975 (mpp) cc_final: 0.2720 (mpp) REVERT: E 32 TYR cc_start: 0.8766 (m-80) cc_final: 0.8299 (m-80) REVERT: E 195 GLU cc_start: 0.4313 (tt0) cc_final: 0.4064 (pt0) REVERT: F 158 TRP cc_start: 0.3844 (m100) cc_final: 0.3392 (m100) REVERT: G 117 ILE cc_start: 0.6402 (OUTLIER) cc_final: 0.5960 (mm) outliers start: 45 outliers final: 36 residues processed: 202 average time/residue: 0.1987 time to fit residues: 65.5139 Evaluate side-chains 194 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 117 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 378 optimal weight: 8.9990 chunk 280 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 296 optimal weight: 6.9990 chunk 388 optimal weight: 40.0000 chunk 31 optimal weight: 0.0670 chunk 253 optimal weight: 0.0060 chunk 285 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 210 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 388 ASN B 872 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.094936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.058781 restraints weight = 123030.363| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.49 r_work: 0.3014 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32512 Z= 0.095 Angle : 0.523 10.121 44389 Z= 0.265 Chirality : 0.044 0.271 5165 Planarity : 0.004 0.079 5621 Dihedral : 3.973 22.712 4259 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.07 % Allowed : 11.34 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 0.59 (0.13), residues: 3908 helix: 2.18 (0.20), residues: 670 sheet: 0.57 (0.15), residues: 1188 loop : -0.29 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.030 0.001 TYR A 904 PHE 0.032 0.001 PHE A 201 TRP 0.011 0.001 TRP B 104 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (32402) covalent geometry : angle 0.51017 / 0.26 (44109) SS BOND : bond 0.00202 / 0.15 ( 50) SS BOND : angle 0.83971 / 0.61 ( 100) hydrogen bonds : bond 0.03310 / 2.19 ( 1278) hydrogen bonds : angle 4.90606 / 3.46 ( 3750) link_BETA1-4 : bond 0.00376 / 0.24 ( 18) link_BETA1-4 : angle 0.86152 / 0.59 ( 54) link_NAG-ASN : bond 0.00470 / 0.24 ( 42) link_NAG-ASN : angle 2.07244 / 1.81 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7934 (m-80) cc_final: 0.7545 (m-80) REVERT: A 153 MET cc_start: 0.5581 (pmm) cc_final: 0.5288 (pmm) REVERT: A 762 GLN cc_start: 0.9076 (mt0) cc_final: 0.8828 (mt0) REVERT: A 936 ASP cc_start: 0.9244 (m-30) cc_final: 0.8902 (m-30) REVERT: B 211 ASN cc_start: 0.8333 (p0) cc_final: 0.7332 (m-40) REVERT: B 226 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8769 (mm) REVERT: B 271 GLN cc_start: 0.9272 (mt0) cc_final: 0.8758 (mp10) REVERT: B 574 ASP cc_start: 0.9186 (p0) cc_final: 0.8897 (p0) REVERT: B 773 GLU cc_start: 0.8985 (tp30) cc_final: 0.8686 (tt0) REVERT: B 858 LEU cc_start: 0.9304 (mt) cc_final: 0.8666 (pt) REVERT: B 954 GLN cc_start: 0.8946 (mt0) cc_final: 0.8703 (mt0) REVERT: B 1002 GLN cc_start: 0.9176 (tt0) cc_final: 0.8812 (tm-30) REVERT: C 170 TYR cc_start: 0.8717 (t80) cc_final: 0.8502 (t80) REVERT: C 378 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8262 (mtmm) REVERT: C 398 ASP cc_start: 0.9002 (m-30) cc_final: 0.8376 (m-30) REVERT: C 460 ASN cc_start: 0.9030 (m-40) cc_final: 0.8593 (t0) REVERT: C 462 LYS cc_start: 0.9256 (mmmt) cc_final: 0.8894 (mppt) REVERT: C 796 ASP cc_start: 0.8958 (t0) cc_final: 0.8432 (p0) REVERT: C 900 MET cc_start: 0.9266 (mtp) cc_final: 0.9055 (mtt) REVERT: C 923 ILE cc_start: 0.9773 (OUTLIER) cc_final: 0.9562 (mp) REVERT: C 1002 GLN cc_start: 0.9219 (tt0) cc_final: 0.8932 (tp40) REVERT: D 11 LEU cc_start: 0.5453 (tp) cc_final: 0.5149 (tp) REVERT: D 34 MET cc_start: 0.3065 (mpp) cc_final: 0.1980 (mmt) REVERT: D 78 LEU cc_start: 0.1237 (OUTLIER) cc_final: 0.0722 (tt) REVERT: D 82 MET cc_start: 0.2937 (mpp) cc_final: 0.2681 (mpp) REVERT: E 32 TYR cc_start: 0.8759 (m-80) cc_final: 0.8288 (m-80) REVERT: E 195 GLU cc_start: 0.4436 (tt0) cc_final: 0.4172 (pt0) REVERT: F 158 TRP cc_start: 0.3605 (m100) cc_final: 0.3142 (m100) REVERT: G 117 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.6147 (mm) outliers start: 37 outliers final: 25 residues processed: 201 average time/residue: 0.1863 time to fit residues: 61.8176 Evaluate side-chains 183 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 117 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 73 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN C 872 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.092961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056523 restraints weight = 123800.569| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 4.47 r_work: 0.2953 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32512 Z= 0.191 Angle : 0.581 9.954 44389 Z= 0.294 Chirality : 0.044 0.280 5165 Planarity : 0.004 0.081 5621 Dihedral : 4.150 21.839 4259 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.07 % Allowed : 11.57 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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: 0.49 (0.13), residues: 3908 helix: 2.11 (0.20), residues: 673 sheet: 0.40 (0.15), residues: 1134 loop : -0.26 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 214 TYR 0.027 0.001 TYR A 904 PHE 0.024 0.001 PHE C 392 TRP 0.010 0.001 TRP B 886 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (32402) covalent geometry : angle 0.56741 / 0.29 (44109) SS BOND : bond 0.00290 / 0.23 ( 50) SS BOND : angle 1.14711 / 0.83 ( 100) hydrogen bonds : bond 0.03765 / 2.50 ( 1278) hydrogen bonds : angle 5.11497 / 3.59 ( 3750) link_BETA1-4 : bond 0.00220 / 0.12 ( 18) link_BETA1-4 : angle 1.14370 / 0.79 ( 54) link_NAG-ASN : bond 0.00512 / 0.29 ( 42) link_NAG-ASN : angle 2.18939 / 1.83 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.8007 (m-80) cc_final: 0.7720 (m-80) REVERT: A 153 MET cc_start: 0.5428 (pmm) cc_final: 0.5120 (pmm) REVERT: A 762 GLN cc_start: 0.9093 (mt0) cc_final: 0.8845 (mt0) REVERT: A 780 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9157 (mm-30) REVERT: A 936 ASP cc_start: 0.9273 (m-30) cc_final: 0.8964 (m-30) REVERT: B 211 ASN cc_start: 0.8363 (p0) cc_final: 0.7316 (m-40) REVERT: B 226 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8834 (mm) REVERT: B 271 GLN cc_start: 0.9340 (mt0) cc_final: 0.9120 (mt0) REVERT: B 458 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8253 (tppt) REVERT: B 574 ASP cc_start: 0.9167 (p0) cc_final: 0.8846 (p0) REVERT: B 773 GLU cc_start: 0.9082 (tp30) cc_final: 0.8755 (tt0) REVERT: B 858 LEU cc_start: 0.9364 (mt) cc_final: 0.8656 (pt) REVERT: B 954 GLN cc_start: 0.8988 (mt0) cc_final: 0.8760 (mt0) REVERT: B 1002 GLN cc_start: 0.9234 (tt0) cc_final: 0.8925 (tm-30) REVERT: C 378 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8237 (mtmm) REVERT: C 398 ASP cc_start: 0.9067 (m-30) cc_final: 0.8458 (m-30) REVERT: C 460 ASN cc_start: 0.9009 (m-40) cc_final: 0.8592 (t0) REVERT: C 462 LYS cc_start: 0.9255 (mmmt) cc_final: 0.8876 (mppt) REVERT: C 923 ILE cc_start: 0.9779 (OUTLIER) cc_final: 0.9560 (mp) REVERT: C 1002 GLN cc_start: 0.9244 (tt0) cc_final: 0.9011 (tp40) REVERT: D 11 LEU cc_start: 0.5357 (tp) cc_final: 0.5151 (tp) REVERT: D 34 MET cc_start: 0.3102 (mpp) cc_final: 0.1892 (mmt) REVERT: D 78 LEU cc_start: 0.1164 (OUTLIER) cc_final: 0.0770 (tt) REVERT: D 82 MET cc_start: 0.3052 (mpp) cc_final: 0.2764 (mpp) REVERT: E 32 TYR cc_start: 0.8790 (m-80) cc_final: 0.8337 (m-80) REVERT: E 195 GLU cc_start: 0.4344 (tt0) cc_final: 0.4072 (pt0) REVERT: F 158 TRP cc_start: 0.3785 (m100) cc_final: 0.3343 (m100) REVERT: G 24 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7798 (mtm-85) REVERT: G 117 ILE cc_start: 0.6486 (OUTLIER) cc_final: 0.6022 (mm) outliers start: 37 outliers final: 30 residues processed: 187 average time/residue: 0.1784 time to fit residues: 56.0524 Evaluate side-chains 189 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 117 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 365 optimal weight: 30.0000 chunk 125 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 373 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 308 optimal weight: 0.6980 chunk 242 optimal weight: 0.8980 chunk 332 optimal weight: 6.9990 chunk 348 optimal weight: 0.0270 chunk 364 optimal weight: 5.9990 overall best weight: 1.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.093325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.056917 restraints weight = 123890.705| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 4.48 r_work: 0.2968 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32512 Z= 0.148 Angle : 0.541 9.348 44389 Z= 0.276 Chirality : 0.044 0.286 5165 Planarity : 0.004 0.080 5621 Dihedral : 4.107 22.571 4259 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.07 % Allowed : 11.65 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % 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 (0.13), residues: 3908 helix: 2.17 (0.20), residues: 685 sheet: 0.39 (0.16), residues: 1106 loop : -0.25 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.027 0.001 TYR A 904 PHE 0.023 0.001 PHE A 201 TRP 0.010 0.001 TRP B 104 HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (32402) covalent geometry : angle 0.52813 / 0.27 (44109) SS BOND : bond 0.00236 / 0.19 ( 50) SS BOND : angle 0.88970 / 0.65 ( 100) hydrogen bonds : bond 0.03523 / 2.34 ( 1278) hydrogen bonds : angle 5.03106 / 3.54 ( 3750) link_BETA1-4 : bond 0.00268 / 0.17 ( 18) link_BETA1-4 : angle 0.86890 / 0.60 ( 54) link_NAG-ASN : bond 0.00460 / 0.24 ( 42) link_NAG-ASN : angle 2.10573 / 1.80 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10563.91 seconds wall clock time: 180 minutes 53.21 seconds (10853.21 seconds total)