Starting phenix.real_space_refine on Sat Jun 28 00:07:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7we7_32441/06_2025/7we7_32441.cif Found real_map, /net/cci-nas-00/data/ceres_data/7we7_32441/06_2025/7we7_32441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7we7_32441/06_2025/7we7_32441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7we7_32441/06_2025/7we7_32441.map" model { file = "/net/cci-nas-00/data/ceres_data/7we7_32441/06_2025/7we7_32441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7we7_32441/06_2025/7we7_32441.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.058 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 135 5.16 5 C 20394 2.51 5 N 5274 2.21 5 O 6292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32095 Number of models: 1 Model: "" Number of chains: 33 Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 809 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "D" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "E" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "G" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "M" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 809 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "N" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 809 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 19.15, per 1000 atoms: 0.60 Number of scatterers: 32095 At special positions: 0 Unit cell: (157.29, 141.24, 233.26, 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 135 16.00 O 6292 8.00 N 5274 7.00 C 20394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 134 " distance=2.03 Simple disulfide: pdb=" SG CYS D 129 " - pdb=" SG CYS D 161 " distance=2.03 Simple disulfide: pdb=" SG CYS D 288 " - pdb=" SG CYS D 298 " distance=2.03 Simple disulfide: pdb=" SG CYS D 333 " - pdb=" SG CYS D 358 " distance=2.03 Simple disulfide: pdb=" SG CYS D 376 " - pdb=" SG CYS D 429 " distance=2.04 Simple disulfide: pdb=" SG CYS D 388 " - pdb=" SG CYS D 522 " distance=2.03 Simple disulfide: pdb=" SG CYS D 477 " - pdb=" SG CYS D 485 " distance=2.03 Simple disulfide: pdb=" SG CYS D 614 " - pdb=" SG CYS D 646 " distance=2.03 Simple disulfide: pdb=" SG CYS D 659 " - pdb=" SG CYS D 668 " distance=2.03 Simple disulfide: pdb=" SG CYS D 735 " - pdb=" SG CYS D 757 " distance=2.03 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 746 " distance=2.03 Simple disulfide: pdb=" SG CYS D1029 " - pdb=" SG CYS D1040 " distance=2.03 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 134 " distance=2.03 Simple disulfide: pdb=" SG CYS E 129 " - pdb=" SG CYS E 161 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 298 " distance=2.03 Simple disulfide: pdb=" SG CYS E 333 " - pdb=" SG CYS E 358 " distance=2.03 Simple disulfide: pdb=" SG CYS E 376 " - pdb=" SG CYS E 429 " distance=2.04 Simple disulfide: pdb=" SG CYS E 388 " - pdb=" SG CYS E 522 " distance=2.03 Simple disulfide: pdb=" SG CYS E 477 " - pdb=" SG CYS E 485 " distance=2.03 Simple disulfide: pdb=" SG CYS E 614 " - pdb=" SG CYS E 646 " distance=2.03 Simple disulfide: pdb=" SG CYS E 659 " - pdb=" SG CYS E 668 " distance=2.03 Simple disulfide: pdb=" SG CYS E 735 " - pdb=" SG CYS E 757 " distance=2.03 Simple disulfide: pdb=" SG CYS E 740 " - pdb=" SG CYS E 746 " distance=2.03 Simple disulfide: pdb=" SG CYS E1029 " - pdb=" SG CYS E1040 " distance=2.03 Simple disulfide: pdb=" SG CYS E1079 " - pdb=" SG CYS E1123 " distance=2.03 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 136 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 163 " distance=2.03 Simple disulfide: pdb=" SG CYS G 290 " - pdb=" SG CYS G 300 " distance=2.03 Simple disulfide: pdb=" SG CYS G 335 " - pdb=" SG CYS G 360 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 431 " distance=2.04 Simple disulfide: pdb=" SG CYS G 390 " - pdb=" SG CYS G 524 " distance=2.03 Simple disulfide: pdb=" SG CYS G 479 " - pdb=" SG CYS G 487 " distance=2.03 Simple disulfide: pdb=" SG CYS G 616 " - pdb=" SG CYS G 648 " distance=2.03 Simple disulfide: pdb=" SG CYS G 661 " - pdb=" SG CYS G 670 " distance=2.03 Simple disulfide: pdb=" SG CYS G 737 " - pdb=" SG CYS G 759 " distance=2.03 Simple disulfide: pdb=" SG CYS G 742 " - pdb=" SG CYS G 748 " distance=2.03 Simple disulfide: pdb=" SG CYS G1031 " - pdb=" SG CYS G1042 " distance=2.03 Simple disulfide: pdb=" SG CYS G1081 " - pdb=" SG CYS G1125 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=1.94 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.51 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " 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=6, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 1 " - " ASN D 231 " " NAG B 1 " - " ASN D 328 " " NAG C 1 " - " ASN D 714 " " NAG D1302 " - " ASN D1155 " " NAG D1303 " - " ASN D 143 " " NAG D1304 " - " ASN D 17 " " NAG D1305 " - " ASN D 61 " " NAG D1306 " - " ASN D 600 " " NAG D1307 " - " ASN D 654 " " NAG D1308 " - " ASN D 613 " " NAG D1309 " - " ASN D 706 " " NAG E1301 " - " ASN E1155 " " NAG E1302 " - " ASN E 123 " " NAG E1303 " - " ASN E 143 " " NAG E1304 " - " ASN E 17 " " NAG E1305 " - " ASN E 61 " " NAG E1306 " - " ASN E 600 " " NAG E1307 " - " ASN E 654 " " NAG E1308 " - " ASN E 613 " " NAG E1309 " - " ASN E 706 " " NAG F 1 " - " ASN D1071 " " NAG G1301 " - " ASN G1157 " " NAG G1302 " - " ASN G 125 " " NAG G1303 " - " ASN G 145 " " NAG G1304 " - " ASN G 17 " " NAG G1305 " - " ASN G 61 " " NAG G1306 " - " ASN G 602 " " NAG G1307 " - " ASN G 656 " " NAG G1308 " - " ASN G 615 " " NAG G1309 " - " ASN G 708 " " NAG I 1 " - " ASN D 798 " " NAG O 1 " - " ASN D1095 " " NAG P 1 " - " ASN D1131 " " NAG S 1 " - " ASN E 714 " " NAG U 1 " - " ASN E 798 " " NAG V 1 " - " ASN E1095 " " NAG W 1 " - " ASN E1131 " " NAG X 1 " - " ASN G 233 " " NAG Z 1 " - " ASN G 716 " " NAG b 1 " - " ASN G 800 " " NAG c 1 " - " ASN G1097 " " NAG d 1 " - " ASN G1133 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.41 Conformation dependent library (CDL) restraints added in 4.0 seconds 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7416 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 67 sheets defined 21.2% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.85 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.562A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.222A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 Processing helix chain 'D' and resid 334 through 340 removed outlier: 3.823A pdb=" N VAL D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 362 through 367 removed outlier: 3.501A pdb=" N ASN D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 402 through 408 removed outlier: 5.347A pdb=" N ARG D 405 " --> pdb=" O ASP D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 616 through 621 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 743 through 752 removed outlier: 3.722A pdb=" N GLN D 752 " --> pdb=" O ASN D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 779 removed outlier: 3.620A pdb=" N LEU D 760 " --> pdb=" O PHE D 756 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 767 " --> pdb=" O ALA D 763 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP D 772 " --> pdb=" O ALA D 768 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS D 773 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN D 776 " --> pdb=" O ASP D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 822 Processing helix chain 'D' and resid 863 through 879 removed outlier: 3.528A pdb=" N ALA D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN D 869 " --> pdb=" O GLU D 865 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 907 removed outlier: 3.664A pdb=" N MET D 899 " --> pdb=" O PHE D 895 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR D 901 " --> pdb=" O MET D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 915 removed outlier: 3.838A pdb=" N TYR D 914 " --> pdb=" O GLN D 910 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 915 " --> pdb=" O ASN D 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 910 through 915' Processing helix chain 'D' and resid 916 through 938 removed outlier: 3.672A pdb=" N ASN D 922 " --> pdb=" O LYS D 918 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN D 932 " --> pdb=" O ILE D 928 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP D 933 " --> pdb=" O GLY D 929 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR D 938 " --> pdb=" O SER D 934 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 963 removed outlier: 3.535A pdb=" N ASN D 952 " --> pdb=" O VAL D 948 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN D 957 " --> pdb=" O ALA D 953 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 974 through 979 removed outlier: 4.013A pdb=" N PHE D 978 " --> pdb=" O LEU D 974 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 1029 removed outlier: 4.265A pdb=" N GLU D 987 " --> pdb=" O LYS D 983 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL D 988 " --> pdb=" O VAL D 984 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 993 " --> pdb=" O GLN D 989 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY D 996 " --> pdb=" O ARG D 992 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D1021 " --> pdb=" O ALA D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1113 through 1115 No H-bonds generated for 'chain 'D' and resid 1113 through 1115' Processing helix chain 'D' and resid 1138 through 1158 removed outlier: 3.578A pdb=" N PHE D1145 " --> pdb=" O GLU D1141 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS D1151 " --> pdb=" O GLU D1147 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 299 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 380 through 384 removed outlier: 3.582A pdb=" N LEU E 384 " --> pdb=" O PRO E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 419 Processing helix chain 'E' and resid 615 through 620 removed outlier: 3.665A pdb=" N VAL E 619 " --> pdb=" O THR E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 636 removed outlier: 3.558A pdb=" N TYR E 633 " --> pdb=" O TRP E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 741 Processing helix chain 'E' and resid 743 through 751 removed outlier: 3.698A pdb=" N ASN E 748 " --> pdb=" O THR E 744 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU E 749 " --> pdb=" O GLU E 745 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 751 " --> pdb=" O SER E 747 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 756 removed outlier: 6.979A pdb=" N SER E 755 " --> pdb=" O GLN E 752 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE E 756 " --> pdb=" O TYR E 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 752 through 756' Processing helix chain 'E' and resid 757 through 775 removed outlier: 3.530A pdb=" N LYS E 761 " --> pdb=" O CYS E 757 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 762 " --> pdb=" O THR E 758 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP E 772 " --> pdb=" O ALA E 768 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR E 775 " --> pdb=" O GLN E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 776 through 778 No H-bonds generated for 'chain 'E' and resid 776 through 778' Processing helix chain 'E' and resid 813 through 823 removed outlier: 3.761A pdb=" N LEU E 818 " --> pdb=" O PHE E 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 847 through 853 removed outlier: 3.721A pdb=" N LYS E 851 " --> pdb=" O ILE E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 863 through 878 removed outlier: 3.720A pdb=" N THR E 878 " --> pdb=" O LEU E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 883 through 887 Processing helix chain 'E' and resid 894 through 907 removed outlier: 3.852A pdb=" N MET E 899 " --> pdb=" O PHE E 895 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA E 900 " --> pdb=" O ALA E 896 " (cutoff:3.500A) Processing helix chain 'E' and resid 910 through 915 removed outlier: 3.732A pdb=" N TYR E 914 " --> pdb=" O GLN E 910 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 938 removed outlier: 3.524A pdb=" N LYS E 930 " --> pdb=" O SER E 926 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 931 " --> pdb=" O ALA E 927 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN E 932 " --> pdb=" O ILE E 928 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER E 936 " --> pdb=" O GLN E 932 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR E 938 " --> pdb=" O SER E 934 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 963 removed outlier: 4.450A pdb=" N VAL E 948 " --> pdb=" O LYS E 944 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 963 " --> pdb=" O LEU E 959 " (cutoff:3.500A) Processing helix chain 'E' and resid 973 through 981 removed outlier: 4.050A pdb=" N ILE E 977 " --> pdb=" O VAL E 973 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE E 978 " --> pdb=" O LEU E 974 " (cutoff:3.500A) Processing helix chain 'E' and resid 982 through 1029 removed outlier: 4.139A pdb=" N GLU E 987 " --> pdb=" O LYS E 983 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL E 988 " --> pdb=" O VAL E 984 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG E 992 " --> pdb=" O VAL E 988 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU E 993 " --> pdb=" O GLN E 989 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE E1010 " --> pdb=" O THR E1006 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER E1018 " --> pdb=" O GLU E1014 " (cutoff:3.500A) Processing helix chain 'E' and resid 1113 through 1115 No H-bonds generated for 'chain 'E' and resid 1113 through 1115' Processing helix chain 'E' and resid 1137 through 1144 removed outlier: 4.038A pdb=" N GLU E1141 " --> pdb=" O PRO E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1145 through 1158 Processing helix chain 'G' and resid 293 through 302 Processing helix chain 'G' and resid 336 through 342 Processing helix chain 'G' and resid 364 through 370 Processing helix chain 'G' and resid 382 through 388 removed outlier: 4.205A pdb=" N LEU G 386 " --> pdb=" O PRO G 383 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASN G 387 " --> pdb=" O THR G 384 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP G 388 " --> pdb=" O LYS G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 410 removed outlier: 4.982A pdb=" N ARG G 407 " --> pdb=" O ASP G 404 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA G 410 " --> pdb=" O ARG G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 421 Processing helix chain 'G' and resid 618 through 623 Processing helix chain 'G' and resid 737 through 743 removed outlier: 3.904A pdb=" N ILE G 741 " --> pdb=" O CYS G 737 " (cutoff:3.500A) Processing helix chain 'G' and resid 745 through 752 removed outlier: 3.564A pdb=" N LEU G 751 " --> pdb=" O GLU G 747 " (cutoff:3.500A) Processing helix chain 'G' and resid 753 through 756 removed outlier: 3.575A pdb=" N GLY G 756 " --> pdb=" O LEU G 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 753 through 756' Processing helix chain 'G' and resid 759 through 781 removed outlier: 3.693A pdb=" N THR G 777 " --> pdb=" O GLN G 773 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 823 removed outlier: 3.735A pdb=" N LEU G 820 " --> pdb=" O PHE G 816 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE G 822 " --> pdb=" O GLU G 818 " (cutoff:3.500A) Processing helix chain 'G' and resid 865 through 880 removed outlier: 4.461A pdb=" N GLN G 871 " --> pdb=" O GLU G 867 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR G 872 " --> pdb=" O MET G 868 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR G 873 " --> pdb=" O ILE G 869 " (cutoff:3.500A) Processing helix chain 'G' and resid 885 through 889 removed outlier: 3.769A pdb=" N GLY G 888 " --> pdb=" O TRP G 885 " (cutoff:3.500A) Processing helix chain 'G' and resid 896 through 909 removed outlier: 3.695A pdb=" N MET G 901 " --> pdb=" O PHE G 897 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ALA G 902 " --> pdb=" O ALA G 898 " (cutoff:3.500A) Processing helix chain 'G' and resid 912 through 917 removed outlier: 3.689A pdb=" N TYR G 916 " --> pdb=" O GLN G 912 " (cutoff:3.500A) Processing helix chain 'G' and resid 918 through 940 removed outlier: 3.741A pdb=" N ALA G 929 " --> pdb=" O GLN G 925 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE G 933 " --> pdb=" O ALA G 929 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN G 934 " --> pdb=" O ILE G 930 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP G 935 " --> pdb=" O GLY G 931 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER G 938 " --> pdb=" O GLN G 934 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR G 940 " --> pdb=" O SER G 936 " (cutoff:3.500A) Processing helix chain 'G' and resid 941 through 943 No H-bonds generated for 'chain 'G' and resid 941 through 943' Processing helix chain 'G' and resid 944 through 964 removed outlier: 3.575A pdb=" N ASP G 949 " --> pdb=" O GLY G 945 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL G 950 " --> pdb=" O LYS G 946 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL G 951 " --> pdb=" O LEU G 947 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN G 954 " --> pdb=" O VAL G 950 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN G 959 " --> pdb=" O ALA G 955 " (cutoff:3.500A) Processing helix chain 'G' and resid 965 through 967 No H-bonds generated for 'chain 'G' and resid 965 through 967' Processing helix chain 'G' and resid 975 through 983 removed outlier: 3.623A pdb=" N ILE G 979 " --> pdb=" O VAL G 975 " (cutoff:3.500A) Processing helix chain 'G' and resid 984 through 1031 removed outlier: 4.045A pdb=" N GLU G 989 " --> pdb=" O LYS G 985 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL G 990 " --> pdb=" O VAL G 986 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN G 991 " --> pdb=" O GLU G 987 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY G 998 " --> pdb=" O ARG G 994 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR G1006 " --> pdb=" O SER G1002 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG G1013 " --> pdb=" O GLN G1009 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA G1019 " --> pdb=" O ALA G1015 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU G1023 " --> pdb=" O ALA G1019 " (cutoff:3.500A) Processing helix chain 'G' and resid 1115 through 1117 No H-bonds generated for 'chain 'G' and resid 1115 through 1117' Processing helix chain 'G' and resid 1141 through 1160 removed outlier: 3.925A pdb=" N SER G1146 " --> pdb=" O PRO G1142 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE G1147 " --> pdb=" O GLU G1143 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU G1149 " --> pdb=" O ASP G1145 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU G1150 " --> pdb=" O SER G1146 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER G1160 " --> pdb=" O LYS G1156 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'M' and resid 80 through 84 removed outlier: 4.066A pdb=" N GLU M 84 " --> pdb=" O SER M 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'N' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 removed outlier: 4.486A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AA3, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.941A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 10 Processing sheet with id=AA6, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 31 removed outlier: 7.851A pdb=" N ASN D 61 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR D 266 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 261 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN D 183 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER D 200 " --> pdb=" O PRO D 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.718A pdb=" N ASP D 284 " --> pdb=" O LYS D 275 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 82 through 83 removed outlier: 3.742A pdb=" N GLY D 101 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 128 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE D 163 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 311 removed outlier: 3.779A pdb=" N THR D 596 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR D 609 " --> pdb=" O CYS D 646 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS D 646 " --> pdb=" O TYR D 609 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY D 645 " --> pdb=" O THR D 642 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 351 through 355 removed outlier: 3.628A pdb=" N ASN D 351 " --> pdb=" O SER D 396 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER D 396 " --> pdb=" O ASN D 351 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 430 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS D 375 " --> pdb=" O VAL D 430 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 358 through 359 removed outlier: 7.323A pdb=" N CYS D 358 " --> pdb=" O CYS D 522 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 449 through 451 Processing sheet with id=AB5, first strand: chain 'D' and resid 470 through 471 removed outlier: 3.601A pdb=" N TYR D 470 " --> pdb=" O TYR D 486 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 539 through 540 removed outlier: 3.640A pdb=" N PHE D 540 " --> pdb=" O LEU D 543 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 548 through 551 removed outlier: 3.536A pdb=" N THR D 585 " --> pdb=" O VAL D 548 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 661 through 662 removed outlier: 3.734A pdb=" N GLN D 672 " --> pdb=" O SER D 688 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 708 through 712 Processing sheet with id=AC1, first strand: chain 'D' and resid 715 through 725 removed outlier: 3.635A pdb=" N SER D 718 " --> pdb=" O THR D1063 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR D1064 " --> pdb=" O HIS D1045 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N HIS D1045 " --> pdb=" O TYR D1064 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 732 through 733 Processing sheet with id=AC3, first strand: chain 'D' and resid 785 through 787 removed outlier: 5.290A pdb=" N ILE D 785 " --> pdb=" O ASN E 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 1117 through 1122 removed outlier: 3.512A pdb=" N SER D1120 " --> pdb=" O ALA D1084 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA D1084 " --> pdb=" O SER D1120 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 27 through 31 removed outlier: 7.927A pdb=" N ASN E 61 " --> pdb=" O TYR E 266 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR E 266 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE E 196 " --> pdb=" O ASP E 225 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP E 225 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE E 198 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS E 202 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N ALA E 219 " --> pdb=" O HIS E 202 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL E 36 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 42 through 44 removed outlier: 6.535A pdb=" N GLY G 565 " --> pdb=" O ASP G 573 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 47 through 55 removed outlier: 3.726A pdb=" N ASP E 284 " --> pdb=" O LYS E 275 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 82 through 83 Processing sheet with id=AC9, first strand: chain 'E' and resid 109 through 114 removed outlier: 6.042A pdb=" N THR E 112 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E 131 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL E 118 " --> pdb=" O VAL E 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 109 through 114 removed outlier: 6.042A pdb=" N THR E 112 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E 131 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL E 128 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE E 163 " --> pdb=" O VAL E 128 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 308 through 315 removed outlier: 3.670A pdb=" N THR E 596 " --> pdb=" O GLY E 308 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL E 592 " --> pdb=" O THR E 312 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN E 314 " --> pdb=" O GLY E 590 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLY E 590 " --> pdb=" O ASN E 314 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY E 591 " --> pdb=" O GLN E 610 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 321 through 325 removed outlier: 4.338A pdb=" N GLU E 321 " --> pdb=" O CYS E 535 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 321 through 325 removed outlier: 4.338A pdb=" N GLU E 321 " --> pdb=" O CYS E 535 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP E 583 " --> pdb=" O THR E 550 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 351 through 355 removed outlier: 4.096A pdb=" N ASN E 351 " --> pdb=" O SER E 396 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER E 396 " --> pdb=" O ASN E 351 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL E 392 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS E 429 " --> pdb=" O LEU E 510 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA E 432 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 358 through 359 removed outlier: 7.372A pdb=" N CYS E 358 " --> pdb=" O CYS E 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 449 through 451 Processing sheet with id=AD8, first strand: chain 'E' and resid 470 through 471 Processing sheet with id=AD9, first strand: chain 'E' and resid 651 through 657 removed outlier: 6.699A pdb=" N GLU E 651 " --> pdb=" O ALA E 691 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N THR E 693 " --> pdb=" O GLU E 651 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N VAL E 653 " --> pdb=" O THR E 693 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER E 688 " --> pdb=" O GLN E 672 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN E 672 " --> pdb=" O SER E 688 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR E 692 " --> pdb=" O CYS E 668 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 708 through 712 removed outlier: 3.628A pdb=" N ILE E 711 " --> pdb=" O LYS E1070 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR E1073 " --> pdb=" O SER E1094 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E1075 " --> pdb=" O PHE E1092 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE E1092 " --> pdb=" O ALA E1075 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL E1091 " --> pdb=" O THR E1102 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E1102 " --> pdb=" O VAL E1091 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 715 through 725 removed outlier: 7.182A pdb=" N GLY E1056 " --> pdb=" O SER E1052 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N SER E1052 " --> pdb=" O GLY E1056 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL E1058 " --> pdb=" O PRO E1050 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU E1060 " --> pdb=" O SER E1048 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER E1048 " --> pdb=" O LEU E1060 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL E1062 " --> pdb=" O LEU E1046 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 732 through 733 Processing sheet with id=AE4, first strand: chain 'E' and resid 1117 through 1122 removed outlier: 3.523A pdb=" N PHE E1086 " --> pdb=" O PHE E1118 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER E1120 " --> pdb=" O ALA E1084 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA E1084 " --> pdb=" O SER E1120 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 27 through 30 removed outlier: 7.947A pdb=" N ASN G 61 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR G 268 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA G 263 " --> pdb=" O ILE G 95 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N SER G 202 " --> pdb=" O PRO G 224 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 36 through 37 removed outlier: 6.442A pdb=" N VAL G 36 " --> pdb=" O LEU G 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'G' and resid 48 through 55 removed outlier: 3.634A pdb=" N ASP G 286 " --> pdb=" O LYS G 277 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 103 through 106 removed outlier: 3.861A pdb=" N PHE G 165 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 310 through 313 removed outlier: 3.557A pdb=" N THR G 598 " --> pdb=" O GLY G 310 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS G 648 " --> pdb=" O TYR G 611 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 355 through 357 removed outlier: 4.538A pdb=" N VAL G 432 " --> pdb=" O LYS G 377 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS G 377 " --> pdb=" O VAL G 432 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR G 375 " --> pdb=" O ALA G 434 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 360 through 361 removed outlier: 6.827A pdb=" N CYS G 360 " --> pdb=" O CYS G 524 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 451 through 453 Processing sheet with id=AF4, first strand: chain 'G' and resid 472 through 473 removed outlier: 3.558A pdb=" N TYR G 472 " --> pdb=" O TYR G 488 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 541 through 542 removed outlier: 3.593A pdb=" N PHE G 542 " --> pdb=" O LEU G 545 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 550 through 551 Processing sheet with id=AF7, first strand: chain 'G' and resid 653 through 659 removed outlier: 3.564A pdb=" N ALA G 693 " --> pdb=" O GLU G 653 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR G 695 " --> pdb=" O VAL G 655 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASN G 657 " --> pdb=" O THR G 695 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 710 through 714 removed outlier: 3.680A pdb=" N THR G1075 " --> pdb=" O SER G1096 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 717 through 727 removed outlier: 3.504A pdb=" N MET G1049 " --> pdb=" O VAL G1064 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR G1066 " --> pdb=" O HIS G1047 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N HIS G1047 " --> pdb=" O TYR G1066 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 732 through 734 removed outlier: 4.273A pdb=" N LYS G 732 " --> pdb=" O LEU G 860 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER G 734 " --> pdb=" O THR G 858 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 1119 through 1124 removed outlier: 6.164A pdb=" N VAL G1121 " --> pdb=" O PHE G1088 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE G1088 " --> pdb=" O VAL G1121 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY G1123 " --> pdb=" O ALA G1086 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AG4, first strand: chain 'J' and resid 58 through 60 removed outlier: 3.564A pdb=" N GLY J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL J 93 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AG6, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AG7, first strand: chain 'M' and resid 46 through 49 removed outlier: 6.721A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 46 through 49 removed outlier: 6.721A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.523A pdb=" N ALA K 118 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 19 through 23 removed outlier: 4.185A pdb=" N THR K 78 " --> pdb=" O ASP K 73 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP K 73 " --> pdb=" O THR K 78 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.032A pdb=" N ALA N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.032A pdb=" N ALA N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 18 through 23 1070 hydrogen bonds defined for protein. 2793 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: 14.86 Time building geometry restraints manager: 9.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8978 1.33 - 1.46: 8197 1.46 - 1.58: 15484 1.58 - 1.71: 0 1.71 - 1.83: 171 Bond restraints: 32830 Sorted by residual: bond pdb=" N ARG M 55 " pdb=" CA ARG M 55 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.87e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" N VAL K 37 " pdb=" CA VAL K 37 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.14e-02 7.69e+03 1.30e+01 bond pdb=" N ILE N 49 " pdb=" CA ILE N 49 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.14e-02 7.69e+03 1.29e+01 bond pdb=" N VAL H 93 " pdb=" CA VAL H 93 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.29e+01 ... (remaining 32825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 42251 1.63 - 3.26: 2057 3.26 - 4.89: 278 4.89 - 6.52: 42 6.52 - 8.15: 12 Bond angle restraints: 44640 Sorted by residual: angle pdb=" CA PRO M 56 " pdb=" C PRO M 56 " pdb=" O PRO M 56 " ideal model delta sigma weight residual 121.31 116.63 4.68 7.40e-01 1.83e+00 4.00e+01 angle pdb=" N LEU E 139 " pdb=" CA LEU E 139 " pdb=" C LEU E 139 " ideal model delta sigma weight residual 112.92 105.30 7.62 1.23e+00 6.61e-01 3.84e+01 angle pdb=" CA GLY J 114 " pdb=" C GLY J 114 " pdb=" O GLY J 114 " ideal model delta sigma weight residual 122.23 118.27 3.96 6.90e-01 2.10e+00 3.29e+01 angle pdb=" CA GLY K 114 " pdb=" C GLY K 114 " pdb=" O GLY K 114 " ideal model delta sigma weight residual 122.23 118.37 3.86 6.90e-01 2.10e+00 3.14e+01 angle pdb=" CA GLY H 114 " pdb=" C GLY H 114 " pdb=" O GLY H 114 " ideal model delta sigma weight residual 121.77 117.58 4.19 8.60e-01 1.35e+00 2.37e+01 ... (remaining 44635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 19157 23.62 - 47.24: 1123 47.24 - 70.86: 128 70.86 - 94.48: 54 94.48 - 118.10: 27 Dihedral angle restraints: 20489 sinusoidal: 8936 harmonic: 11553 Sorted by residual: dihedral pdb=" CB CYS G 479 " pdb=" SG CYS G 479 " pdb=" SG CYS G 487 " pdb=" CB CYS G 487 " ideal model delta sinusoidal sigma weight residual 93.00 37.84 55.16 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CB CYS E 477 " pdb=" SG CYS E 477 " pdb=" SG CYS E 485 " pdb=" CB CYS E 485 " ideal model delta sinusoidal sigma weight residual 93.00 147.89 -54.89 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CB CYS E 740 " pdb=" SG CYS E 740 " pdb=" SG CYS E 746 " pdb=" CB CYS E 746 " ideal model delta sinusoidal sigma weight residual -86.00 -32.69 -53.31 1 1.00e+01 1.00e-02 3.86e+01 ... (remaining 20486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 5004 0.116 - 0.232: 185 0.232 - 0.347: 24 0.347 - 0.463: 1 0.463 - 0.579: 1 Chirality restraints: 5215 Sorted by residual: chirality pdb=" C1 NAG E1302 " pdb=" ND2 ASN E 123 " pdb=" C2 NAG E1302 " pdb=" O5 NAG E1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" CA ASN G 146 " pdb=" N ASN G 146 " pdb=" C ASN G 146 " pdb=" CB ASN G 146 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C1 NAG E1304 " pdb=" ND2 ASN E 17 " pdb=" C2 NAG E1304 " pdb=" O5 NAG E1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 5212 not shown) Planarity restraints: 5709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E1303 " -0.151 2.00e-02 2.50e+03 1.25e-01 1.96e+02 pdb=" C7 NAG E1303 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG E1303 " -0.113 2.00e-02 2.50e+03 pdb=" N2 NAG E1303 " 0.202 2.00e-02 2.50e+03 pdb=" O7 NAG E1303 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E1302 " 0.137 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" C7 NAG E1302 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG E1302 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG E1302 " -0.183 2.00e-02 2.50e+03 pdb=" O7 NAG E1302 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E1304 " 0.100 2.00e-02 2.50e+03 8.26e-02 8.53e+01 pdb=" C7 NAG E1304 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG E1304 " 0.076 2.00e-02 2.50e+03 pdb=" N2 NAG E1304 " -0.131 2.00e-02 2.50e+03 pdb=" O7 NAG E1304 " -0.016 2.00e-02 2.50e+03 ... (remaining 5706 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 7 2.08 - 2.79: 7433 2.79 - 3.49: 44358 3.49 - 4.20: 75749 4.20 - 4.90: 128630 Nonbonded interactions: 256177 Sorted by model distance: nonbonded pdb=" CG PHE H 106 " pdb=" OG SER D 443 " model vdw 1.378 3.260 nonbonded pdb=" CD1 PHE H 106 " pdb=" OG SER D 443 " model vdw 1.453 3.340 nonbonded pdb=" OG SER E 443 " pdb=" CB PHE J 106 " model vdw 1.710 3.440 nonbonded pdb=" OG SER E 443 " pdb=" CG PHE J 106 " model vdw 1.939 3.260 nonbonded pdb=" CB PHE H 106 " pdb=" OG SER D 443 " model vdw 1.976 3.440 ... (remaining 256172 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'V' selection = chain 'W' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.360 Check model and map are aligned: 0.250 Set scattering table: 0.330 Process input model: 75.950 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.006 0.483 32949 Z= 0.366 Angle : 0.787 31.534 44934 Z= 0.471 Chirality : 0.055 0.579 5215 Planarity : 0.004 0.125 5667 Dihedral : 15.069 118.100 12938 Min Nonbonded Distance : 1.378 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.95 % Favored : 94.92 % Rotamer: Outliers : 0.87 % Allowed : 1.45 % Favored : 97.69 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 3939 helix: -0.98 (0.19), residues: 725 sheet: -0.36 (0.17), residues: 903 loop : -1.00 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 632 HIS 0.003 0.001 HIS D1080 PHE 0.017 0.001 PHE G 198 TYR 0.014 0.001 TYR H 94 ARG 0.009 0.000 ARG G 155 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 42) link_NAG-ASN : angle 2.37354 ( 126) link_BETA1-4 : bond 0.00481 ( 26) link_BETA1-4 : angle 1.21823 ( 78) hydrogen bonds : bond 0.25237 ( 1046) hydrogen bonds : angle 9.42946 ( 2793) SS BOND : bond 0.07330 ( 45) SS BOND : angle 3.81970 ( 90) covalent geometry : bond 0.00514 (32830) covalent geometry : angle 0.75902 (44640) Misc. bond : bond 0.00267 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 SER cc_start: 0.3548 (OUTLIER) cc_final: 0.3178 (m) REVERT: H 45 LEU cc_start: 0.7475 (mm) cc_final: 0.7133 (mm) REVERT: D 132 GLN cc_start: 0.8656 (mm110) cc_final: 0.8038 (tm-30) REVERT: E 172 MET cc_start: 0.2658 (mtt) cc_final: 0.1513 (mtt) REVERT: E 559 PHE cc_start: 0.7833 (p90) cc_final: 0.7581 (p90) REVERT: E 1147 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8039 (mp0) REVERT: J 111 TRP cc_start: 0.1699 (m-90) cc_final: 0.0925 (m-90) outliers start: 30 outliers final: 10 residues processed: 212 average time/residue: 0.4266 time to fit residues: 150.1925 Evaluate side-chains 131 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 4.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain M residue 16 GLN Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 356 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 110 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1033 GLN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 852 GLN G 925 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 113 GLN M 39 GLN N 38 GLN N 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.111664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.074727 restraints weight = 122009.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.074824 restraints weight = 76472.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.074355 restraints weight = 57881.123| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32949 Z= 0.183 Angle : 0.651 12.612 44934 Z= 0.327 Chirality : 0.046 0.373 5215 Planarity : 0.004 0.048 5667 Dihedral : 9.553 99.624 5841 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.59 % Favored : 94.39 % Rotamer: Outliers : 0.67 % Allowed : 6.94 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3939 helix: -0.73 (0.18), residues: 768 sheet: -0.25 (0.17), residues: 928 loop : -1.00 (0.13), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 104 HIS 0.005 0.001 HIS G 624 PHE 0.017 0.001 PHE L 101 TYR 0.024 0.001 TYR N 50 ARG 0.005 0.001 ARG G 814 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 42) link_NAG-ASN : angle 1.90773 ( 126) link_BETA1-4 : bond 0.00529 ( 26) link_BETA1-4 : angle 1.88602 ( 78) hydrogen bonds : bond 0.05412 ( 1046) hydrogen bonds : angle 6.73597 ( 2793) SS BOND : bond 0.00316 ( 45) SS BOND : angle 1.10993 ( 90) covalent geometry : bond 0.00414 (32830) covalent geometry : angle 0.63814 (44640) Misc. bond : bond 0.00222 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 3.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.8104 (t0) cc_final: 0.7744 (t0) REVERT: H 76 THR cc_start: 0.8542 (p) cc_final: 0.8228 (p) REVERT: L 16 GLN cc_start: 0.6502 (pt0) cc_final: 0.6164 (pm20) REVERT: D 999 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7860 (tm-30) REVERT: E 172 MET cc_start: 0.3449 (mtt) cc_final: 0.2181 (mtt) REVERT: E 217 PHE cc_start: 0.6877 (OUTLIER) cc_final: 0.6132 (m-80) REVERT: E 559 PHE cc_start: 0.7559 (p90) cc_final: 0.7268 (p90) REVERT: G 368 TYR cc_start: 0.7967 (t80) cc_final: 0.7530 (t80) REVERT: J 111 TRP cc_start: 0.2862 (m-90) cc_final: 0.1770 (m-90) outliers start: 23 outliers final: 16 residues processed: 164 average time/residue: 0.4097 time to fit residues: 116.1204 Evaluate side-chains 140 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 146 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 304 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 177 optimal weight: 20.0000 chunk 241 optimal weight: 0.0470 chunk 278 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 954 GLN ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 750 ASN G 852 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.111635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.074393 restraints weight = 123162.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.074131 restraints weight = 76936.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.074305 restraints weight = 61987.925| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32949 Z= 0.161 Angle : 0.604 10.237 44934 Z= 0.302 Chirality : 0.045 0.356 5215 Planarity : 0.004 0.050 5667 Dihedral : 8.049 96.602 5837 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 1.01 % Allowed : 9.92 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 3939 helix: -0.55 (0.18), residues: 770 sheet: -0.25 (0.17), residues: 933 loop : -0.99 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 104 HIS 0.003 0.001 HIS E 49 PHE 0.018 0.001 PHE N 63 TYR 0.025 0.001 TYR H 108 ARG 0.007 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 42) link_NAG-ASN : angle 1.82783 ( 126) link_BETA1-4 : bond 0.00512 ( 26) link_BETA1-4 : angle 1.80426 ( 78) hydrogen bonds : bond 0.04505 ( 1046) hydrogen bonds : angle 6.21137 ( 2793) SS BOND : bond 0.00253 ( 45) SS BOND : angle 0.88720 ( 90) covalent geometry : bond 0.00367 (32830) covalent geometry : angle 0.59243 (44640) Misc. bond : bond 0.00218 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 3.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7983 (t0) cc_final: 0.7577 (t0) REVERT: L 16 GLN cc_start: 0.6719 (pt0) cc_final: 0.6413 (pm20) REVERT: D 999 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7770 (tm-30) REVERT: E 172 MET cc_start: 0.3333 (mtt) cc_final: 0.2070 (mtt) REVERT: E 217 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.5999 (m-80) REVERT: E 559 PHE cc_start: 0.7523 (p90) cc_final: 0.7243 (p90) REVERT: G 368 TYR cc_start: 0.7965 (t80) cc_final: 0.7478 (t80) REVERT: G 901 MET cc_start: 0.9080 (tpp) cc_final: 0.8874 (mmm) REVERT: G 1049 MET cc_start: 0.8359 (ptp) cc_final: 0.8053 (ptp) REVERT: K 48 MET cc_start: 0.2352 (tmm) cc_final: 0.0237 (mtm) outliers start: 35 outliers final: 19 residues processed: 162 average time/residue: 0.3958 time to fit residues: 111.7912 Evaluate side-chains 142 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 283 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 318 optimal weight: 6.9990 chunk 381 optimal weight: 30.0000 chunk 262 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 334 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 175 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 916 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 852 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN M 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.120884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.084921 restraints weight = 130437.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.079944 restraints weight = 102573.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.080704 restraints weight = 92079.406| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32949 Z= 0.182 Angle : 0.612 10.187 44934 Z= 0.305 Chirality : 0.045 0.351 5215 Planarity : 0.004 0.050 5667 Dihedral : 7.192 92.646 5833 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 1.71 % Allowed : 11.98 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 3939 helix: -0.41 (0.19), residues: 770 sheet: -0.22 (0.17), residues: 923 loop : -0.99 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP J 111 HIS 0.005 0.001 HIS J 110 PHE 0.020 0.001 PHE G 92 TYR 0.027 0.001 TYR H 108 ARG 0.008 0.000 ARG D 902 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 42) link_NAG-ASN : angle 1.83977 ( 126) link_BETA1-4 : bond 0.00499 ( 26) link_BETA1-4 : angle 1.76010 ( 78) hydrogen bonds : bond 0.04130 ( 1046) hydrogen bonds : angle 6.00470 ( 2793) SS BOND : bond 0.00462 ( 45) SS BOND : angle 1.04734 ( 90) covalent geometry : bond 0.00418 (32830) covalent geometry : angle 0.59978 (44640) Misc. bond : bond 0.00214 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 3.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7820 (t0) cc_final: 0.7578 (t0) REVERT: L 28 ASN cc_start: 0.7402 (t0) cc_final: 0.6831 (m-40) REVERT: D 999 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7571 (tm-30) REVERT: D 1009 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8898 (mt) REVERT: E 172 MET cc_start: 0.3798 (mtt) cc_final: 0.2926 (mtt) REVERT: E 217 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6037 (m-80) REVERT: E 559 PHE cc_start: 0.7564 (p90) cc_final: 0.7246 (p90) REVERT: G 368 TYR cc_start: 0.7877 (t80) cc_final: 0.7318 (t80) REVERT: G 901 MET cc_start: 0.9290 (tpp) cc_final: 0.9045 (mmm) REVERT: K 48 MET cc_start: 0.2011 (tmm) cc_final: 0.0253 (mtm) outliers start: 59 outliers final: 33 residues processed: 176 average time/residue: 0.3876 time to fit residues: 118.1006 Evaluate side-chains 151 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 3.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 948 VAL Chi-restraints excluded: chain E residue 995 THR Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 769 ILE Chi-restraints excluded: chain G residue 780 VAL Chi-restraints excluded: chain G residue 914 VAL Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 291 optimal weight: 10.0000 chunk 321 optimal weight: 0.8980 chunk 220 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 347 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 484 ASN D1085 HIS ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 543 ASN G 852 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.113752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.079843 restraints weight = 124502.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.076591 restraints weight = 85677.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.077321 restraints weight = 78881.736| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32949 Z= 0.183 Angle : 0.605 10.167 44934 Z= 0.302 Chirality : 0.045 0.342 5215 Planarity : 0.004 0.050 5667 Dihedral : 6.797 89.805 5832 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.44 % Rotamer: Outliers : 1.71 % Allowed : 13.63 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 3939 helix: -0.32 (0.19), residues: 764 sheet: -0.16 (0.17), residues: 896 loop : -0.99 (0.13), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP J 111 HIS 0.003 0.001 HIS E 49 PHE 0.026 0.001 PHE G 374 TYR 0.031 0.001 TYR H 108 ARG 0.005 0.000 ARG D 902 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 42) link_NAG-ASN : angle 1.83174 ( 126) link_BETA1-4 : bond 0.00475 ( 26) link_BETA1-4 : angle 1.68783 ( 78) hydrogen bonds : bond 0.04015 ( 1046) hydrogen bonds : angle 5.88010 ( 2793) SS BOND : bond 0.00351 ( 45) SS BOND : angle 1.05686 ( 90) covalent geometry : bond 0.00419 (32830) covalent geometry : angle 0.59357 (44640) Misc. bond : bond 0.00217 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 133 time to evaluate : 3.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7770 (t0) cc_final: 0.7441 (t0) REVERT: L 28 ASN cc_start: 0.6982 (t0) cc_final: 0.6459 (m-40) REVERT: D 756 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6640 (t80) REVERT: D 782 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8508 (p) REVERT: D 999 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7686 (tm-30) REVERT: E 172 MET cc_start: 0.3631 (mtt) cc_final: 0.2787 (mtt) REVERT: E 217 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.5946 (m-80) REVERT: E 559 PHE cc_start: 0.7529 (p90) cc_final: 0.7290 (p90) REVERT: G 610 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9093 (tt) REVERT: K 48 MET cc_start: 0.2210 (tmm) cc_final: 0.0466 (mtm) outliers start: 59 outliers final: 41 residues processed: 182 average time/residue: 0.3992 time to fit residues: 127.3111 Evaluate side-chains 165 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 4.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 782 VAL Chi-restraints excluded: chain D residue 788 THR Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 990 ILE Chi-restraints excluded: chain D residue 1101 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 570 THR Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 948 VAL Chi-restraints excluded: chain E residue 995 THR Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 379 TYR Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 769 ILE Chi-restraints excluded: chain G residue 780 VAL Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain G residue 972 ILE Chi-restraints excluded: chain G residue 975 VAL Chi-restraints excluded: chain G residue 1007 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 80 optimal weight: 1.9990 chunk 337 optimal weight: 0.2980 chunk 338 optimal weight: 1.9990 chunk 385 optimal weight: 50.0000 chunk 363 optimal weight: 30.0000 chunk 82 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 386 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 327 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 484 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 687 GLN E1002 GLN ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 803 GLN G 852 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.111923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.074395 restraints weight = 122103.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.074462 restraints weight = 77732.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.074935 restraints weight = 58186.236| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32949 Z= 0.123 Angle : 0.577 10.769 44934 Z= 0.287 Chirality : 0.044 0.330 5215 Planarity : 0.004 0.051 5667 Dihedral : 6.399 84.838 5832 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.74 % Rotamer: Outliers : 1.85 % Allowed : 14.58 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 3939 helix: -0.12 (0.19), residues: 760 sheet: -0.14 (0.17), residues: 898 loop : -0.94 (0.13), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP J 111 HIS 0.007 0.001 HIS E 502 PHE 0.034 0.001 PHE G 373 TYR 0.035 0.001 TYR H 94 ARG 0.013 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 42) link_NAG-ASN : angle 1.75074 ( 126) link_BETA1-4 : bond 0.00461 ( 26) link_BETA1-4 : angle 1.67905 ( 78) hydrogen bonds : bond 0.03652 ( 1046) hydrogen bonds : angle 5.67817 ( 2793) SS BOND : bond 0.00276 ( 45) SS BOND : angle 0.88002 ( 90) covalent geometry : bond 0.00273 (32830) covalent geometry : angle 0.56558 (44640) Misc. bond : bond 0.00204 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 137 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7766 (t0) cc_final: 0.7414 (t0) REVERT: L 28 ASN cc_start: 0.6851 (t0) cc_final: 0.6312 (m-40) REVERT: D 737 MET cc_start: 0.7753 (tmm) cc_final: 0.7474 (ttt) REVERT: D 756 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6565 (t80) REVERT: D 999 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7588 (tm-30) REVERT: E 132 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8410 (tp-100) REVERT: E 172 MET cc_start: 0.3655 (mtt) cc_final: 0.2814 (mtt) REVERT: E 217 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6154 (m-80) REVERT: E 559 PHE cc_start: 0.7503 (p90) cc_final: 0.7284 (p90) REVERT: G 610 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8995 (tt) REVERT: K 48 MET cc_start: 0.2105 (tmm) cc_final: 0.0437 (mtm) outliers start: 64 outliers final: 40 residues processed: 191 average time/residue: 0.4057 time to fit residues: 136.6182 Evaluate side-chains 161 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 4.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 906 ILE Chi-restraints excluded: chain E residue 995 THR Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 379 TYR Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 769 ILE Chi-restraints excluded: chain G residue 914 VAL Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain G residue 972 ILE Chi-restraints excluded: chain G residue 975 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 271 optimal weight: 20.0000 chunk 108 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 339 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 387 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 chunk 316 optimal weight: 0.8980 chunk 260 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 975 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 HIS ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 852 GLN G1105 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN M 32 ASN M 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.112426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.076342 restraints weight = 122547.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.074913 restraints weight = 74166.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.075579 restraints weight = 61078.899| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 32949 Z= 0.111 Angle : 0.579 12.217 44934 Z= 0.286 Chirality : 0.044 0.331 5215 Planarity : 0.004 0.051 5667 Dihedral : 6.066 77.368 5832 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 1.74 % Allowed : 15.10 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.13), residues: 3939 helix: 0.05 (0.19), residues: 755 sheet: -0.10 (0.17), residues: 873 loop : -0.93 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP J 111 HIS 0.004 0.001 HIS E 502 PHE 0.024 0.001 PHE G 373 TYR 0.036 0.001 TYR N 50 ARG 0.010 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 42) link_NAG-ASN : angle 1.76702 ( 126) link_BETA1-4 : bond 0.00469 ( 26) link_BETA1-4 : angle 1.69490 ( 78) hydrogen bonds : bond 0.03485 ( 1046) hydrogen bonds : angle 5.51747 ( 2793) SS BOND : bond 0.00254 ( 45) SS BOND : angle 1.07245 ( 90) covalent geometry : bond 0.00249 (32830) covalent geometry : angle 0.56680 (44640) Misc. bond : bond 0.00199 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 129 time to evaluate : 3.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7816 (t0) cc_final: 0.7477 (t0) REVERT: H 108 TYR cc_start: 0.6042 (m-80) cc_final: 0.5837 (m-80) REVERT: L 28 ASN cc_start: 0.6627 (t0) cc_final: 0.6128 (m-40) REVERT: D 737 MET cc_start: 0.7823 (tmm) cc_final: 0.7582 (tmm) REVERT: D 756 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6569 (t80) REVERT: D 999 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7509 (tm-30) REVERT: D 1002 GLN cc_start: 0.9069 (mm110) cc_final: 0.8818 (mm110) REVERT: E 132 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8442 (tp-100) REVERT: E 172 MET cc_start: 0.3887 (mtt) cc_final: 0.2979 (mtt) REVERT: E 559 PHE cc_start: 0.7560 (p90) cc_final: 0.7275 (p90) REVERT: E 852 PHE cc_start: 0.8391 (m-10) cc_final: 0.8038 (m-80) REVERT: G 610 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8963 (tt) REVERT: K 48 MET cc_start: 0.1876 (tmm) cc_final: 0.0539 (mtm) outliers start: 60 outliers final: 38 residues processed: 177 average time/residue: 0.3877 time to fit residues: 120.5756 Evaluate side-chains 163 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 4.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1101 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 906 ILE Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 379 TYR Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 914 VAL Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain G residue 972 ILE Chi-restraints excluded: chain G residue 975 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 29 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 270 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 380 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 975 ASN ** D 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1033 GLN D1105 ASN D1116 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 672 GLN ** G 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 ASN G 627 GLN G 803 GLN G 852 GLN G 913 ASN G1105 GLN ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.118234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 135)---------------| | r_work = 0.3712 r_free = 0.3712 target = 0.082322 restraints weight = 129214.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.076221 restraints weight = 112251.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.077294 restraints weight = 121450.602| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 32949 Z= 0.387 Angle : 0.805 11.989 44934 Z= 0.403 Chirality : 0.049 0.356 5215 Planarity : 0.005 0.072 5667 Dihedral : 6.763 60.429 5832 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.24 % Favored : 92.71 % Rotamer: Outliers : 2.08 % Allowed : 15.77 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 3939 helix: -0.56 (0.18), residues: 767 sheet: -0.35 (0.17), residues: 906 loop : -1.14 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP G 104 HIS 0.011 0.002 HIS E1045 PHE 0.030 0.002 PHE D 885 TYR 0.030 0.002 TYR D 366 ARG 0.014 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 42) link_NAG-ASN : angle 2.21647 ( 126) link_BETA1-4 : bond 0.00559 ( 26) link_BETA1-4 : angle 1.94576 ( 78) hydrogen bonds : bond 0.04840 ( 1046) hydrogen bonds : angle 6.20440 ( 2793) SS BOND : bond 0.00742 ( 45) SS BOND : angle 1.42425 ( 90) covalent geometry : bond 0.00898 (32830) covalent geometry : angle 0.79273 (44640) Misc. bond : bond 0.00245 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 132 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7856 (t0) cc_final: 0.7504 (t0) REVERT: L 28 ASN cc_start: 0.6863 (t0) cc_final: 0.6451 (m-40) REVERT: D 132 GLN cc_start: 0.8849 (mm110) cc_final: 0.8622 (mm110) REVERT: D 756 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6702 (t80) REVERT: D 999 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7748 (tm-30) REVERT: E 172 MET cc_start: 0.4337 (mtt) cc_final: 0.3476 (mtt) REVERT: E 217 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.6098 (m-80) REVERT: K 48 MET cc_start: 0.1748 (tmm) cc_final: 0.1092 (tmm) outliers start: 72 outliers final: 50 residues processed: 192 average time/residue: 0.3851 time to fit residues: 128.5162 Evaluate side-chains 168 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 116 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 788 THR Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1101 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain E residue 875 LEU Chi-restraints excluded: chain E residue 906 ILE Chi-restraints excluded: chain E residue 931 ILE Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 948 VAL Chi-restraints excluded: chain E residue 995 THR Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 379 TYR Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 780 VAL Chi-restraints excluded: chain G residue 914 VAL Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain G residue 972 ILE Chi-restraints excluded: chain G residue 975 VAL Chi-restraints excluded: chain G residue 1007 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain K residue 110 HIS Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 274 optimal weight: 5.9990 chunk 330 optimal weight: 0.6980 chunk 67 optimal weight: 0.0070 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 169 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 271 optimal weight: 20.0000 chunk 288 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1116 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 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 = 0.4362 r_free = 0.4362 target = 0.120296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3747 r_free = 0.3747 target = 0.083888 restraints weight = 129911.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.078814 restraints weight = 102642.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.079936 restraints weight = 87071.998| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32949 Z= 0.167 Angle : 0.646 17.140 44934 Z= 0.319 Chirality : 0.045 0.302 5215 Planarity : 0.004 0.080 5667 Dihedral : 6.301 58.068 5832 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 1.59 % Allowed : 16.67 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 3939 helix: -0.16 (0.19), residues: 760 sheet: -0.35 (0.17), residues: 923 loop : -1.02 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.002 TRP J 111 HIS 0.006 0.001 HIS D 516 PHE 0.030 0.001 PHE E 559 TYR 0.030 0.001 TYR D 366 ARG 0.008 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 42) link_NAG-ASN : angle 1.86019 ( 126) link_BETA1-4 : bond 0.00496 ( 26) link_BETA1-4 : angle 1.91860 ( 78) hydrogen bonds : bond 0.03888 ( 1046) hydrogen bonds : angle 5.78564 ( 2793) SS BOND : bond 0.00342 ( 45) SS BOND : angle 1.01953 ( 90) covalent geometry : bond 0.00379 (32830) covalent geometry : angle 0.63340 (44640) Misc. bond : bond 0.00844 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 120 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7874 (t0) cc_final: 0.7523 (t0) REVERT: L 28 ASN cc_start: 0.6949 (t0) cc_final: 0.6362 (m-40) REVERT: D 756 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6637 (t80) REVERT: D 999 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7586 (tm-30) REVERT: E 172 MET cc_start: 0.4414 (mtt) cc_final: 0.3723 (mtt) REVERT: E 217 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.6023 (m-80) outliers start: 55 outliers final: 45 residues processed: 166 average time/residue: 0.3870 time to fit residues: 113.5108 Evaluate side-chains 164 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 117 time to evaluate : 5.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 788 THR Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1101 VAL Chi-restraints excluded: chain D residue 1116 ASN Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 906 ILE Chi-restraints excluded: chain E residue 931 ILE Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 995 THR Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 379 TYR Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 730 MET Chi-restraints excluded: chain G residue 780 VAL Chi-restraints excluded: chain G residue 914 VAL Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain G residue 972 ILE Chi-restraints excluded: chain G residue 975 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 56 optimal weight: 0.4980 chunk 251 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 363 optimal weight: 50.0000 chunk 334 optimal weight: 0.6980 chunk 316 optimal weight: 0.0670 chunk 371 optimal weight: 40.0000 chunk 13 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1116 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 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 = 0.4235 r_free = 0.4235 target = 0.111346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.073058 restraints weight = 121332.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.073267 restraints weight = 75698.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.073074 restraints weight = 61668.227| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.203 32949 Z= 0.178 Angle : 0.750 59.196 44934 Z= 0.397 Chirality : 0.045 0.302 5215 Planarity : 0.004 0.066 5667 Dihedral : 6.291 58.082 5831 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.54 % Rotamer: Outliers : 1.48 % Allowed : 16.81 % Favored : 81.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3939 helix: -0.16 (0.19), residues: 767 sheet: -0.36 (0.17), residues: 923 loop : -1.04 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.002 TRP J 111 HIS 0.004 0.001 HIS E 502 PHE 0.024 0.001 PHE G 55 TYR 0.075 0.002 TYR J 95 ARG 0.007 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 42) link_NAG-ASN : angle 1.85750 ( 126) link_BETA1-4 : bond 0.00484 ( 26) link_BETA1-4 : angle 1.91891 ( 78) hydrogen bonds : bond 0.03853 ( 1046) hydrogen bonds : angle 5.78108 ( 2793) SS BOND : bond 0.00338 ( 45) SS BOND : angle 0.99381 ( 90) covalent geometry : bond 0.00397 (32830) covalent geometry : angle 0.74073 (44640) Misc. bond : bond 0.00550 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 118 time to evaluate : 5.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7880 (t0) cc_final: 0.7470 (t0) REVERT: L 28 ASN cc_start: 0.6561 (t0) cc_final: 0.5962 (m-40) REVERT: D 756 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6642 (t80) REVERT: D 999 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7648 (tm-30) REVERT: D 1047 MET cc_start: 0.8230 (ptp) cc_final: 0.8026 (ptp) REVERT: D 1116 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8257 (t0) REVERT: E 172 MET cc_start: 0.4260 (mtt) cc_final: 0.3577 (mtt) REVERT: E 217 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6045 (m-80) outliers start: 51 outliers final: 47 residues processed: 160 average time/residue: 0.5918 time to fit residues: 167.2556 Evaluate side-chains 168 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 118 time to evaluate : 3.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 693 THR Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 1101 VAL Chi-restraints excluded: chain D residue 1116 ASN Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 875 LEU Chi-restraints excluded: chain E residue 906 ILE Chi-restraints excluded: chain E residue 931 ILE Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 995 THR Chi-restraints excluded: chain G residue 55 PHE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 379 TYR Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 730 MET Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 780 VAL Chi-restraints excluded: chain G residue 914 VAL Chi-restraints excluded: chain G residue 962 VAL Chi-restraints excluded: chain G residue 972 ILE Chi-restraints excluded: chain G residue 975 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 349 optimal weight: 5.9990 chunk 392 optimal weight: 30.0000 chunk 230 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 296 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 361 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1116 ASN ** D1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 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 = 0.4365 r_free = 0.4365 target = 0.120467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.082152 restraints weight = 129259.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.078238 restraints weight = 95181.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.078968 restraints weight = 84789.417| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.275 32949 Z= 0.195 Angle : 0.740 47.697 44934 Z= 0.424 Chirality : 0.045 0.302 5215 Planarity : 0.004 0.066 5667 Dihedral : 6.291 58.082 5831 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.54 % Rotamer: Outliers : 1.45 % Allowed : 16.84 % Favored : 81.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3939 helix: -0.16 (0.19), residues: 767 sheet: -0.36 (0.17), residues: 923 loop : -1.04 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.002 TRP J 111 HIS 0.004 0.001 HIS E 502 PHE 0.024 0.001 PHE G 55 TYR 0.075 0.002 TYR J 95 ARG 0.007 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 42) link_NAG-ASN : angle 1.85750 ( 126) link_BETA1-4 : bond 0.00484 ( 26) link_BETA1-4 : angle 1.91890 ( 78) hydrogen bonds : bond 0.03853 ( 1046) hydrogen bonds : angle 5.78108 ( 2793) SS BOND : bond 0.00338 ( 45) SS BOND : angle 0.99380 ( 90) covalent geometry : bond 0.00427 (32830) covalent geometry : angle 0.72994 (44640) Misc. bond : bond 0.00550 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11210.79 seconds wall clock time: 202 minutes 0.09 seconds (12120.09 seconds total)