Starting phenix.real_space_refine on Fri Mar 6 04:59:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oan_12777/03_2026/7oan_12777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oan_12777/03_2026/7oan_12777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oan_12777/03_2026/7oan_12777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oan_12777/03_2026/7oan_12777.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oan_12777/03_2026/7oan_12777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oan_12777/03_2026/7oan_12777.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 132 5.16 5 C 17886 2.51 5 N 4638 2.21 5 O 5547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28203 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 8192 Classifications: {'peptide': 1049} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 53, 'TRANS': 995} Chain breaks: 7 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 8192 Classifications: {'peptide': 1049} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 53, 'TRANS': 995} Chain breaks: 7 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 8192 Classifications: {'peptide': 1049} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 53, 'TRANS': 995} Chain breaks: 7 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 901 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 901 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 901 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.60, per 1000 atoms: 0.20 Number of scatterers: 28203 At special positions: 0 Unit cell: (139.92, 149.46, 201.4, 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 132 16.00 O 5547 8.00 N 4638 7.00 C 17886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 50 " - pdb=" SG CYS F 104 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 50 " - pdb=" SG CYS G 104 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 50 " - pdb=" SG CYS H 104 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 17 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 17 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 165 " " NAG C1312 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6534 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 60 sheets defined 22.1% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.147A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.673A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.955A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.410A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.591A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.148A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.672A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.956A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.410A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.590A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.148A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.672A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.955A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.410A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.591A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.286A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.286A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.437A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.936A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.579A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.620A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.912A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.430A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.302A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.302A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.328A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.627A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.648A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.033A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.419A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.434A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.286A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.286A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.437A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.936A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.579A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.621A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 141 through 143 Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.911A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.301A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.301A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.327A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.648A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.033A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.420A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.433A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.287A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.287A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.936A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.578A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.621A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 141 through 143 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.911A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.301A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.301A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.328A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.648A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.033A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.420A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.434A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 3 through 8 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.211A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER F 120 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL F 12 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG F 38 " --> pdb=" O ARG F 47 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.211A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER F 120 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL F 12 " --> pdb=" O SER F 120 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 3 through 8 Processing sheet with id=AG2, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.210A pdb=" N GLY G 10 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER G 120 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL G 12 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ARG G 38 " --> pdb=" O ARG G 47 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.210A pdb=" N GLY G 10 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER G 120 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL G 12 " --> pdb=" O SER G 120 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AG5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.210A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER H 120 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL H 12 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ARG H 38 " --> pdb=" O ARG H 47 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.210A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER H 120 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL H 12 " --> pdb=" O SER H 120 " (cutoff:3.500A) 1243 hydrogen bonds defined for protein. 3342 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: 6.58 Time building geometry restraints manager: 2.68 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: 8423 1.33 - 1.45: 4267 1.45 - 1.57: 15954 1.57 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 28812 Sorted by residual: bond pdb=" N VAL C 213 " pdb=" CA VAL C 213 " ideal model delta sigma weight residual 1.456 1.489 -0.033 9.50e-03 1.11e+04 1.19e+01 bond pdb=" N VAL A 213 " pdb=" CA VAL A 213 " ideal model delta sigma weight residual 1.456 1.489 -0.033 9.50e-03 1.11e+04 1.18e+01 bond pdb=" N VAL B 213 " pdb=" CA VAL B 213 " ideal model delta sigma weight residual 1.456 1.489 -0.033 9.50e-03 1.11e+04 1.18e+01 bond pdb=" N VAL A1068 " pdb=" CA VAL A1068 " ideal model delta sigma weight residual 1.456 1.486 -0.029 8.70e-03 1.32e+04 1.13e+01 bond pdb=" N VAL C1068 " pdb=" CA VAL C1068 " ideal model delta sigma weight residual 1.456 1.486 -0.029 8.70e-03 1.32e+04 1.12e+01 ... (remaining 28807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 31953 1.49 - 2.98: 6797 2.98 - 4.47: 388 4.47 - 5.96: 30 5.96 - 7.45: 18 Bond angle restraints: 39186 Sorted by residual: angle pdb=" CA ASP C 745 " pdb=" CB ASP C 745 " pdb=" CG ASP C 745 " ideal model delta sigma weight residual 112.60 117.99 -5.39 1.00e+00 1.00e+00 2.91e+01 angle pdb=" CA ASP A 745 " pdb=" CB ASP A 745 " pdb=" CG ASP A 745 " ideal model delta sigma weight residual 112.60 117.97 -5.37 1.00e+00 1.00e+00 2.88e+01 angle pdb=" CA ASP B 745 " pdb=" CB ASP B 745 " pdb=" CG ASP B 745 " ideal model delta sigma weight residual 112.60 117.96 -5.36 1.00e+00 1.00e+00 2.87e+01 angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 113.18 106.56 6.62 1.33e+00 5.65e-01 2.48e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.18 106.60 6.58 1.33e+00 5.65e-01 2.45e+01 ... (remaining 39181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 16519 17.79 - 35.58: 1123 35.58 - 53.37: 277 53.37 - 71.16: 42 71.16 - 88.95: 48 Dihedral angle restraints: 18009 sinusoidal: 7845 harmonic: 10164 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -178.05 -88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -178.05 -88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 -178.09 -88.91 1 1.00e+01 1.00e-02 9.42e+01 ... (remaining 18006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 4623 0.204 - 0.408: 6 0.408 - 0.612: 3 0.612 - 0.816: 3 0.816 - 1.019: 3 Chirality restraints: 4638 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.59e+01 ... (remaining 4635 not shown) Planarity restraints: 5043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 506 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO B 507 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 507 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 507 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 506 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C 507 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 507 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 507 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 506 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 507 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 507 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 507 " -0.029 5.00e-02 4.00e+02 ... (remaining 5040 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 298 2.63 - 3.20: 25022 3.20 - 3.77: 43116 3.77 - 4.33: 62494 4.33 - 4.90: 100805 Nonbonded interactions: 231735 Sorted by model distance: nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.066 3.040 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.067 3.040 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.068 3.040 nonbonded pdb=" OG1 THR C 393 " pdb=" O GLU C 516 " model vdw 2.130 3.040 nonbonded pdb=" OG1 THR B 393 " pdb=" O GLU B 516 " model vdw 2.130 3.040 ... (remaining 231730 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.980 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.011 0.042 28926 Z= 0.832 Angle : 1.162 15.361 39480 Z= 0.798 Chirality : 0.076 1.019 4638 Planarity : 0.004 0.054 4992 Dihedral : 13.391 88.590 11331 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.02 % Favored : 95.80 % Rotamer: Outliers : 1.35 % Allowed : 1.35 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 3456 helix: 0.64 (0.20), residues: 693 sheet: -0.30 (0.16), residues: 837 loop : -0.97 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 237 TYR 0.022 0.003 TYR C 265 PHE 0.019 0.003 PHE B 497 TRP 0.022 0.003 TRP F 111 HIS 0.005 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.01148 (28812) covalent geometry : angle 1.12646 (39186) SS BOND : bond 0.00653 ( 48) SS BOND : angle 0.90132 ( 96) hydrogen bonds : bond 0.12813 ( 1168) hydrogen bonds : angle 7.73781 ( 3342) link_BETA1-4 : bond 0.00262 ( 15) link_BETA1-4 : angle 1.47674 ( 45) link_NAG-ASN : bond 0.01106 ( 51) link_NAG-ASN : angle 4.73981 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 262 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.9118 (p90) cc_final: 0.8785 (p90) REVERT: A 360 ASN cc_start: 0.9441 (m-40) cc_final: 0.8991 (t0) REVERT: A 370 ASN cc_start: 0.9215 (m-40) cc_final: 0.8939 (p0) REVERT: A 402 ILE cc_start: 0.9311 (pt) cc_final: 0.9047 (pp) REVERT: A 421 TYR cc_start: 0.8822 (m-80) cc_final: 0.8376 (m-10) REVERT: A 453 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7662 (p90) REVERT: A 456 PHE cc_start: 0.8631 (m-80) cc_final: 0.8120 (m-10) REVERT: B 140 PHE cc_start: 0.9130 (p90) cc_final: 0.8870 (p90) REVERT: B 370 ASN cc_start: 0.9176 (m-40) cc_final: 0.8847 (p0) REVERT: B 402 ILE cc_start: 0.9353 (pt) cc_final: 0.9073 (pp) REVERT: B 408 ARG cc_start: 0.9182 (pmt-80) cc_final: 0.8971 (pmt-80) REVERT: B 421 TYR cc_start: 0.8788 (m-80) cc_final: 0.8311 (m-10) REVERT: B 453 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7569 (p90) REVERT: B 456 PHE cc_start: 0.8695 (m-80) cc_final: 0.8136 (m-10) REVERT: B 492 LEU cc_start: 0.8874 (tp) cc_final: 0.8557 (tm) REVERT: C 140 PHE cc_start: 0.9078 (p90) cc_final: 0.8785 (p90) REVERT: C 360 ASN cc_start: 0.9457 (m-40) cc_final: 0.9059 (t0) REVERT: C 370 ASN cc_start: 0.9216 (m-40) cc_final: 0.8969 (p0) REVERT: C 402 ILE cc_start: 0.9288 (pt) cc_final: 0.9076 (pp) REVERT: C 408 ARG cc_start: 0.9141 (pmt-80) cc_final: 0.8894 (pmt-80) REVERT: C 453 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7858 (p90) REVERT: C 456 PHE cc_start: 0.8731 (m-80) cc_final: 0.7899 (m-10) REVERT: F 29 LEU cc_start: 0.8968 (mt) cc_final: 0.8723 (mt) REVERT: F 54 PHE cc_start: 0.8699 (t80) cc_final: 0.8287 (t80) REVERT: G 54 PHE cc_start: 0.8656 (t80) cc_final: 0.7858 (t80) REVERT: H 29 LEU cc_start: 0.8913 (mt) cc_final: 0.8550 (tp) REVERT: H 54 PHE cc_start: 0.8831 (t80) cc_final: 0.8226 (t80) outliers start: 41 outliers final: 3 residues processed: 291 average time/residue: 0.6914 time to fit residues: 232.8677 Evaluate side-chains 155 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain C residue 453 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.0470 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 613 GLN C 957 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.102276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.060035 restraints weight = 71023.437| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.39 r_work: 0.2782 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28926 Z= 0.133 Angle : 0.644 15.072 39480 Z= 0.324 Chirality : 0.050 0.609 4638 Planarity : 0.004 0.045 4992 Dihedral : 6.695 59.878 5156 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.25 % Allowed : 6.44 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3456 helix: 2.13 (0.20), residues: 642 sheet: -0.05 (0.17), residues: 804 loop : -0.83 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 31 TYR 0.017 0.001 TYR F 109 PHE 0.019 0.001 PHE C 497 TRP 0.015 0.002 TRP C 258 HIS 0.003 0.001 HIS F 32 Details of bonding type rmsd covalent geometry : bond 0.00289 (28812) covalent geometry : angle 0.59424 (39186) SS BOND : bond 0.00225 ( 48) SS BOND : angle 0.59656 ( 96) hydrogen bonds : bond 0.04362 ( 1168) hydrogen bonds : angle 5.98066 ( 3342) link_BETA1-4 : bond 0.00284 ( 15) link_BETA1-4 : angle 1.10238 ( 45) link_NAG-ASN : bond 0.00720 ( 51) link_NAG-ASN : angle 3.99416 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.9160 (p90) cc_final: 0.8926 (p90) REVERT: A 360 ASN cc_start: 0.9499 (m-40) cc_final: 0.9010 (t0) REVERT: A 370 ASN cc_start: 0.9109 (m-40) cc_final: 0.8864 (p0) REVERT: A 421 TYR cc_start: 0.8914 (m-80) cc_final: 0.8438 (m-10) REVERT: A 456 PHE cc_start: 0.8586 (m-80) cc_final: 0.8282 (m-10) REVERT: A 1002 GLN cc_start: 0.8742 (tt0) cc_final: 0.8540 (tt0) REVERT: B 140 PHE cc_start: 0.9190 (p90) cc_final: 0.8945 (p90) REVERT: B 370 ASN cc_start: 0.9026 (m-40) cc_final: 0.8788 (p0) REVERT: B 408 ARG cc_start: 0.9225 (pmt-80) cc_final: 0.8936 (pmt-80) REVERT: B 421 TYR cc_start: 0.8858 (m-80) cc_final: 0.8373 (m-10) REVERT: B 456 PHE cc_start: 0.8638 (m-80) cc_final: 0.8253 (m-10) REVERT: B 492 LEU cc_start: 0.8972 (tp) cc_final: 0.8705 (tm) REVERT: B 950 ASP cc_start: 0.8586 (m-30) cc_final: 0.8205 (m-30) REVERT: C 140 PHE cc_start: 0.9144 (p90) cc_final: 0.8855 (p90) REVERT: C 360 ASN cc_start: 0.9534 (m-40) cc_final: 0.9049 (t0) REVERT: C 408 ARG cc_start: 0.9150 (pmt-80) cc_final: 0.8791 (pmt-80) REVERT: C 421 TYR cc_start: 0.8866 (m-80) cc_final: 0.8446 (m-10) REVERT: C 456 PHE cc_start: 0.8625 (m-80) cc_final: 0.8269 (m-10) REVERT: C 950 ASP cc_start: 0.8598 (m-30) cc_final: 0.8267 (m-30) REVERT: F 2 VAL cc_start: 0.1253 (OUTLIER) cc_final: 0.1028 (m) REVERT: F 54 PHE cc_start: 0.8816 (t80) cc_final: 0.8213 (t80) REVERT: F 100 VAL cc_start: 0.6522 (OUTLIER) cc_final: 0.6205 (t) REVERT: G 2 VAL cc_start: 0.1682 (OUTLIER) cc_final: 0.1476 (m) REVERT: G 54 PHE cc_start: 0.8732 (t80) cc_final: 0.8017 (t80) REVERT: H 29 LEU cc_start: 0.8689 (mt) cc_final: 0.8398 (tp) REVERT: H 54 PHE cc_start: 0.8795 (t80) cc_final: 0.8099 (t80) REVERT: H 77 ASN cc_start: 0.7963 (t0) cc_final: 0.7284 (t0) outliers start: 38 outliers final: 14 residues processed: 187 average time/residue: 0.6607 time to fit residues: 144.0702 Evaluate side-chains 148 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 79 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 323 optimal weight: 20.0000 chunk 291 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 269 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 675 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.099414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.056524 restraints weight = 70742.855| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.40 r_work: 0.2716 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 28926 Z= 0.224 Angle : 0.647 15.632 39480 Z= 0.325 Chirality : 0.049 0.550 4638 Planarity : 0.004 0.037 4992 Dihedral : 5.880 50.832 5142 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.55 % Allowed : 8.05 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3456 helix: 2.05 (0.20), residues: 660 sheet: 0.11 (0.17), residues: 840 loop : -0.84 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 214 TYR 0.022 0.002 TYR C 396 PHE 0.017 0.001 PHE A 565 TRP 0.015 0.001 TRP B 258 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00514 (28812) covalent geometry : angle 0.60333 (39186) SS BOND : bond 0.00282 ( 48) SS BOND : angle 0.66458 ( 96) hydrogen bonds : bond 0.04478 ( 1168) hydrogen bonds : angle 5.69229 ( 3342) link_BETA1-4 : bond 0.00146 ( 15) link_BETA1-4 : angle 1.03477 ( 45) link_NAG-ASN : bond 0.00590 ( 51) link_NAG-ASN : angle 3.77489 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.9235 (p90) cc_final: 0.8969 (p90) REVERT: A 360 ASN cc_start: 0.9519 (m-40) cc_final: 0.9010 (t0) REVERT: A 370 ASN cc_start: 0.9135 (m-40) cc_final: 0.8883 (p0) REVERT: A 421 TYR cc_start: 0.8956 (m-80) cc_final: 0.8392 (m-10) REVERT: A 456 PHE cc_start: 0.8598 (m-80) cc_final: 0.8394 (m-10) REVERT: A 603 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8491 (t0) REVERT: A 675 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7610 (pp30) REVERT: B 140 PHE cc_start: 0.9228 (p90) cc_final: 0.8918 (p90) REVERT: B 370 ASN cc_start: 0.9059 (m-40) cc_final: 0.8792 (p0) REVERT: B 408 ARG cc_start: 0.9231 (pmt-80) cc_final: 0.8862 (pmt-80) REVERT: B 421 TYR cc_start: 0.8899 (m-80) cc_final: 0.8383 (m-10) REVERT: B 456 PHE cc_start: 0.8650 (m-80) cc_final: 0.8247 (m-10) REVERT: B 902 MET cc_start: 0.9113 (tpp) cc_final: 0.8904 (tpt) REVERT: B 950 ASP cc_start: 0.8742 (m-30) cc_final: 0.8362 (m-30) REVERT: C 140 PHE cc_start: 0.9186 (p90) cc_final: 0.8840 (p90) REVERT: C 360 ASN cc_start: 0.9572 (m-40) cc_final: 0.9059 (t0) REVERT: C 408 ARG cc_start: 0.9228 (pmt-80) cc_final: 0.8909 (pmt-80) REVERT: C 421 TYR cc_start: 0.8870 (m-80) cc_final: 0.8410 (m-10) REVERT: C 456 PHE cc_start: 0.8630 (m-80) cc_final: 0.8246 (m-10) REVERT: C 603 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8506 (t0) REVERT: C 1010 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8469 (mp10) REVERT: F 54 PHE cc_start: 0.8827 (t80) cc_final: 0.8297 (t80) REVERT: F 55 ASP cc_start: 0.9064 (t70) cc_final: 0.8482 (p0) REVERT: F 76 MET cc_start: 0.4381 (pmt) cc_final: 0.4075 (pmt) REVERT: F 80 TYR cc_start: 0.7441 (m-80) cc_final: 0.7059 (m-10) REVERT: G 2 VAL cc_start: 0.2087 (OUTLIER) cc_final: 0.1876 (m) REVERT: G 54 PHE cc_start: 0.8801 (t80) cc_final: 0.8260 (t80) REVERT: G 55 ASP cc_start: 0.9186 (t70) cc_final: 0.8902 (p0) REVERT: G 76 MET cc_start: 0.4416 (OUTLIER) cc_final: 0.4206 (pmt) REVERT: G 80 TYR cc_start: 0.7311 (m-80) cc_final: 0.6763 (m-10) REVERT: H 54 PHE cc_start: 0.8917 (t80) cc_final: 0.8279 (t80) outliers start: 47 outliers final: 24 residues processed: 186 average time/residue: 0.6548 time to fit residues: 142.0240 Evaluate side-chains 164 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 272 optimal weight: 2.9990 chunk 229 optimal weight: 30.0000 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 285 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 345 optimal weight: 30.0000 chunk 237 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 957 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.103202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.063177 restraints weight = 72230.091| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.23 r_work: 0.2761 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28926 Z= 0.130 Angle : 0.583 14.216 39480 Z= 0.294 Chirality : 0.048 0.528 4638 Planarity : 0.003 0.038 4992 Dihedral : 5.370 48.131 5142 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.48 % Allowed : 8.94 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3456 helix: 2.21 (0.20), residues: 663 sheet: 0.14 (0.17), residues: 798 loop : -0.70 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 214 TYR 0.016 0.001 TYR B1067 PHE 0.022 0.001 PHE C 168 TRP 0.019 0.001 TRP C 258 HIS 0.001 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00290 (28812) covalent geometry : angle 0.54049 (39186) SS BOND : bond 0.00197 ( 48) SS BOND : angle 0.48443 ( 96) hydrogen bonds : bond 0.03874 ( 1168) hydrogen bonds : angle 5.44834 ( 3342) link_BETA1-4 : bond 0.00304 ( 15) link_BETA1-4 : angle 0.88684 ( 45) link_NAG-ASN : bond 0.00573 ( 51) link_NAG-ASN : angle 3.54785 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASN cc_start: 0.9121 (m-40) cc_final: 0.8885 (p0) REVERT: A 456 PHE cc_start: 0.8654 (m-80) cc_final: 0.8200 (m-10) REVERT: A 1072 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: B 140 PHE cc_start: 0.9204 (p90) cc_final: 0.8924 (p90) REVERT: B 408 ARG cc_start: 0.9251 (pmt-80) cc_final: 0.9034 (ppt170) REVERT: B 421 TYR cc_start: 0.8847 (m-80) cc_final: 0.8314 (m-10) REVERT: B 456 PHE cc_start: 0.8595 (m-80) cc_final: 0.8298 (m-10) REVERT: B 902 MET cc_start: 0.9011 (tpp) cc_final: 0.8680 (tpt) REVERT: B 950 ASP cc_start: 0.8732 (m-30) cc_final: 0.8370 (m-30) REVERT: C 140 PHE cc_start: 0.9181 (p90) cc_final: 0.8864 (p90) REVERT: C 186 PHE cc_start: 0.7842 (m-10) cc_final: 0.7611 (m-80) REVERT: C 408 ARG cc_start: 0.9244 (pmt-80) cc_final: 0.8939 (pmt-80) REVERT: C 421 TYR cc_start: 0.8856 (m-80) cc_final: 0.8431 (m-10) REVERT: C 456 PHE cc_start: 0.8615 (m-80) cc_final: 0.8278 (m-10) REVERT: C 950 ASP cc_start: 0.9035 (m-30) cc_final: 0.8767 (m-30) REVERT: C 1010 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8433 (mp10) REVERT: F 54 PHE cc_start: 0.8838 (t80) cc_final: 0.8287 (t80) REVERT: F 55 ASP cc_start: 0.9412 (t70) cc_final: 0.9060 (p0) REVERT: F 76 MET cc_start: 0.4568 (pmt) cc_final: 0.4131 (pmt) REVERT: F 80 TYR cc_start: 0.7434 (m-80) cc_final: 0.7059 (m-10) REVERT: G 2 VAL cc_start: 0.2347 (OUTLIER) cc_final: 0.1762 (m) REVERT: G 54 PHE cc_start: 0.8917 (t80) cc_final: 0.8328 (t80) REVERT: G 55 ASP cc_start: 0.9269 (t70) cc_final: 0.9004 (t70) REVERT: G 76 MET cc_start: 0.4551 (pmt) cc_final: 0.4133 (pmm) REVERT: H 54 PHE cc_start: 0.8919 (t80) cc_final: 0.8290 (t80) REVERT: H 76 MET cc_start: 0.4735 (pmt) cc_final: 0.4283 (pmm) outliers start: 45 outliers final: 14 residues processed: 179 average time/residue: 0.6983 time to fit residues: 144.9335 Evaluate side-chains 146 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 286 optimal weight: 5.9990 chunk 150 optimal weight: 0.1980 chunk 106 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 21 optimal weight: 50.0000 chunk 59 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 299 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 675 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.099971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.057565 restraints weight = 70434.629| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.35 r_work: 0.2788 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28926 Z= 0.145 Angle : 0.584 13.908 39480 Z= 0.293 Chirality : 0.048 0.508 4638 Planarity : 0.003 0.047 4992 Dihedral : 5.076 49.409 5142 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.68 % Allowed : 9.43 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.14), residues: 3456 helix: 2.32 (0.20), residues: 663 sheet: 0.24 (0.17), residues: 855 loop : -0.66 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 52 TYR 0.021 0.001 TYR H 109 PHE 0.017 0.001 PHE B 565 TRP 0.019 0.001 TRP C 258 HIS 0.002 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00328 (28812) covalent geometry : angle 0.54488 (39186) SS BOND : bond 0.00213 ( 48) SS BOND : angle 0.49686 ( 96) hydrogen bonds : bond 0.03831 ( 1168) hydrogen bonds : angle 5.33562 ( 3342) link_BETA1-4 : bond 0.00269 ( 15) link_BETA1-4 : angle 0.93450 ( 45) link_NAG-ASN : bond 0.00550 ( 51) link_NAG-ASN : angle 3.41686 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASN cc_start: 0.9064 (m-40) cc_final: 0.8840 (p0) REVERT: A 456 PHE cc_start: 0.8673 (m-80) cc_final: 0.8237 (m-10) REVERT: A 900 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9065 (mtm) REVERT: B 140 PHE cc_start: 0.9200 (p90) cc_final: 0.8912 (p90) REVERT: B 408 ARG cc_start: 0.9277 (pmt-80) cc_final: 0.9051 (ppt170) REVERT: B 456 PHE cc_start: 0.8555 (m-80) cc_final: 0.8047 (m-10) REVERT: B 950 ASP cc_start: 0.8747 (m-30) cc_final: 0.8365 (m-30) REVERT: C 140 PHE cc_start: 0.9179 (p90) cc_final: 0.8792 (p90) REVERT: C 408 ARG cc_start: 0.9245 (pmt-80) cc_final: 0.8938 (pmt-80) REVERT: C 421 TYR cc_start: 0.8856 (m-80) cc_final: 0.8424 (m-10) REVERT: C 950 ASP cc_start: 0.8929 (m-30) cc_final: 0.8571 (m-30) REVERT: C 1010 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8401 (mp10) REVERT: F 54 PHE cc_start: 0.8876 (t80) cc_final: 0.8343 (t80) REVERT: F 55 ASP cc_start: 0.9430 (t70) cc_final: 0.9075 (p0) REVERT: G 2 VAL cc_start: 0.2256 (OUTLIER) cc_final: 0.2048 (m) REVERT: G 54 PHE cc_start: 0.8973 (t80) cc_final: 0.8419 (t80) REVERT: G 55 ASP cc_start: 0.9132 (t70) cc_final: 0.8822 (t0) REVERT: G 76 MET cc_start: 0.4340 (pmt) cc_final: 0.3868 (pmm) REVERT: H 52 ARG cc_start: 0.8346 (ttm110) cc_final: 0.7790 (ttp-110) REVERT: H 54 PHE cc_start: 0.8953 (t80) cc_final: 0.8431 (t80) REVERT: H 55 ASP cc_start: 0.9043 (t70) cc_final: 0.8352 (p0) REVERT: H 76 MET cc_start: 0.4814 (pmt) cc_final: 0.4342 (pmm) outliers start: 51 outliers final: 18 residues processed: 176 average time/residue: 0.6400 time to fit residues: 131.7835 Evaluate side-chains 143 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 17 optimal weight: 9.9990 chunk 322 optimal weight: 30.0000 chunk 168 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 247 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 309 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 762 GLN B 675 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 907 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.098177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.055840 restraints weight = 71072.548| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.28 r_work: 0.2723 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 28926 Z= 0.317 Angle : 0.667 14.989 39480 Z= 0.334 Chirality : 0.050 0.522 4638 Planarity : 0.004 0.041 4992 Dihedral : 5.220 51.530 5142 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.78 % Allowed : 10.36 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3456 helix: 1.94 (0.20), residues: 678 sheet: 0.07 (0.16), residues: 891 loop : -0.57 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 214 TYR 0.026 0.002 TYR A 396 PHE 0.019 0.002 PHE B 565 TRP 0.025 0.001 TRP C 258 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00729 (28812) covalent geometry : angle 0.63040 (39186) SS BOND : bond 0.00340 ( 48) SS BOND : angle 0.75659 ( 96) hydrogen bonds : bond 0.04587 ( 1168) hydrogen bonds : angle 5.53940 ( 3342) link_BETA1-4 : bond 0.00126 ( 15) link_BETA1-4 : angle 1.04197 ( 45) link_NAG-ASN : bond 0.00520 ( 51) link_NAG-ASN : angle 3.48994 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 140 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8157 (m-10) cc_final: 0.7675 (m-80) REVERT: A 370 ASN cc_start: 0.9100 (m-40) cc_final: 0.8875 (p0) REVERT: A 456 PHE cc_start: 0.8715 (m-80) cc_final: 0.8241 (m-10) REVERT: A 1072 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: B 140 PHE cc_start: 0.9208 (p90) cc_final: 0.8906 (p90) REVERT: B 186 PHE cc_start: 0.8144 (m-10) cc_final: 0.7629 (m-80) REVERT: B 408 ARG cc_start: 0.9298 (pmt-80) cc_final: 0.8907 (pmt-80) REVERT: B 456 PHE cc_start: 0.8575 (m-80) cc_final: 0.8340 (m-10) REVERT: B 1072 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: C 140 PHE cc_start: 0.9222 (p90) cc_final: 0.8808 (p90) REVERT: C 186 PHE cc_start: 0.8187 (m-10) cc_final: 0.7890 (m-80) REVERT: C 408 ARG cc_start: 0.9267 (pmt-80) cc_final: 0.8952 (pmt-80) REVERT: C 421 TYR cc_start: 0.8875 (m-80) cc_final: 0.8385 (m-10) REVERT: C 950 ASP cc_start: 0.8839 (m-30) cc_final: 0.8445 (m-30) REVERT: C 1010 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8319 (mp10) REVERT: C 1072 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8467 (mp0) REVERT: F 54 PHE cc_start: 0.8935 (t80) cc_final: 0.8382 (t80) REVERT: F 55 ASP cc_start: 0.9435 (t70) cc_final: 0.9024 (p0) REVERT: F 76 MET cc_start: 0.5021 (pmt) cc_final: 0.4604 (pmm) REVERT: G 54 PHE cc_start: 0.9049 (t80) cc_final: 0.8487 (t80) REVERT: G 76 MET cc_start: 0.5161 (OUTLIER) cc_final: 0.4625 (pmm) REVERT: H 52 ARG cc_start: 0.8465 (ttm110) cc_final: 0.8021 (ttp-110) REVERT: H 54 PHE cc_start: 0.9057 (t80) cc_final: 0.8459 (t80) REVERT: H 55 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8316 (p0) REVERT: H 76 MET cc_start: 0.5146 (OUTLIER) cc_final: 0.4855 (pmm) outliers start: 54 outliers final: 23 residues processed: 182 average time/residue: 0.6659 time to fit residues: 141.3132 Evaluate side-chains 153 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 62 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 170 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 chunk 314 optimal weight: 40.0000 chunk 234 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 762 GLN B 675 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN G 74 ASN G 82 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.099250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.056945 restraints weight = 70171.003| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.32 r_work: 0.2770 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28926 Z= 0.140 Angle : 0.610 13.710 39480 Z= 0.304 Chirality : 0.049 0.557 4638 Planarity : 0.004 0.064 4992 Dihedral : 5.095 50.504 5142 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.51 % Allowed : 11.05 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.14), residues: 3456 helix: 2.03 (0.20), residues: 684 sheet: 0.16 (0.17), residues: 867 loop : -0.53 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 214 TYR 0.017 0.001 TYR C 265 PHE 0.024 0.001 PHE B 168 TRP 0.039 0.001 TRP C 258 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00315 (28812) covalent geometry : angle 0.56922 (39186) SS BOND : bond 0.00214 ( 48) SS BOND : angle 0.53883 ( 96) hydrogen bonds : bond 0.03958 ( 1168) hydrogen bonds : angle 5.36456 ( 3342) link_BETA1-4 : bond 0.00278 ( 15) link_BETA1-4 : angle 0.88157 ( 45) link_NAG-ASN : bond 0.00637 ( 51) link_NAG-ASN : angle 3.54276 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8072 (m-10) cc_final: 0.7608 (m-80) REVERT: A 370 ASN cc_start: 0.9074 (m-40) cc_final: 0.8858 (p0) REVERT: A 456 PHE cc_start: 0.8694 (m-80) cc_final: 0.8478 (m-10) REVERT: A 1072 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8403 (mp0) REVERT: B 140 PHE cc_start: 0.9198 (p90) cc_final: 0.8912 (p90) REVERT: B 186 PHE cc_start: 0.8086 (m-10) cc_final: 0.7716 (m-80) REVERT: B 408 ARG cc_start: 0.9285 (pmt-80) cc_final: 0.8878 (pmt-80) REVERT: B 456 PHE cc_start: 0.8836 (m-80) cc_final: 0.8106 (m-10) REVERT: B 489 TYR cc_start: 0.8496 (m-80) cc_final: 0.8243 (m-80) REVERT: B 902 MET cc_start: 0.9147 (mmm) cc_final: 0.8779 (tpt) REVERT: B 1072 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8423 (mp0) REVERT: C 140 PHE cc_start: 0.9194 (p90) cc_final: 0.8819 (p90) REVERT: C 186 PHE cc_start: 0.8136 (m-10) cc_final: 0.7847 (m-80) REVERT: C 408 ARG cc_start: 0.9264 (pmt-80) cc_final: 0.8926 (pmt-80) REVERT: C 462 LYS cc_start: 0.8628 (mppt) cc_final: 0.8383 (pttm) REVERT: C 1010 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8301 (mp10) REVERT: C 1072 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8520 (mp0) REVERT: F 54 PHE cc_start: 0.8934 (t80) cc_final: 0.8355 (t80) REVERT: F 55 ASP cc_start: 0.9366 (t70) cc_final: 0.9059 (t0) REVERT: F 76 MET cc_start: 0.4884 (pmt) cc_final: 0.4289 (pmm) REVERT: G 54 PHE cc_start: 0.9009 (t80) cc_final: 0.8473 (t80) REVERT: G 76 MET cc_start: 0.4795 (pmt) cc_final: 0.4277 (pmm) REVERT: H 52 ARG cc_start: 0.8403 (ttm110) cc_final: 0.8010 (ttp-110) REVERT: H 54 PHE cc_start: 0.9214 (t80) cc_final: 0.8773 (t80) REVERT: H 55 ASP cc_start: 0.9050 (t70) cc_final: 0.8410 (p0) REVERT: H 76 MET cc_start: 0.4979 (OUTLIER) cc_final: 0.4448 (pmm) outliers start: 46 outliers final: 25 residues processed: 179 average time/residue: 0.6628 time to fit residues: 138.5783 Evaluate side-chains 155 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 322 optimal weight: 40.0000 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 312 optimal weight: 30.0000 chunk 251 optimal weight: 20.0000 chunk 326 optimal weight: 40.0000 chunk 314 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 675 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.098719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.056607 restraints weight = 70819.079| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.31 r_work: 0.2740 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 28926 Z= 0.214 Angle : 0.625 13.774 39480 Z= 0.312 Chirality : 0.048 0.502 4638 Planarity : 0.004 0.056 4992 Dihedral : 5.074 51.414 5142 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.71 % Allowed : 11.11 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3456 helix: 1.98 (0.20), residues: 681 sheet: 0.18 (0.17), residues: 861 loop : -0.54 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 214 TYR 0.019 0.001 TYR B 265 PHE 0.021 0.001 PHE B 565 TRP 0.045 0.002 TRP B 258 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00488 (28812) covalent geometry : angle 0.58655 (39186) SS BOND : bond 0.00277 ( 48) SS BOND : angle 0.63781 ( 96) hydrogen bonds : bond 0.04169 ( 1168) hydrogen bonds : angle 5.36383 ( 3342) link_BETA1-4 : bond 0.00174 ( 15) link_BETA1-4 : angle 0.96919 ( 45) link_NAG-ASN : bond 0.00559 ( 51) link_NAG-ASN : angle 3.50312 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8156 (m-10) cc_final: 0.7681 (m-80) REVERT: A 370 ASN cc_start: 0.9099 (m-40) cc_final: 0.8893 (p0) REVERT: A 456 PHE cc_start: 0.8891 (m-80) cc_final: 0.8376 (m-10) REVERT: A 1072 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: B 186 PHE cc_start: 0.8206 (m-10) cc_final: 0.7796 (m-80) REVERT: B 408 ARG cc_start: 0.9304 (pmt-80) cc_final: 0.8900 (pmt-80) REVERT: B 456 PHE cc_start: 0.8843 (m-80) cc_final: 0.8032 (m-10) REVERT: B 489 TYR cc_start: 0.8504 (m-80) cc_final: 0.8203 (m-80) REVERT: B 1072 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8516 (mp0) REVERT: C 24 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8527 (mm) REVERT: C 140 PHE cc_start: 0.9219 (p90) cc_final: 0.8859 (p90) REVERT: C 186 PHE cc_start: 0.8234 (m-10) cc_final: 0.7920 (m-80) REVERT: C 408 ARG cc_start: 0.9281 (pmt-80) cc_final: 0.8919 (pmt-80) REVERT: C 456 PHE cc_start: 0.7618 (m-80) cc_final: 0.7307 (m-80) REVERT: C 1010 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8348 (mp10) REVERT: C 1072 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: F 54 PHE cc_start: 0.8949 (t80) cc_final: 0.8337 (t80) REVERT: F 76 MET cc_start: 0.4925 (pmt) cc_final: 0.4395 (pmm) REVERT: G 52 ARG cc_start: 0.8304 (mtm110) cc_final: 0.7788 (mtm-85) REVERT: G 54 PHE cc_start: 0.9038 (t80) cc_final: 0.8574 (t80) REVERT: G 55 ASP cc_start: 0.9108 (t0) cc_final: 0.8731 (p0) REVERT: G 76 MET cc_start: 0.5060 (OUTLIER) cc_final: 0.4612 (pmm) REVERT: H 52 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8045 (ttp-110) REVERT: H 54 PHE cc_start: 0.9244 (t80) cc_final: 0.8854 (t80) REVERT: H 55 ASP cc_start: 0.9058 (t70) cc_final: 0.8439 (p0) REVERT: H 76 MET cc_start: 0.5151 (OUTLIER) cc_final: 0.4656 (pmm) outliers start: 52 outliers final: 26 residues processed: 176 average time/residue: 0.6431 time to fit residues: 133.2308 Evaluate side-chains 157 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 168 optimal weight: 0.9980 chunk 268 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 279 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 309 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.100279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.058342 restraints weight = 70936.004| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.35 r_work: 0.2791 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28926 Z= 0.118 Angle : 0.599 12.611 39480 Z= 0.299 Chirality : 0.047 0.484 4638 Planarity : 0.004 0.072 4992 Dihedral : 4.918 50.690 5142 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.28 % Allowed : 11.87 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3456 helix: 2.21 (0.20), residues: 681 sheet: 0.19 (0.17), residues: 873 loop : -0.45 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 214 TYR 0.017 0.001 TYR A 265 PHE 0.028 0.001 PHE C 168 TRP 0.054 0.002 TRP B 258 HIS 0.003 0.000 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00265 (28812) covalent geometry : angle 0.56296 (39186) SS BOND : bond 0.00167 ( 48) SS BOND : angle 0.43796 ( 96) hydrogen bonds : bond 0.03652 ( 1168) hydrogen bonds : angle 5.12003 ( 3342) link_BETA1-4 : bond 0.00343 ( 15) link_BETA1-4 : angle 0.87375 ( 45) link_NAG-ASN : bond 0.00573 ( 51) link_NAG-ASN : angle 3.33303 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8080 (m-10) cc_final: 0.7624 (m-80) REVERT: A 456 PHE cc_start: 0.8876 (m-80) cc_final: 0.8438 (m-10) REVERT: A 489 TYR cc_start: 0.8530 (m-80) cc_final: 0.8322 (m-80) REVERT: A 1072 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8434 (mp0) REVERT: B 140 PHE cc_start: 0.9214 (p90) cc_final: 0.8924 (p90) REVERT: B 186 PHE cc_start: 0.8160 (m-10) cc_final: 0.7760 (m-80) REVERT: B 408 ARG cc_start: 0.9306 (pmt-80) cc_final: 0.9007 (pmt-80) REVERT: B 456 PHE cc_start: 0.8813 (m-80) cc_final: 0.8035 (m-10) REVERT: B 489 TYR cc_start: 0.8542 (m-80) cc_final: 0.8204 (m-80) REVERT: B 740 MET cc_start: 0.9299 (tpp) cc_final: 0.9071 (tpt) REVERT: B 902 MET cc_start: 0.9134 (mmm) cc_final: 0.8835 (tpt) REVERT: B 950 ASP cc_start: 0.8764 (m-30) cc_final: 0.8520 (m-30) REVERT: B 1072 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: C 24 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8523 (mm) REVERT: C 140 PHE cc_start: 0.9191 (p90) cc_final: 0.8858 (p90) REVERT: C 186 PHE cc_start: 0.8166 (m-10) cc_final: 0.7853 (m-80) REVERT: C 214 ARG cc_start: 0.8866 (mmm160) cc_final: 0.8549 (tpp-160) REVERT: C 408 ARG cc_start: 0.9284 (pmt-80) cc_final: 0.8910 (pmt-80) REVERT: C 462 LYS cc_start: 0.9092 (mtmm) cc_final: 0.8851 (pmmt) REVERT: C 1072 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8539 (mp0) REVERT: F 54 PHE cc_start: 0.9003 (t80) cc_final: 0.8501 (t80) REVERT: F 76 MET cc_start: 0.4658 (pmt) cc_final: 0.4191 (pmm) REVERT: G 54 PHE cc_start: 0.9060 (t80) cc_final: 0.8541 (t80) REVERT: G 76 MET cc_start: 0.4821 (OUTLIER) cc_final: 0.4309 (pmm) REVERT: H 52 ARG cc_start: 0.8402 (ttm110) cc_final: 0.8023 (ttp-110) REVERT: H 54 PHE cc_start: 0.9248 (t80) cc_final: 0.8841 (t80) REVERT: H 55 ASP cc_start: 0.9023 (t70) cc_final: 0.8333 (p0) REVERT: H 76 MET cc_start: 0.5013 (pmt) cc_final: 0.4521 (pmm) outliers start: 39 outliers final: 22 residues processed: 168 average time/residue: 0.6972 time to fit residues: 136.3480 Evaluate side-chains 155 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 97 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 304 optimal weight: 0.7980 chunk 219 optimal weight: 10.0000 chunk 54 optimal weight: 0.0970 chunk 111 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.099927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.057768 restraints weight = 70356.150| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.33 r_work: 0.2797 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28926 Z= 0.116 Angle : 0.593 14.960 39480 Z= 0.295 Chirality : 0.047 0.510 4638 Planarity : 0.004 0.069 4992 Dihedral : 4.830 51.098 5142 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.08 % Allowed : 12.06 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3456 helix: 2.34 (0.20), residues: 669 sheet: 0.22 (0.17), residues: 879 loop : -0.45 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 214 TYR 0.017 0.001 TYR A 265 PHE 0.026 0.001 PHE A 168 TRP 0.039 0.001 TRP B 258 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00259 (28812) covalent geometry : angle 0.55681 (39186) SS BOND : bond 0.00166 ( 48) SS BOND : angle 0.44503 ( 96) hydrogen bonds : bond 0.03616 ( 1168) hydrogen bonds : angle 5.06766 ( 3342) link_BETA1-4 : bond 0.00310 ( 15) link_BETA1-4 : angle 0.91140 ( 45) link_NAG-ASN : bond 0.00529 ( 51) link_NAG-ASN : angle 3.29916 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8096 (m-10) cc_final: 0.7638 (m-80) REVERT: A 456 PHE cc_start: 0.8912 (m-80) cc_final: 0.8486 (m-10) REVERT: A 489 TYR cc_start: 0.8521 (m-80) cc_final: 0.8307 (m-80) REVERT: A 1072 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8434 (mp0) REVERT: B 140 PHE cc_start: 0.9246 (p90) cc_final: 0.8937 (p90) REVERT: B 186 PHE cc_start: 0.8170 (m-10) cc_final: 0.7760 (m-80) REVERT: B 408 ARG cc_start: 0.9306 (pmt-80) cc_final: 0.9005 (pmt-80) REVERT: B 456 PHE cc_start: 0.8796 (m-80) cc_final: 0.8053 (m-10) REVERT: B 489 TYR cc_start: 0.8515 (m-80) cc_final: 0.8177 (m-80) REVERT: B 740 MET cc_start: 0.9301 (tpp) cc_final: 0.9069 (tpt) REVERT: B 950 ASP cc_start: 0.8759 (m-30) cc_final: 0.8518 (m-30) REVERT: B 1072 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: C 24 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8532 (mm) REVERT: C 140 PHE cc_start: 0.9207 (p90) cc_final: 0.8840 (p90) REVERT: C 186 PHE cc_start: 0.8168 (m-10) cc_final: 0.7847 (m-80) REVERT: C 214 ARG cc_start: 0.8849 (mmm160) cc_final: 0.8550 (tpp-160) REVERT: C 408 ARG cc_start: 0.9298 (pmt-80) cc_final: 0.8917 (pmt-80) REVERT: C 462 LYS cc_start: 0.9057 (mtmm) cc_final: 0.8716 (pmtt) REVERT: C 1072 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8512 (mp0) REVERT: F 54 PHE cc_start: 0.8991 (t80) cc_final: 0.8463 (t80) REVERT: F 55 ASP cc_start: 0.8912 (t0) cc_final: 0.8653 (t0) REVERT: F 76 MET cc_start: 0.4600 (pmt) cc_final: 0.4115 (pmm) REVERT: G 2 VAL cc_start: 0.1633 (OUTLIER) cc_final: 0.1357 (m) REVERT: G 52 ARG cc_start: 0.8339 (ttm110) cc_final: 0.8080 (mtm-85) REVERT: G 54 PHE cc_start: 0.9061 (t80) cc_final: 0.8642 (t80) REVERT: G 55 ASP cc_start: 0.9131 (t0) cc_final: 0.8733 (p0) REVERT: G 76 MET cc_start: 0.4700 (OUTLIER) cc_final: 0.4214 (pmm) REVERT: H 52 ARG cc_start: 0.8357 (ttm110) cc_final: 0.7986 (ttp-110) REVERT: H 54 PHE cc_start: 0.9266 (t80) cc_final: 0.8861 (t80) REVERT: H 55 ASP cc_start: 0.9027 (t70) cc_final: 0.8348 (p0) REVERT: H 76 MET cc_start: 0.4949 (pmt) cc_final: 0.4519 (pmm) outliers start: 33 outliers final: 21 residues processed: 159 average time/residue: 0.6778 time to fit residues: 126.0296 Evaluate side-chains 152 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 21 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 199 optimal weight: 0.4980 chunk 125 optimal weight: 30.0000 chunk 197 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 762 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.097813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.054915 restraints weight = 70842.318| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.37 r_work: 0.2732 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 28926 Z= 0.247 Angle : 0.640 13.170 39480 Z= 0.322 Chirality : 0.048 0.475 4638 Planarity : 0.004 0.064 4992 Dihedral : 5.060 52.922 5142 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.15 % Allowed : 12.13 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3456 helix: 1.89 (0.20), residues: 702 sheet: 0.16 (0.17), residues: 867 loop : -0.41 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 214 TYR 0.019 0.001 TYR B 265 PHE 0.025 0.001 PHE C 168 TRP 0.034 0.002 TRP B 258 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00565 (28812) covalent geometry : angle 0.60983 (39186) SS BOND : bond 0.00302 ( 48) SS BOND : angle 0.72490 ( 96) hydrogen bonds : bond 0.04313 ( 1168) hydrogen bonds : angle 5.28917 ( 3342) link_BETA1-4 : bond 0.00143 ( 15) link_BETA1-4 : angle 1.02149 ( 45) link_NAG-ASN : bond 0.00529 ( 51) link_NAG-ASN : angle 3.14782 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8663.65 seconds wall clock time: 148 minutes 34.68 seconds (8914.68 seconds total)