Starting phenix.real_space_refine on Sun Jul 5 13:52:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oan_12777/07_2026/7oan_12777.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oan_12777/07_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_12777/07_2026/7oan_12777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oan_12777/07_2026/7oan_12777.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7oan_12777/07_2026/7oan_12777.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oan_12777/07_2026/7oan_12777.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oan_12777/07_2026/7oan_12777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oan_12777/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 12 Time building chain proxies: 5.70, 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: 2.09 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: 1.32 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: 7.81 Time building geometry restraints manager: 2.83 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: 15271 17.79 - 35.58: 1057 35.58 - 53.37: 209 53.37 - 71.16: 38 71.16 - 88.95: 48 Dihedral angle restraints: 16623 sinusoidal: 6459 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 16620 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: 0.08 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: 2.690 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.540 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 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 : 13.539 88.590 9945 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/Z covalent geometry : bond 0.01148 / 0.83 (28812) covalent geometry : angle 1.12646 / 0.79 (39186) SS BOND : bond 0.00653 / 0.42 ( 48) SS BOND : angle 0.90132 / 0.65 ( 96) hydrogen bonds : bond 0.12813 / 8.64 ( 1168) hydrogen bonds : angle 7.73781 / 5.44 ( 3342) link_BETA1-4 : bond 0.00262 / 0.19 ( 15) link_BETA1-4 : angle 1.47674 / 0.91 ( 45) link_NAG-ASN : bond 0.01106 / 0.71 ( 51) link_NAG-ASN : angle 4.73981 / 3.22 ( 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 : 1.032 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: 0.6055 time to fit residues: 204.8440 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 : 0.620 ------------------------------------------------------------------------------- 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: 1.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3856 r_free = 0.3856 target = 0.101985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.059797 restraints weight = 70909.901| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.41 r_work: 0.2769 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1625 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= 0.141 Angle : 0.648 14.444 39480 Z= 0.326 Chirality : 0.050 0.579 4638 Planarity : 0.004 0.044 4992 Dihedral : 5.012 46.809 3770 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.28 % Allowed : 6.28 % Favored : 92.44 % 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: -0.11 (0.14), residues: 3456 helix: 2.11 (0.20), residues: 645 sheet: -0.05 (0.17), residues: 804 loop : -0.82 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 31 TYR 0.019 0.001 TYR F 109 PHE 0.015 0.001 PHE A 497 TRP 0.016 0.002 TRP C 258 HIS 0.003 0.001 HIS F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (28812) covalent geometry : angle 0.60192 / 0.32 (39186) SS BOND : bond 0.00244 / 0.17 ( 48) SS BOND : angle 0.62732 / 0.44 ( 96) hydrogen bonds : bond 0.04282 / 2.86 ( 1168) hydrogen bonds : angle 5.94787 / 4.18 ( 3342) link_BETA1-4 : bond 0.00400 / 0.29 ( 15) link_BETA1-4 : angle 1.06695 / 0.72 ( 45) link_NAG-ASN : bond 0.00637 / 0.41 ( 51) link_NAG-ASN : angle 3.86876 / 2.65 ( 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: 39 poor density : 161 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.9166 (p90) cc_final: 0.8921 (p90) REVERT: A 360 ASN cc_start: 0.9508 (m-40) cc_final: 0.9012 (t0) REVERT: A 370 ASN cc_start: 0.9128 (m-40) cc_final: 0.8877 (p0) REVERT: A 421 TYR cc_start: 0.8940 (m-80) cc_final: 0.8440 (m-10) REVERT: A 456 PHE cc_start: 0.8598 (m-80) cc_final: 0.8287 (m-10) REVERT: A 1002 GLN cc_start: 0.8762 (tt0) cc_final: 0.8551 (tt0) REVERT: A 1029 MET cc_start: 0.9608 (OUTLIER) cc_final: 0.9282 (tpp) REVERT: B 140 PHE cc_start: 0.9183 (p90) cc_final: 0.8922 (p90) REVERT: B 370 ASN cc_start: 0.9050 (m-40) cc_final: 0.8800 (p0) REVERT: B 408 ARG cc_start: 0.9222 (pmt-80) cc_final: 0.8925 (pmt-80) REVERT: B 421 TYR cc_start: 0.8857 (m-80) cc_final: 0.8369 (m-10) REVERT: B 456 PHE cc_start: 0.8651 (m-80) cc_final: 0.8262 (m-10) REVERT: B 492 LEU cc_start: 0.8975 (tp) cc_final: 0.8709 (tm) REVERT: B 950 ASP cc_start: 0.8599 (m-30) cc_final: 0.8217 (m-30) REVERT: B 1029 MET cc_start: 0.9601 (OUTLIER) cc_final: 0.9384 (tpp) REVERT: C 140 PHE cc_start: 0.9146 (p90) cc_final: 0.8843 (p90) REVERT: C 360 ASN cc_start: 0.9549 (m-40) cc_final: 0.9064 (t0) REVERT: C 408 ARG cc_start: 0.9155 (pmt-80) cc_final: 0.8842 (pmt-80) REVERT: C 421 TYR cc_start: 0.8870 (m-80) cc_final: 0.8454 (m-10) REVERT: C 456 PHE cc_start: 0.8635 (m-80) cc_final: 0.8275 (m-10) REVERT: C 950 ASP cc_start: 0.8614 (m-30) cc_final: 0.8263 (m-30) REVERT: F 2 VAL cc_start: 0.1265 (OUTLIER) cc_final: 0.1022 (m) REVERT: F 54 PHE cc_start: 0.8823 (t80) cc_final: 0.8216 (t80) REVERT: F 100 VAL cc_start: 0.6506 (OUTLIER) cc_final: 0.6250 (t) REVERT: G 2 VAL cc_start: 0.1720 (OUTLIER) cc_final: 0.1512 (m) REVERT: G 54 PHE cc_start: 0.8736 (t80) cc_final: 0.8020 (t80) REVERT: H 29 LEU cc_start: 0.8696 (mt) cc_final: 0.8393 (tp) REVERT: H 54 PHE cc_start: 0.8799 (t80) cc_final: 0.8106 (t80) REVERT: H 77 ASN cc_start: 0.8085 (t0) cc_final: 0.7440 (t0) outliers start: 39 outliers final: 13 residues processed: 186 average time/residue: 0.6049 time to fit residues: 132.2492 Evaluate side-chains 151 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 LEU 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 B residue 1029 MET 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 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: 6.9990 chunk 291 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 269 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 187 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 675 GLN A 762 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 675 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.100693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058357 restraints weight = 70893.589| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.37 r_work: 0.2744 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28926 Z= 0.168 Angle : 0.615 14.575 39480 Z= 0.310 Chirality : 0.048 0.511 4638 Planarity : 0.003 0.036 4992 Dihedral : 4.586 18.968 3756 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.71 % Allowed : 7.86 % Favored : 90.43 % 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: 0.00 (0.14), residues: 3456 helix: 2.17 (0.20), residues: 663 sheet: 0.14 (0.17), residues: 846 loop : -0.85 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 214 TYR 0.024 0.001 TYR C 396 PHE 0.018 0.001 PHE A 565 TRP 0.012 0.001 TRP B 258 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (28812) covalent geometry : angle 0.57323 / 0.30 (39186) SS BOND : bond 0.00253 / 0.18 ( 48) SS BOND : angle 0.56283 / 0.40 ( 96) hydrogen bonds : bond 0.04204 / 2.79 ( 1168) hydrogen bonds : angle 5.58112 / 3.93 ( 3342) link_BETA1-4 : bond 0.00190 / 0.15 ( 15) link_BETA1-4 : angle 1.00009 / 0.68 ( 45) link_NAG-ASN : bond 0.00570 / 0.37 ( 51) link_NAG-ASN : angle 3.60250 / 2.47 ( 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 206 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.9239 (p90) cc_final: 0.8976 (p90) REVERT: A 360 ASN cc_start: 0.9520 (m-40) cc_final: 0.9004 (t0) REVERT: A 370 ASN cc_start: 0.9105 (m-40) cc_final: 0.8857 (p0) REVERT: A 421 TYR cc_start: 0.8930 (m-80) cc_final: 0.8421 (m-10) REVERT: A 456 PHE cc_start: 0.8578 (m-80) cc_final: 0.8375 (m-10) REVERT: A 675 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7648 (pp30) REVERT: B 140 PHE cc_start: 0.9247 (p90) cc_final: 0.8934 (p90) REVERT: B 370 ASN cc_start: 0.9055 (m-40) cc_final: 0.8801 (p0) REVERT: B 408 ARG cc_start: 0.9244 (pmt-80) cc_final: 0.8887 (pmt-80) REVERT: B 421 TYR cc_start: 0.8868 (m-80) cc_final: 0.8359 (m-10) REVERT: B 456 PHE cc_start: 0.8641 (m-80) cc_final: 0.8228 (m-10) REVERT: B 950 ASP cc_start: 0.8704 (m-30) cc_final: 0.8321 (m-30) REVERT: C 140 PHE cc_start: 0.9182 (p90) cc_final: 0.8830 (p90) REVERT: C 186 PHE cc_start: 0.7839 (m-10) cc_final: 0.7614 (m-80) REVERT: C 360 ASN cc_start: 0.9575 (m-40) cc_final: 0.9056 (t0) REVERT: C 408 ARG cc_start: 0.9227 (pmt-80) cc_final: 0.8901 (pmt-80) REVERT: C 421 TYR cc_start: 0.8864 (m-80) cc_final: 0.8429 (m-10) REVERT: C 456 PHE cc_start: 0.8617 (m-80) cc_final: 0.8225 (m-10) REVERT: F 2 VAL cc_start: 0.1536 (OUTLIER) cc_final: 0.1244 (m) REVERT: F 54 PHE cc_start: 0.8846 (t80) cc_final: 0.8318 (t80) REVERT: F 55 ASP cc_start: 0.9090 (t70) cc_final: 0.8510 (p0) REVERT: F 76 MET cc_start: 0.4528 (OUTLIER) cc_final: 0.4056 (pmm) REVERT: G 2 VAL cc_start: 0.2020 (OUTLIER) cc_final: 0.1808 (m) REVERT: G 54 PHE cc_start: 0.8863 (t80) cc_final: 0.8324 (t80) REVERT: G 55 ASP cc_start: 0.9150 (t70) cc_final: 0.8787 (p0) REVERT: G 76 MET cc_start: 0.3880 (OUTLIER) cc_final: 0.3601 (pmm) REVERT: H 54 PHE cc_start: 0.8950 (t80) cc_final: 0.8309 (t80) outliers start: 52 outliers final: 22 residues processed: 196 average time/residue: 0.5941 time to fit residues: 137.1618 Evaluate side-chains 162 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 582 LEU 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 331 ASN Chi-restraints excluded: chain B residue 645 THR 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 786 LYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 76 MET 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: 3.9990 chunk 229 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 204 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 345 optimal weight: 50.0000 chunk 237 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 675 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 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 = 0.3820 r_free = 0.3820 target = 0.099458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.056986 restraints weight = 70855.785| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.41 r_work: 0.2712 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28926 Z= 0.219 Angle : 0.618 14.286 39480 Z= 0.309 Chirality : 0.049 0.514 4638 Planarity : 0.003 0.035 4992 Dihedral : 4.570 22.022 3756 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.48 % Allowed : 9.17 % Favored : 89.35 % 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: 0.07 (0.14), residues: 3456 helix: 2.12 (0.20), residues: 663 sheet: 0.13 (0.17), residues: 852 loop : -0.73 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 214 TYR 0.019 0.001 TYR B 396 PHE 0.019 0.001 PHE B 168 TRP 0.019 0.001 TRP C 258 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (28812) covalent geometry : angle 0.57879 / 0.30 (39186) SS BOND : bond 0.00273 / 0.19 ( 48) SS BOND : angle 0.61143 / 0.44 ( 96) hydrogen bonds : bond 0.04247 / 2.81 ( 1168) hydrogen bonds : angle 5.54523 / 3.91 ( 3342) link_BETA1-4 : bond 0.00221 / 0.16 ( 15) link_BETA1-4 : angle 0.98547 / 0.66 ( 45) link_NAG-ASN : bond 0.00520 / 0.34 ( 51) link_NAG-ASN : angle 3.51647 / 2.41 ( 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 185 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.9230 (p90) cc_final: 0.8994 (p90) REVERT: A 370 ASN cc_start: 0.9131 (m-40) cc_final: 0.8883 (p0) REVERT: A 456 PHE cc_start: 0.8679 (m-80) cc_final: 0.8216 (m-10) REVERT: A 1072 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: B 140 PHE cc_start: 0.9207 (p90) cc_final: 0.8880 (p90) REVERT: B 370 ASN cc_start: 0.9075 (m-40) cc_final: 0.8872 (p0) REVERT: B 408 ARG cc_start: 0.9260 (pmt-80) cc_final: 0.9038 (ppt170) REVERT: B 421 TYR cc_start: 0.8884 (m-80) cc_final: 0.8348 (m-10) REVERT: B 456 PHE cc_start: 0.8623 (m-80) cc_final: 0.8316 (m-10) REVERT: B 902 MET cc_start: 0.9107 (mmm) cc_final: 0.8681 (tpt) REVERT: C 140 PHE cc_start: 0.9200 (p90) cc_final: 0.8768 (p90) REVERT: C 186 PHE cc_start: 0.7961 (m-10) cc_final: 0.7682 (m-80) REVERT: C 408 ARG cc_start: 0.9250 (pmt-80) cc_final: 0.8921 (pmt-80) REVERT: C 421 TYR cc_start: 0.8876 (m-80) cc_final: 0.8439 (m-10) REVERT: C 456 PHE cc_start: 0.8635 (m-80) cc_final: 0.8296 (m-10) REVERT: C 950 ASP cc_start: 0.8988 (m-30) cc_final: 0.8711 (m-30) REVERT: F 54 PHE cc_start: 0.8851 (t80) cc_final: 0.8286 (t80) REVERT: F 55 ASP cc_start: 0.9412 (t70) cc_final: 0.9058 (p0) REVERT: F 76 MET cc_start: 0.4836 (pmt) cc_final: 0.4256 (pmm) REVERT: G 2 VAL cc_start: 0.2466 (OUTLIER) cc_final: 0.1870 (m) REVERT: G 54 PHE cc_start: 0.8959 (t80) cc_final: 0.8394 (t80) REVERT: G 76 MET cc_start: 0.4674 (pmt) cc_final: 0.4144 (pmm) REVERT: H 54 PHE cc_start: 0.8934 (t80) cc_final: 0.8317 (t80) REVERT: H 76 MET cc_start: 0.4511 (pmt) cc_final: 0.4043 (pmm) outliers start: 45 outliers final: 18 residues processed: 173 average time/residue: 0.6455 time to fit residues: 130.4979 Evaluate side-chains 144 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 645 THR Chi-restraints excluded: chain B residue 1072 GLU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 286 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 0.0170 chunk 294 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 21 optimal weight: 40.0000 chunk 59 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 299 optimal weight: 1.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.101054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.059071 restraints weight = 70717.698| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.35 r_work: 0.2796 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28926 Z= 0.120 Angle : 0.579 13.132 39480 Z= 0.290 Chirality : 0.048 0.491 4638 Planarity : 0.003 0.049 4992 Dihedral : 4.323 17.660 3756 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.64 % Allowed : 9.57 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.14), residues: 3456 helix: 2.33 (0.20), residues: 663 sheet: 0.24 (0.17), residues: 855 loop : -0.67 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 214 TYR 0.023 0.001 TYR B 396 PHE 0.016 0.001 PHE B 565 TRP 0.028 0.001 TRP C 258 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (28812) covalent geometry : angle 0.54109 / 0.28 (39186) SS BOND : bond 0.00182 / 0.13 ( 48) SS BOND : angle 0.44315 / 0.31 ( 96) hydrogen bonds : bond 0.03713 / 2.48 ( 1168) hydrogen bonds : angle 5.29495 / 3.74 ( 3342) link_BETA1-4 : bond 0.00332 / 0.24 ( 15) link_BETA1-4 : angle 0.88113 / 0.58 ( 45) link_NAG-ASN : bond 0.00634 / 0.43 ( 51) link_NAG-ASN : angle 3.36202 / 2.29 ( 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 189 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.9210 (p90) cc_final: 0.8999 (p90) REVERT: A 370 ASN cc_start: 0.9135 (m-40) cc_final: 0.8933 (p0) REVERT: A 456 PHE cc_start: 0.8662 (m-80) cc_final: 0.8247 (m-10) REVERT: B 140 PHE cc_start: 0.9216 (p90) cc_final: 0.8935 (p90) REVERT: B 408 ARG cc_start: 0.9279 (pmt-80) cc_final: 0.8924 (pmt-80) REVERT: B 417 LYS cc_start: 0.9651 (mmtt) cc_final: 0.9447 (mmtt) REVERT: B 456 PHE cc_start: 0.8579 (m-80) cc_final: 0.8066 (m-10) REVERT: B 902 MET cc_start: 0.9121 (mmm) cc_final: 0.8848 (tpt) REVERT: B 950 ASP cc_start: 0.8732 (m-30) cc_final: 0.8372 (m-30) REVERT: C 140 PHE cc_start: 0.9181 (p90) cc_final: 0.8814 (p90) REVERT: C 408 ARG cc_start: 0.9250 (pmt-80) cc_final: 0.8932 (pmt-80) REVERT: C 421 TYR cc_start: 0.8854 (m-80) cc_final: 0.8417 (m-10) REVERT: C 950 ASP cc_start: 0.8837 (m-30) cc_final: 0.8456 (m-30) REVERT: F 54 PHE cc_start: 0.8898 (t80) cc_final: 0.8347 (t80) REVERT: F 55 ASP cc_start: 0.9425 (t70) cc_final: 0.9021 (p0) REVERT: G 2 VAL cc_start: 0.2225 (OUTLIER) cc_final: 0.2021 (m) REVERT: G 54 PHE cc_start: 0.8956 (t80) cc_final: 0.8416 (t80) REVERT: H 54 PHE cc_start: 0.8956 (t80) cc_final: 0.8351 (t80) REVERT: H 76 MET cc_start: 0.4699 (pmt) cc_final: 0.4217 (pmm) outliers start: 50 outliers final: 18 residues processed: 173 average time/residue: 0.6286 time to fit residues: 126.8996 Evaluate side-chains 143 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 331 ASN 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 F residue 2 VAL Chi-restraints excluded: chain F residue 80 TYR 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 80 TYR 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: 2.9990 chunk 157 optimal weight: 9.9990 chunk 125 optimal weight: 30.0000 chunk 51 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 309 optimal weight: 0.0870 chunk 87 optimal weight: 6.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 675 GLN B 370 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** H 73 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 = 0.3810 r_free = 0.3810 target = 0.097656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.054850 restraints weight = 70715.980| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.34 r_work: 0.2721 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 28926 Z= 0.299 Angle : 0.662 14.223 39480 Z= 0.330 Chirality : 0.049 0.500 4638 Planarity : 0.004 0.042 4992 Dihedral : 4.555 20.057 3756 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.04 % Allowed : 10.12 % Favored : 87.84 % 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: 1.92 (0.20), residues: 678 sheet: 0.07 (0.17), residues: 870 loop : -0.55 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 214 TYR 0.024 0.002 TYR A 396 PHE 0.020 0.002 PHE C 168 TRP 0.026 0.001 TRP C 258 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.30 (28812) covalent geometry : angle 0.62773 / 0.32 (39186) SS BOND : bond 0.00379 / 0.26 ( 48) SS BOND : angle 0.77109 / 0.55 ( 96) hydrogen bonds : bond 0.04580 / 3.01 ( 1168) hydrogen bonds : angle 5.52712 / 3.90 ( 3342) link_BETA1-4 : bond 0.00127 / 0.10 ( 15) link_BETA1-4 : angle 1.02846 / 0.69 ( 45) link_NAG-ASN : bond 0.00503 / 0.34 ( 51) link_NAG-ASN : angle 3.38220 / 2.34 ( 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 196 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 134 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.9188 (p90) cc_final: 0.8962 (p90) REVERT: A 186 PHE cc_start: 0.8162 (m-10) cc_final: 0.7684 (m-80) REVERT: A 370 ASN cc_start: 0.9078 (m-40) cc_final: 0.8864 (p0) REVERT: A 456 PHE cc_start: 0.8717 (m-80) cc_final: 0.8255 (m-10) REVERT: A 1072 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: B 18 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7051 (tp) REVERT: B 140 PHE cc_start: 0.9209 (p90) cc_final: 0.8903 (p90) REVERT: B 186 PHE cc_start: 0.8147 (m-10) cc_final: 0.7774 (m-80) REVERT: B 408 ARG cc_start: 0.9282 (pmt-80) cc_final: 0.8895 (pmt-80) REVERT: B 456 PHE cc_start: 0.8585 (m-80) cc_final: 0.8367 (m-10) REVERT: B 902 MET cc_start: 0.9199 (mmm) cc_final: 0.8774 (tpt) REVERT: B 1072 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8345 (mp0) REVERT: C 140 PHE cc_start: 0.9240 (p90) cc_final: 0.8813 (p90) REVERT: C 186 PHE cc_start: 0.8181 (m-10) cc_final: 0.7896 (m-80) REVERT: C 408 ARG cc_start: 0.9273 (pmt-80) cc_final: 0.8953 (pmt-80) REVERT: C 456 PHE cc_start: 0.8097 (m-10) cc_final: 0.7446 (m-10) REVERT: C 1072 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8476 (mp0) REVERT: F 54 PHE cc_start: 0.8953 (t80) cc_final: 0.8397 (t80) REVERT: F 55 ASP cc_start: 0.9332 (t70) cc_final: 0.8700 (p0) REVERT: F 76 MET cc_start: 0.4912 (pmt) cc_final: 0.4296 (pmm) REVERT: G 54 PHE cc_start: 0.9053 (t80) cc_final: 0.8546 (t80) REVERT: G 55 ASP cc_start: 0.9181 (t70) cc_final: 0.8690 (p0) REVERT: G 76 MET cc_start: 0.4893 (pmt) cc_final: 0.4323 (pmm) REVERT: H 54 PHE cc_start: 0.9021 (t80) cc_final: 0.8315 (t80) REVERT: H 76 MET cc_start: 0.5103 (OUTLIER) cc_final: 0.4613 (pmm) outliers start: 62 outliers final: 24 residues processed: 182 average time/residue: 0.6134 time to fit residues: 132.3327 Evaluate side-chains 150 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 1072 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 516 GLU 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 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 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: 0.7980 chunk 9 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 178 optimal weight: 0.5980 chunk 154 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 chunk 314 optimal weight: 40.0000 chunk 234 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 675 GLN A 762 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 218 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.099579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.057306 restraints weight = 69980.126| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.32 r_work: 0.2783 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28926 Z= 0.128 Angle : 0.587 12.783 39480 Z= 0.294 Chirality : 0.047 0.486 4638 Planarity : 0.003 0.052 4992 Dihedral : 4.326 18.036 3756 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.28 % Allowed : 11.34 % Favored : 87.38 % 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: 2.06 (0.20), residues: 684 sheet: 0.12 (0.17), residues: 876 loop : -0.51 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 214 TYR 0.018 0.001 TYR A 396 PHE 0.023 0.001 PHE C 168 TRP 0.035 0.001 TRP C 258 HIS 0.001 0.000 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (28812) covalent geometry : angle 0.55396 / 0.29 (39186) SS BOND : bond 0.00195 / 0.14 ( 48) SS BOND : angle 0.48855 / 0.33 ( 96) hydrogen bonds : bond 0.03803 / 2.54 ( 1168) hydrogen bonds : angle 5.25862 / 3.71 ( 3342) link_BETA1-4 : bond 0.00309 / 0.23 ( 15) link_BETA1-4 : angle 0.84362 / 0.55 ( 45) link_NAG-ASN : bond 0.00571 / 0.37 ( 51) link_NAG-ASN : angle 3.16020 / 2.19 ( 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 173 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8055 (m-10) cc_final: 0.7596 (m-80) REVERT: A 456 PHE cc_start: 0.8703 (m-80) cc_final: 0.8484 (m-10) REVERT: A 1002 GLN cc_start: 0.8848 (tt0) cc_final: 0.8630 (tt0) REVERT: A 1072 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: B 18 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7171 (tp) REVERT: B 140 PHE cc_start: 0.9196 (p90) cc_final: 0.8919 (p90) REVERT: B 186 PHE cc_start: 0.8072 (m-10) cc_final: 0.7703 (m-80) REVERT: B 378 LYS cc_start: 0.8595 (mppt) cc_final: 0.8379 (mptt) REVERT: B 408 ARG cc_start: 0.9289 (pmt-80) cc_final: 0.8878 (pmt-80) REVERT: B 456 PHE cc_start: 0.8857 (m-80) cc_final: 0.8110 (m-10) REVERT: B 489 TYR cc_start: 0.8541 (m-80) cc_final: 0.8289 (m-80) REVERT: B 902 MET cc_start: 0.9112 (mmm) cc_final: 0.8673 (tpt) REVERT: B 950 ASP cc_start: 0.8750 (m-30) cc_final: 0.8365 (m-30) REVERT: B 1072 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8462 (mp0) REVERT: C 24 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8502 (mm) REVERT: C 140 PHE cc_start: 0.9203 (p90) cc_final: 0.8830 (p90) REVERT: C 186 PHE cc_start: 0.8109 (m-10) cc_final: 0.7829 (m-80) REVERT: C 214 ARG cc_start: 0.8775 (mmm160) cc_final: 0.8435 (tpp80) REVERT: C 378 LYS cc_start: 0.8637 (mppt) cc_final: 0.8366 (mptt) REVERT: C 408 ARG cc_start: 0.9276 (pmt-80) cc_final: 0.8908 (pmt-80) REVERT: C 456 PHE cc_start: 0.7889 (m-10) cc_final: 0.7485 (m-10) REVERT: C 1072 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: F 54 PHE cc_start: 0.8925 (t80) cc_final: 0.8335 (t80) REVERT: F 76 MET cc_start: 0.4693 (pmt) cc_final: 0.4130 (pmm) REVERT: G 54 PHE cc_start: 0.9049 (t80) cc_final: 0.8545 (t80) REVERT: G 55 ASP cc_start: 0.9129 (t70) cc_final: 0.8644 (p0) REVERT: G 76 MET cc_start: 0.5034 (pmt) cc_final: 0.4498 (pmm) REVERT: H 54 PHE cc_start: 0.9198 (t80) cc_final: 0.8778 (t80) REVERT: H 76 MET cc_start: 0.4956 (pmt) cc_final: 0.4420 (pmm) outliers start: 39 outliers final: 21 residues processed: 168 average time/residue: 0.6511 time to fit residues: 128.3093 Evaluate side-chains 153 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 18 LEU Chi-restraints excluded: chain B residue 176 LEU 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 558 LYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 55 ASP 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 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: 10.0000 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 312 optimal weight: 20.0000 chunk 251 optimal weight: 1.9990 chunk 326 optimal weight: 50.0000 chunk 314 optimal weight: 20.0000 chunk 100 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN A 762 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 GLN ** H 73 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 = 0.3840 r_free = 0.3840 target = 0.098711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.056340 restraints weight = 71076.503| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.31 r_work: 0.2742 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28926 Z= 0.238 Angle : 0.628 13.228 39480 Z= 0.313 Chirality : 0.048 0.478 4638 Planarity : 0.004 0.050 4992 Dihedral : 4.390 18.347 3756 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.38 % Allowed : 11.54 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3456 helix: 1.98 (0.20), residues: 684 sheet: 0.15 (0.17), residues: 867 loop : -0.51 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 214 TYR 0.019 0.001 TYR B 265 PHE 0.023 0.001 PHE B 168 TRP 0.033 0.001 TRP A 258 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (28812) covalent geometry : angle 0.59408 / 0.31 (39186) SS BOND : bond 0.00283 / 0.20 ( 48) SS BOND : angle 0.67455 / 0.48 ( 96) hydrogen bonds : bond 0.04196 / 2.77 ( 1168) hydrogen bonds : angle 5.33308 / 3.77 ( 3342) link_BETA1-4 : bond 0.00148 / 0.11 ( 15) link_BETA1-4 : angle 0.96180 / 0.64 ( 45) link_NAG-ASN : bond 0.00461 / 0.31 ( 51) link_NAG-ASN : angle 3.30093 / 2.25 ( 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 170 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8128 (m-10) cc_final: 0.7660 (m-80) REVERT: A 456 PHE cc_start: 0.8838 (m-80) cc_final: 0.8052 (m-10) REVERT: A 1072 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: B 18 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6994 (tp) REVERT: B 186 PHE cc_start: 0.8177 (m-10) cc_final: 0.7788 (m-80) REVERT: B 378 LYS cc_start: 0.8568 (mppt) cc_final: 0.8261 (mmtp) REVERT: B 408 ARG cc_start: 0.9305 (pmt-80) cc_final: 0.8933 (ppt170) REVERT: B 456 PHE cc_start: 0.8843 (m-80) cc_final: 0.8358 (m-10) REVERT: B 950 ASP cc_start: 0.8785 (m-30) cc_final: 0.8381 (m-30) REVERT: B 1072 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: C 140 PHE cc_start: 0.9214 (p90) cc_final: 0.8840 (p90) REVERT: C 186 PHE cc_start: 0.8200 (m-10) cc_final: 0.7906 (m-80) REVERT: C 378 LYS cc_start: 0.8613 (mppt) cc_final: 0.8320 (mptt) REVERT: C 408 ARG cc_start: 0.9283 (pmt-80) cc_final: 0.8921 (pmt-80) REVERT: C 456 PHE cc_start: 0.7970 (m-80) cc_final: 0.7544 (m-10) REVERT: C 1072 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8555 (mp0) REVERT: F 54 PHE cc_start: 0.9005 (t80) cc_final: 0.8480 (t80) REVERT: F 76 MET cc_start: 0.4877 (pmt) cc_final: 0.4311 (pmm) REVERT: G 54 PHE cc_start: 0.9081 (t80) cc_final: 0.8599 (t80) REVERT: G 55 ASP cc_start: 0.9052 (t70) cc_final: 0.8278 (p0) REVERT: G 76 MET cc_start: 0.5002 (pmt) cc_final: 0.4502 (pmm) REVERT: H 54 PHE cc_start: 0.9251 (t80) cc_final: 0.8824 (t80) REVERT: H 76 MET cc_start: 0.5160 (pmt) cc_final: 0.4674 (pmm) outliers start: 42 outliers final: 25 residues processed: 164 average time/residue: 0.6021 time to fit residues: 115.9048 Evaluate side-chains 151 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 18 LEU 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 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 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1145 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 168 optimal weight: 0.7980 chunk 268 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 279 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 80 optimal weight: 0.5980 chunk 309 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.099464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.057278 restraints weight = 70414.007| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.32 r_work: 0.2788 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28926 Z= 0.126 Angle : 0.594 12.283 39480 Z= 0.297 Chirality : 0.047 0.468 4638 Planarity : 0.004 0.069 4992 Dihedral : 4.249 17.026 3756 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.08 % Allowed : 12.10 % Favored : 86.82 % 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: 2.15 (0.20), residues: 684 sheet: 0.16 (0.17), residues: 888 loop : -0.42 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 214 TYR 0.017 0.001 TYR B 265 PHE 0.020 0.001 PHE B 565 TRP 0.025 0.001 TRP A 258 HIS 0.003 0.000 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (28812) covalent geometry : angle 0.56213 / 0.29 (39186) SS BOND : bond 0.00194 / 0.13 ( 48) SS BOND : angle 0.46172 / 0.32 ( 96) hydrogen bonds : bond 0.03721 / 2.47 ( 1168) hydrogen bonds : angle 5.13883 / 3.63 ( 3342) link_BETA1-4 : bond 0.00296 / 0.22 ( 15) link_BETA1-4 : angle 0.86977 / 0.57 ( 45) link_NAG-ASN : bond 0.00565 / 0.36 ( 51) link_NAG-ASN : angle 3.13505 / 2.15 ( 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 169 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8133 (m-10) cc_final: 0.7682 (m-80) REVERT: A 1072 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: B 18 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.7019 (tp) REVERT: B 140 PHE cc_start: 0.9212 (p90) cc_final: 0.8905 (p90) REVERT: B 186 PHE cc_start: 0.8185 (m-10) cc_final: 0.7782 (m-80) REVERT: B 214 ARG cc_start: 0.8845 (mmm160) cc_final: 0.8515 (tpt170) REVERT: B 378 LYS cc_start: 0.8636 (mppt) cc_final: 0.8255 (mmtt) REVERT: B 408 ARG cc_start: 0.9301 (pmt-80) cc_final: 0.8913 (ppt170) REVERT: B 456 PHE cc_start: 0.8856 (m-80) cc_final: 0.8089 (m-10) REVERT: B 489 TYR cc_start: 0.8617 (m-80) cc_final: 0.8255 (m-80) REVERT: B 740 MET cc_start: 0.9347 (tpp) cc_final: 0.9113 (tpt) REVERT: B 902 MET cc_start: 0.9065 (mmm) cc_final: 0.8669 (tpt) REVERT: B 950 ASP cc_start: 0.8768 (m-30) cc_final: 0.8520 (m-30) REVERT: B 1072 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8540 (mp0) REVERT: C 24 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8528 (mm) REVERT: C 140 PHE cc_start: 0.9204 (p90) cc_final: 0.8865 (p90) REVERT: C 186 PHE cc_start: 0.8163 (m-10) cc_final: 0.7862 (m-80) REVERT: C 214 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8453 (tpp80) REVERT: C 378 LYS cc_start: 0.8623 (mppt) cc_final: 0.8255 (mmtp) REVERT: C 408 ARG cc_start: 0.9282 (pmt-80) cc_final: 0.8904 (pmt-80) REVERT: C 456 PHE cc_start: 0.7833 (m-80) cc_final: 0.7434 (m-10) REVERT: C 1072 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: F 54 PHE cc_start: 0.8985 (t80) cc_final: 0.8476 (t80) REVERT: F 76 MET cc_start: 0.4768 (pmt) cc_final: 0.4242 (pmm) REVERT: G 54 PHE cc_start: 0.9068 (t80) cc_final: 0.8489 (t80) REVERT: G 76 MET cc_start: 0.4965 (pmt) cc_final: 0.4548 (pmm) REVERT: H 52 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7852 (ttp-110) REVERT: H 54 PHE cc_start: 0.9269 (t80) cc_final: 0.8853 (t80) REVERT: H 55 ASP cc_start: 0.8987 (t0) cc_final: 0.8332 (p0) REVERT: H 76 MET cc_start: 0.5083 (OUTLIER) cc_final: 0.4600 (pmm) outliers start: 33 outliers final: 19 residues processed: 161 average time/residue: 0.6129 time to fit residues: 116.0638 Evaluate side-chains 152 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 18 LEU 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 645 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1145 LEU 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 76 MET 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: 0.6980 chunk 110 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 304 optimal weight: 0.6980 chunk 219 optimal weight: 9.9990 chunk 54 optimal weight: 0.0970 chunk 111 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.100265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.058421 restraints weight = 70299.763| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.32 r_work: 0.2809 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28926 Z= 0.108 Angle : 0.575 11.568 39480 Z= 0.287 Chirality : 0.046 0.447 4638 Planarity : 0.004 0.067 4992 Dihedral : 4.121 17.436 3756 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.95 % Allowed : 12.36 % Favored : 86.69 % 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: 0.48 (0.14), residues: 3456 helix: 2.35 (0.20), residues: 672 sheet: 0.26 (0.17), residues: 888 loop : -0.37 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 214 TYR 0.017 0.001 TYR A 265 PHE 0.026 0.001 PHE B 168 TRP 0.025 0.001 TRP A 258 HIS 0.002 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (28812) covalent geometry : angle 0.54408 / 0.28 (39186) SS BOND : bond 0.00149 / 0.10 ( 48) SS BOND : angle 0.45978 / 0.31 ( 96) hydrogen bonds : bond 0.03491 / 2.33 ( 1168) hydrogen bonds : angle 4.99776 / 3.53 ( 3342) link_BETA1-4 : bond 0.00314 / 0.23 ( 15) link_BETA1-4 : angle 0.86888 / 0.58 ( 45) link_NAG-ASN : bond 0.00534 / 0.34 ( 51) link_NAG-ASN : angle 3.00387 / 2.05 ( 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 167 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8132 (m-10) cc_final: 0.7657 (m-80) REVERT: A 214 ARG cc_start: 0.8905 (mmm160) cc_final: 0.8564 (tpt170) REVERT: A 462 LYS cc_start: 0.8989 (mtmm) cc_final: 0.8723 (pmmt) REVERT: A 489 TYR cc_start: 0.8639 (m-80) cc_final: 0.8365 (m-80) REVERT: A 1072 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: B 186 PHE cc_start: 0.8173 (m-10) cc_final: 0.7755 (m-80) REVERT: B 378 LYS cc_start: 0.8634 (mppt) cc_final: 0.8234 (mmtt) REVERT: B 408 ARG cc_start: 0.9313 (pmt-80) cc_final: 0.8911 (ppt170) REVERT: B 456 PHE cc_start: 0.8836 (m-80) cc_final: 0.8054 (m-10) REVERT: B 489 TYR cc_start: 0.8609 (m-80) cc_final: 0.8212 (m-80) REVERT: B 492 LEU cc_start: 0.8919 (tp) cc_final: 0.8701 (tm) REVERT: B 740 MET cc_start: 0.9306 (tpp) cc_final: 0.9078 (tpt) REVERT: B 902 MET cc_start: 0.9078 (mmm) cc_final: 0.8699 (tpt) REVERT: B 950 ASP cc_start: 0.8738 (m-30) cc_final: 0.8525 (m-30) REVERT: B 1072 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8529 (mp0) REVERT: C 24 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8543 (mm) REVERT: C 140 PHE cc_start: 0.9224 (p90) cc_final: 0.8880 (p90) REVERT: C 186 PHE cc_start: 0.8146 (m-10) cc_final: 0.7831 (m-80) REVERT: C 378 LYS cc_start: 0.8618 (mppt) cc_final: 0.8268 (mptt) REVERT: C 408 ARG cc_start: 0.9304 (pmt-80) cc_final: 0.8919 (pmt-80) REVERT: C 950 ASP cc_start: 0.8770 (m-30) cc_final: 0.8540 (m-30) REVERT: F 54 PHE cc_start: 0.9039 (t80) cc_final: 0.8667 (t80) REVERT: F 55 ASP cc_start: 0.9065 (t0) cc_final: 0.8453 (p0) REVERT: F 76 MET cc_start: 0.4765 (pmt) cc_final: 0.4261 (pmm) REVERT: G 2 VAL cc_start: 0.1526 (OUTLIER) cc_final: 0.1238 (m) REVERT: G 52 ARG cc_start: 0.8446 (ttm110) cc_final: 0.8037 (mtm-85) REVERT: G 54 PHE cc_start: 0.9020 (t80) cc_final: 0.8399 (t80) REVERT: G 55 ASP cc_start: 0.9154 (t0) cc_final: 0.8700 (p0) REVERT: G 76 MET cc_start: 0.4995 (pmt) cc_final: 0.4559 (pmm) REVERT: H 52 ARG cc_start: 0.8317 (ttm110) cc_final: 0.7865 (ttp-110) REVERT: H 54 PHE cc_start: 0.9271 (t80) cc_final: 0.8846 (t80) REVERT: H 55 ASP cc_start: 0.8979 (t0) cc_final: 0.8263 (p0) REVERT: H 76 MET cc_start: 0.4941 (OUTLIER) cc_final: 0.4515 (pmm) outliers start: 29 outliers final: 17 residues processed: 160 average time/residue: 0.6384 time to fit residues: 120.7184 Evaluate side-chains 151 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 645 THR Chi-restraints excluded: chain C residue 1145 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 21 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 chunk 199 optimal weight: 0.6980 chunk 125 optimal weight: 30.0000 chunk 197 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** G 74 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 = 0.3866 r_free = 0.3866 target = 0.100070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058138 restraints weight = 70909.355| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.34 r_work: 0.2784 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3383 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= 0.146 Angle : 0.583 11.736 39480 Z= 0.292 Chirality : 0.046 0.441 4638 Planarity : 0.004 0.063 4992 Dihedral : 4.130 16.993 3756 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.92 % Allowed : 12.62 % Favored : 86.46 % 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: 0.49 (0.14), residues: 3456 helix: 2.36 (0.20), residues: 669 sheet: 0.29 (0.17), residues: 888 loop : -0.37 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 214 TYR 0.018 0.001 TYR A 265 PHE 0.021 0.001 PHE B 565 TRP 0.033 0.001 TRP B 258 HIS 0.003 0.000 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (28812) covalent geometry : angle 0.55293 / 0.29 (39186) SS BOND : bond 0.00195 / 0.14 ( 48) SS BOND : angle 0.49202 / 0.34 ( 96) hydrogen bonds : bond 0.03683 / 2.44 ( 1168) hydrogen bonds : angle 5.01880 / 3.55 ( 3342) link_BETA1-4 : bond 0.00256 / 0.19 ( 15) link_BETA1-4 : angle 0.90603 / 0.60 ( 45) link_NAG-ASN : bond 0.00498 / 0.32 ( 51) link_NAG-ASN : angle 2.99145 / 2.06 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8127.11 seconds wall clock time: 139 minutes 35.96 seconds (8375.96 seconds total)