Starting phenix.real_space_refine on Fri Mar 6 01:40:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zhd_11218/03_2026/6zhd_11218.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zhd_11218/03_2026/6zhd_11218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zhd_11218/03_2026/6zhd_11218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zhd_11218/03_2026/6zhd_11218.map" model { file = "/net/cci-nas-00/data/ceres_data/6zhd_11218/03_2026/6zhd_11218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zhd_11218/03_2026/6zhd_11218.cif" } resolution = 3.7 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 117 5.16 5 C 17150 2.51 5 N 4408 2.21 5 O 5252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26927 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7646 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 49, 'TRANS': 937} Chain breaks: 9 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7677 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 7659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7659 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 7 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 1007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} bond proxies already assigned to first conformer: 1019 Chain: "E" Number of atoms: 1007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} bond proxies already assigned to first conformer: 1019 Chain: "F" Number of atoms: 1007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} bond proxies already assigned to first conformer: 1019 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.20, per 1000 atoms: 0.27 Number of scatterers: 26927 At special positions: 0 Unit cell: (129.32, 135.68, 218.36, 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 117 16.00 O 5252 8.00 N 4408 7.00 C 17150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 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=2.03 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=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.06 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.05 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=2.06 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=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.07 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.06 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.05 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1310 " - " ASN A 603 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 657 " " NAG A1313 " - " ASN A 709 " " NAG A1318 " - " ASN A1074 " " NAG A1323 " - " ASN A 165 " " NAG A1324 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1313 " - " ASN B1074 " " NAG B1318 " - " ASN B 343 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 61 " " NAG C1405 " - " ASN C 234 " " NAG C1408 " - " ASN C 331 " " NAG C1409 " - " ASN C 603 " " NAG C1410 " - " ASN C 616 " " NAG C1411 " - " ASN C 657 " " NAG C1424 " - " ASN C 165 " " NAG G 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 282 " " NAG J 1 " - " ASN A 331 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 122 " " NAG T 1 " - " ASN C 282 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6260 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 54 sheets defined 25.5% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.960A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.275A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.650A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.097A 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 removed outlier: 3.673A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.669A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.405A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.093A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.033A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.275A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.675A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.649A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.114A 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 removed outlier: 3.696A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.636A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.413A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.092A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.025A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.283A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 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 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.645A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.103A 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 removed outlier: 3.661A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.635A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.324A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.085A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 31 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'E' and resid 28 through 31 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 105 through 111 Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.647A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.568A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.581A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.549A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 327 removed outlier: 6.655A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.489A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.559A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.864A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.955A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.193A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.681A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.378A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.654A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.575A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.584A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.585A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.129A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.476A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.548A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.857A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.798A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.194A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.760A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.379A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.652A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.878A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.736A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.580A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.137A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.487A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.558A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.865A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.952A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.187A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.377A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 2 through 7 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.183A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.183A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 2 through 7 Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.183A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.183A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 2 through 7 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.183A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N SER F 126 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N MET F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N PHE 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: 6.183A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N SER F 126 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N MET F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) 1189 hydrogen bonds defined for protein. 3156 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: 7.50 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4910 1.32 - 1.45: 8300 1.45 - 1.58: 14161 1.58 - 1.70: 0 1.70 - 1.83: 150 Bond restraints: 27521 Sorted by residual: bond pdb=" CA SER A 968 " pdb=" CB SER A 968 " ideal model delta sigma weight residual 1.531 1.479 0.052 1.58e-02 4.01e+03 1.09e+01 bond pdb=" C PHE B 759 " pdb=" O PHE B 759 " ideal model delta sigma weight residual 1.236 1.199 0.038 1.18e-02 7.18e+03 1.01e+01 bond pdb=" CA SER B 968 " pdb=" CB SER B 968 " ideal model delta sigma weight residual 1.531 1.481 0.050 1.58e-02 4.01e+03 9.94e+00 bond pdb=" CA SER C 596 " pdb=" CB SER C 596 " ideal model delta sigma weight residual 1.532 1.481 0.051 1.74e-02 3.30e+03 8.49e+00 bond pdb=" CA SER B1003 " pdb=" CB SER B1003 " ideal model delta sigma weight residual 1.528 1.483 0.045 1.56e-02 4.11e+03 8.49e+00 ... (remaining 27516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 31716 1.98 - 3.96: 5093 3.96 - 5.94: 551 5.94 - 7.92: 69 7.92 - 9.90: 16 Bond angle restraints: 37445 Sorted by residual: angle pdb=" C PRO C 600 " pdb=" CA PRO C 600 " pdb=" CB PRO C 600 " ideal model delta sigma weight residual 111.44 101.87 9.57 1.51e+00 4.39e-01 4.02e+01 angle pdb=" C GLN A 913 " pdb=" CA GLN A 913 " pdb=" CB GLN A 913 " ideal model delta sigma weight residual 110.85 100.95 9.90 1.70e+00 3.46e-01 3.39e+01 angle pdb=" CA THR B 961 " pdb=" CB THR B 961 " pdb=" OG1 THR B 961 " ideal model delta sigma weight residual 109.60 101.11 8.49 1.50e+00 4.44e-01 3.21e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.24 -6.54 1.22e+00 6.72e-01 2.87e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.20 -6.50 1.22e+00 6.72e-01 2.84e+01 ... (remaining 37440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 15778 17.55 - 35.10: 1107 35.10 - 52.65: 218 52.65 - 70.20: 46 70.20 - 87.76: 26 Dihedral angle restraints: 17175 sinusoidal: 7424 harmonic: 9751 Sorted by residual: 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 -179.24 -87.76 1 1.00e+01 1.00e-02 9.22e+01 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 -179.78 -87.22 1 1.00e+01 1.00e-02 9.13e+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 -179.82 -87.18 1 1.00e+01 1.00e-02 9.13e+01 ... (remaining 17172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.201: 4235 0.201 - 0.402: 193 0.402 - 0.603: 11 0.603 - 0.804: 0 0.804 - 1.006: 1 Chirality restraints: 4440 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.24e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.18e+02 ... (remaining 4437 not shown) Planarity restraints: 4780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1410 " 0.292 2.00e-02 2.50e+03 2.48e-01 7.69e+02 pdb=" C7 NAG C1410 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG C1410 " 0.180 2.00e-02 2.50e+03 pdb=" N2 NAG C1410 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG C1410 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.225 2.00e-02 2.50e+03 1.84e-01 4.24e+02 pdb=" C7 NAG L 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.295 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " 0.221 2.00e-02 2.50e+03 1.81e-01 4.08e+02 pdb=" C7 NAG B1308 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " -0.290 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " -0.027 2.00e-02 2.50e+03 ... (remaining 4777 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 83 2.56 - 3.14: 21053 3.14 - 3.73: 40323 3.73 - 4.31: 61219 4.31 - 4.90: 98348 Nonbonded interactions: 221026 Sorted by model distance: nonbonded pdb=" O ASN A 81 " pdb=" NE2 GLN A 239 " model vdw 1.973 3.120 nonbonded pdb=" NH1 ARG C 328 " pdb=" OD2 ASP C 578 " model vdw 2.190 3.120 nonbonded pdb=" OH TYR B 200 " pdb=" OH TYR C 396 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR B 200 " pdb=" OE1 GLU C 516 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLU E 6 " pdb=" OE1 GLN E 119 " model vdw 2.240 3.040 ... (remaining 221021 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 110 or (resid 111 through 113 and (name N or name CA or name C or name O or \ name CB )) or resid 116 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 140 \ or resid 166 through 168 or (resid 169 and (name N or name CA or name C or name \ O or name CB )) or resid 170 through 172 or resid 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 210 or (resid \ 211 through 215 and (name N or name CA or name C or name O or name CB )) or res \ id 216 through 241 or (resid 242 through 263 and (name N or name CA or name C or \ name O or name CB )) or resid 265 through 280 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 570 o \ r (resid 571 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 72 through 581 or (resid 582 through 583 and (name N or name CA or name C or nam \ e O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA \ or name C or name O or name CB )) or resid 587 through 660 or (resid 661 and (na \ me N or name CA or name C or name O or name CB )) or resid 662 through 676 or re \ sid 690 through 747 or (resid 748 and (name N or name CA or name C or name O or \ name CB )) or resid 749 through 810 or (resid 811 and (name N or name CA or name \ C or name O or name CB )) or resid 812 through 827 or resid 856 through 939 or \ (resid 940 and (name N or name CA or name C or name O or name CB )) or resid 941 \ through 984 or (resid 985 and (name N or name CA or name C or name O or name CB \ )) or resid 986 through 1143 or (resid 1144 through 1146 and (name N or name CA \ or name C or name O or name CB )) or resid 1147 through 1324)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 111 or (resid 112 through 113 and (name N or name CA o \ r name C or name O or name CB )) or resid 116 through 124 or (resid 125 and (nam \ e N or name CA or name C or name O or name CB )) or resid 126 through 131 or (re \ sid 132 and (name N or name CA or name C or name O or name CB )) or resid 133 or \ (resid 134 through 138 and (name N or name CA or name C or name O or name CB )) \ or resid 139 through 140 or resid 166 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 171 or (resid 172 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 1 \ 96 or resid 200 through 210 or (resid 211 and (name N or name CA or name C or na \ me O or name CB )) or (resid 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 263 or resid 265 through 528 or (resid 529 and (n \ ame N or name CA or name C or name O or name CB )) or resid 530 through 660 or ( \ resid 661 and (name N or name CA or name C or name O or name CB )) or resid 662 \ through 747 or (resid 748 and (name N or name CA or name C or name O or name CB \ )) or resid 749 through 810 or (resid 811 and (name N or name CA or name C or na \ me O or name CB )) or resid 812 through 827 or resid 856 through 939 or (resid 9 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 941 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or r \ esid 986 through 1141 or (resid 1142 and (name N or name CA or name C or name O \ or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N \ or name CA or name C or name O or name CB )) or resid 1147 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 124 or (resid 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 128 or (resid 129 an \ d (name N or name CA or name C or name O or name CB )) or resid 130 through 133 \ or (resid 134 through 138 and (name N or name CA or name C or name O or name CB \ )) or resid 139 through 140 or resid 166 through 187 or (resid 188 and (name N o \ r name CA or name C or name O or name CB )) or resid 189 through 196 or resid 20 \ 0 through 211 or (resid 215 and (name N or name CA or name C or name O or name C \ B )) or resid 216 through 528 or (resid 529 and (name N or name CA or name C or \ name O or name CB )) or resid 530 through 567 or (resid 568 and (name N or name \ CA or name C or name O or name CB )) or resid 569 through 570 or (resid 571 and \ (name N or name CA or name C or name O or name CB )) or resid 572 through 581 or \ (resid 582 through 583 and (name N or name CA or name C or name O or name CB )) \ or resid 584 through 585 or (resid 586 and (name N or name CA or name C or name \ O or name CB )) or resid 587 through 1141 or (resid 1142 and (name N or name CA \ or name C or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and \ (name N or name CA or name C or name O or name CB )) or resid 1147 through 1424 \ )) } ncs_group { reference = (chain 'D' and (resid 1 through 88 or resid 90 through 128)) selection = (chain 'E' and (resid 1 through 88 or resid 90 through 128)) selection = (chain 'F' and (resid 1 through 88 or resid 90 through 128)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 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: 0.040 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.360 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 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 : 0.008 0.052 27629 Z= 0.528 Angle : 1.482 12.056 37727 Z= 0.951 Chirality : 0.103 1.006 4440 Planarity : 0.011 0.248 4734 Dihedral : 12.792 86.121 10789 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 0.74 % Allowed : 4.36 % Favored : 94.90 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.92 (0.13), residues: 3296 helix: -0.62 (0.18), residues: 671 sheet: 0.18 (0.17), residues: 812 loop : -0.95 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG B 328 TYR 0.051 0.006 TYR A 28 PHE 0.043 0.006 PHE B 565 TRP 0.019 0.005 TRP C 64 HIS 0.062 0.004 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00847 (27521) covalent geometry : angle 1.46105 (37445) SS BOND : bond 0.01630 ( 42) SS BOND : angle 3.28998 ( 84) hydrogen bonds : bond 0.13363 ( 1177) hydrogen bonds : angle 6.96408 ( 3156) link_BETA1-4 : bond 0.00657 ( 20) link_BETA1-4 : angle 2.47361 ( 60) link_NAG-ASN : bond 0.01032 ( 46) link_NAG-ASN : angle 3.43967 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.9376 (p90) cc_final: 0.9101 (t80) REVERT: A 386 LYS cc_start: 0.9649 (mmpt) cc_final: 0.9410 (ptpt) REVERT: A 979 ASP cc_start: 0.9664 (m-30) cc_final: 0.9165 (t0) REVERT: A 1107 ARG cc_start: 0.9626 (OUTLIER) cc_final: 0.9347 (ptp-170) REVERT: B 117 LEU cc_start: 0.9409 (mp) cc_final: 0.9144 (tt) REVERT: B 224 GLU cc_start: 0.9652 (OUTLIER) cc_final: 0.9408 (pm20) REVERT: B 229 LEU cc_start: 0.9150 (mt) cc_final: 0.8692 (tp) REVERT: B 869 MET cc_start: 0.9391 (mtp) cc_final: 0.9002 (mtp) REVERT: C 117 LEU cc_start: 0.9374 (mp) cc_final: 0.9038 (tp) REVERT: C 869 MET cc_start: 0.9411 (mtt) cc_final: 0.9181 (mpp) REVERT: D 18 LEU cc_start: 0.4388 (tp) cc_final: 0.3800 (tt) REVERT: D 48 VAL cc_start: 0.8833 (t) cc_final: 0.8600 (t) REVERT: D 73 ASP cc_start: 0.9134 (t0) cc_final: 0.8798 (p0) REVERT: D 84 ASN cc_start: 0.6698 (m-40) cc_final: 0.6312 (m-40) REVERT: D 95 TYR cc_start: 0.9281 (m-80) cc_final: 0.8991 (m-80) REVERT: E 27 ARG cc_start: 0.8659 (ttt180) cc_final: 0.7939 (ptt90) REVERT: E 83 MET cc_start: 0.5893 (mtp) cc_final: 0.5241 (mpp) REVERT: E 88 TYR cc_start: 0.8369 (t80) cc_final: 0.8120 (m-10) REVERT: E 102 VAL cc_start: 0.9046 (t) cc_final: 0.8836 (t) REVERT: E 112 TRP cc_start: 0.8654 (t-100) cc_final: 0.8354 (t-100) REVERT: F 3 GLN cc_start: 0.9304 (tt0) cc_final: 0.9099 (mp10) REVERT: F 67 ARG cc_start: 0.8136 (mtm110) cc_final: 0.7540 (mtm110) REVERT: F 81 LEU cc_start: 0.9490 (tp) cc_final: 0.9041 (tp) REVERT: F 83 MET cc_start: 0.8899 (mtp) cc_final: 0.8631 (mpp) REVERT: F 115 ASP cc_start: 0.8520 (m-30) cc_final: 0.8226 (m-30) outliers start: 21 outliers final: 1 residues processed: 271 average time/residue: 0.2141 time to fit residues: 86.6754 Evaluate side-chains 126 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 804 GLN A 935 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 388 ASN C 607 GLN C 901 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN D 82 GLN E 1 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.057069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.036151 restraints weight = 206818.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.037835 restraints weight = 79685.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.038929 restraints weight = 45401.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.039620 restraints weight = 31414.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.040114 restraints weight = 24828.542| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27629 Z= 0.179 Angle : 0.649 10.813 37727 Z= 0.329 Chirality : 0.044 0.211 4440 Planarity : 0.004 0.035 4734 Dihedral : 6.586 58.983 5002 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.06 % Allowed : 7.07 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3296 helix: 1.11 (0.20), residues: 687 sheet: 0.34 (0.17), residues: 805 loop : -0.41 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 38 TYR 0.024 0.001 TYR B 200 PHE 0.014 0.001 PHE C 135 TRP 0.026 0.001 TRP D 117 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00386 (27521) covalent geometry : angle 0.63108 (37445) SS BOND : bond 0.00264 ( 42) SS BOND : angle 0.79230 ( 84) hydrogen bonds : bond 0.04759 ( 1177) hydrogen bonds : angle 5.69011 ( 3156) link_BETA1-4 : bond 0.00297 ( 20) link_BETA1-4 : angle 1.56816 ( 60) link_NAG-ASN : bond 0.00346 ( 46) link_NAG-ASN : angle 2.37147 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 912 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8746 (p) REVERT: A 979 ASP cc_start: 0.9201 (m-30) cc_final: 0.8645 (t0) REVERT: B 117 LEU cc_start: 0.9169 (mp) cc_final: 0.8848 (tt) REVERT: B 229 LEU cc_start: 0.9023 (mt) cc_final: 0.8516 (tp) REVERT: B 869 MET cc_start: 0.9200 (mtp) cc_final: 0.8766 (mtp) REVERT: C 104 TRP cc_start: 0.8704 (m-90) cc_final: 0.8312 (m-90) REVERT: C 117 LEU cc_start: 0.8793 (mp) cc_final: 0.8417 (tt) REVERT: C 427 ASP cc_start: 0.9207 (m-30) cc_final: 0.8800 (t0) REVERT: C 571 ASP cc_start: 0.8053 (t70) cc_final: 0.7486 (t70) REVERT: C 740 MET cc_start: 0.9131 (tpp) cc_final: 0.8568 (tpp) REVERT: C 756 TYR cc_start: 0.9269 (m-80) cc_final: 0.8945 (m-80) REVERT: C 869 MET cc_start: 0.9258 (mtt) cc_final: 0.9003 (mtm) REVERT: C 990 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8760 (pp20) REVERT: D 34 MET cc_start: 0.7045 (tpp) cc_final: 0.6732 (tpt) REVERT: D 73 ASP cc_start: 0.9216 (t0) cc_final: 0.8812 (p0) REVERT: D 76 LYS cc_start: 0.9376 (tptp) cc_final: 0.9126 (tptp) REVERT: D 82 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6920 (mm-40) REVERT: D 117 TRP cc_start: 0.7473 (m-90) cc_final: 0.6747 (m-90) REVERT: E 27 ARG cc_start: 0.8153 (ttt180) cc_final: 0.7837 (ptt90) REVERT: F 12 MET cc_start: 0.8652 (mmm) cc_final: 0.7772 (tpp) REVERT: F 34 MET cc_start: 0.8901 (mmm) cc_final: 0.8679 (mmm) REVERT: F 46 GLU cc_start: 0.8943 (tt0) cc_final: 0.8692 (pm20) REVERT: F 81 LEU cc_start: 0.9418 (tp) cc_final: 0.8820 (tp) REVERT: F 83 MET cc_start: 0.8674 (mtp) cc_final: 0.8422 (mpp) outliers start: 30 outliers final: 15 residues processed: 164 average time/residue: 0.1813 time to fit residues: 47.1201 Evaluate side-chains 124 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain D residue 82 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 153 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 313 optimal weight: 30.0000 chunk 262 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 955 ASN A1048 HIS B 901 GLN B1048 HIS C 955 ASN C1005 GLN C1048 HIS D 82 GLN E 1 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.056868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.036012 restraints weight = 195289.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.037651 restraints weight = 77426.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.038732 restraints weight = 44654.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.039433 restraints weight = 31145.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.039898 restraints weight = 24534.389| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27629 Z= 0.142 Angle : 0.559 9.779 37727 Z= 0.284 Chirality : 0.043 0.210 4440 Planarity : 0.003 0.049 4734 Dihedral : 5.676 58.741 4993 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.09 % Allowed : 8.23 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3296 helix: 1.87 (0.20), residues: 675 sheet: 0.33 (0.17), residues: 839 loop : -0.17 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.022 0.001 TYR D 116 PHE 0.017 0.001 PHE B 168 TRP 0.016 0.001 TRP D 117 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00297 (27521) covalent geometry : angle 0.54329 (37445) SS BOND : bond 0.00295 ( 42) SS BOND : angle 0.76471 ( 84) hydrogen bonds : bond 0.04104 ( 1177) hydrogen bonds : angle 5.35122 ( 3156) link_BETA1-4 : bond 0.00224 ( 20) link_BETA1-4 : angle 1.47787 ( 60) link_NAG-ASN : bond 0.00227 ( 46) link_NAG-ASN : angle 2.00294 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.9039 (tpp80) REVERT: A 912 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8787 (p) REVERT: A 979 ASP cc_start: 0.9204 (m-30) cc_final: 0.8661 (t0) REVERT: B 117 LEU cc_start: 0.9162 (mp) cc_final: 0.8912 (tt) REVERT: B 229 LEU cc_start: 0.9031 (mt) cc_final: 0.8533 (tp) REVERT: B 869 MET cc_start: 0.9199 (mtp) cc_final: 0.8819 (mtp) REVERT: C 117 LEU cc_start: 0.8709 (mp) cc_final: 0.8389 (tt) REVERT: C 427 ASP cc_start: 0.9229 (m-30) cc_final: 0.8853 (t0) REVERT: C 571 ASP cc_start: 0.8000 (t70) cc_final: 0.7422 (t70) REVERT: C 740 MET cc_start: 0.9220 (tpp) cc_final: 0.8809 (tpp) REVERT: D 73 ASP cc_start: 0.9201 (t0) cc_final: 0.8841 (p0) REVERT: D 81 LEU cc_start: 0.5461 (tp) cc_final: 0.5130 (mp) REVERT: D 117 TRP cc_start: 0.7520 (m-90) cc_final: 0.6756 (m-90) REVERT: E 27 ARG cc_start: 0.8193 (ttt180) cc_final: 0.7832 (ptt90) REVERT: F 46 GLU cc_start: 0.8951 (tt0) cc_final: 0.8725 (pm20) REVERT: F 81 LEU cc_start: 0.9426 (tp) cc_final: 0.8823 (tp) outliers start: 31 outliers final: 16 residues processed: 150 average time/residue: 0.1749 time to fit residues: 42.0234 Evaluate side-chains 128 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 1 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 141 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 309 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 8 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A1011 GLN B 655 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** 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 = 0.3270 r_free = 0.3270 target = 0.055257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.034529 restraints weight = 192749.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.036031 restraints weight = 79732.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.037037 restraints weight = 47189.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.037691 restraints weight = 33624.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.038097 restraints weight = 26966.119| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 27629 Z= 0.271 Angle : 0.619 9.642 37727 Z= 0.309 Chirality : 0.043 0.214 4440 Planarity : 0.004 0.056 4734 Dihedral : 5.380 57.689 4993 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.69 % Allowed : 8.37 % Favored : 89.94 % 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: 0.63 (0.14), residues: 3296 helix: 2.10 (0.21), residues: 667 sheet: 0.29 (0.17), residues: 855 loop : -0.11 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 67 TYR 0.025 0.001 TYR F 88 PHE 0.011 0.001 PHE A 133 TRP 0.013 0.001 TRP D 117 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00576 (27521) covalent geometry : angle 0.60444 (37445) SS BOND : bond 0.00313 ( 42) SS BOND : angle 0.68548 ( 84) hydrogen bonds : bond 0.04150 ( 1177) hydrogen bonds : angle 5.38834 ( 3156) link_BETA1-4 : bond 0.00300 ( 20) link_BETA1-4 : angle 1.59087 ( 60) link_NAG-ASN : bond 0.00473 ( 46) link_NAG-ASN : angle 2.07734 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 110 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9189 (m) REVERT: A 912 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.8911 (p) REVERT: A 979 ASP cc_start: 0.9244 (m-30) cc_final: 0.8710 (t0) REVERT: B 117 LEU cc_start: 0.9255 (mp) cc_final: 0.8871 (tt) REVERT: B 229 LEU cc_start: 0.9148 (mt) cc_final: 0.8654 (tp) REVERT: B 468 ILE cc_start: 0.9645 (OUTLIER) cc_final: 0.9241 (mp) REVERT: B 740 MET cc_start: 0.9000 (ttt) cc_final: 0.8694 (ttt) REVERT: B 869 MET cc_start: 0.9197 (mtp) cc_final: 0.8832 (mtp) REVERT: C 427 ASP cc_start: 0.9232 (m-30) cc_final: 0.8907 (t0) REVERT: C 571 ASP cc_start: 0.7949 (t70) cc_final: 0.7457 (t70) REVERT: C 957 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.9043 (tt0) REVERT: D 12 MET cc_start: 0.1436 (pmm) cc_final: 0.0928 (ptp) REVERT: D 34 MET cc_start: 0.6263 (tpp) cc_final: 0.5905 (tpt) REVERT: D 73 ASP cc_start: 0.9230 (t0) cc_final: 0.8842 (p0) REVERT: D 117 TRP cc_start: 0.7520 (m-90) cc_final: 0.6664 (m-90) REVERT: F 81 LEU cc_start: 0.9082 (tp) cc_final: 0.8813 (tp) outliers start: 48 outliers final: 31 residues processed: 154 average time/residue: 0.1627 time to fit residues: 41.2158 Evaluate side-chains 131 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 29 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 199 optimal weight: 5.9990 chunk 313 optimal weight: 40.0000 chunk 56 optimal weight: 1.9990 chunk 327 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 243 optimal weight: 0.6980 chunk 326 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 955 ASN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.056616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.035640 restraints weight = 240415.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.037356 restraints weight = 86737.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.038482 restraints weight = 48235.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.039211 restraints weight = 33002.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.039724 restraints weight = 25747.487| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27629 Z= 0.101 Angle : 0.522 9.731 37727 Z= 0.265 Chirality : 0.043 0.220 4440 Planarity : 0.003 0.060 4734 Dihedral : 4.857 55.353 4993 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.30 % Allowed : 8.97 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3296 helix: 2.29 (0.21), residues: 667 sheet: 0.35 (0.17), residues: 855 loop : -0.01 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 45 TYR 0.020 0.001 TYR F 88 PHE 0.014 0.001 PHE D 29 TRP 0.024 0.001 TRP D 36 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00214 (27521) covalent geometry : angle 0.51142 (37445) SS BOND : bond 0.00190 ( 42) SS BOND : angle 0.45678 ( 84) hydrogen bonds : bond 0.03681 ( 1177) hydrogen bonds : angle 5.08084 ( 3156) link_BETA1-4 : bond 0.00337 ( 20) link_BETA1-4 : angle 1.23241 ( 60) link_NAG-ASN : bond 0.00231 ( 46) link_NAG-ASN : angle 1.67655 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.9140 (p) REVERT: A 387 LEU cc_start: 0.9665 (mt) cc_final: 0.9435 (mp) REVERT: A 697 MET cc_start: 0.8922 (ttm) cc_final: 0.8587 (ttm) REVERT: A 912 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8853 (p) REVERT: A 979 ASP cc_start: 0.9225 (m-30) cc_final: 0.8681 (t0) REVERT: B 117 LEU cc_start: 0.9228 (mp) cc_final: 0.8847 (tt) REVERT: B 224 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8879 (mp0) REVERT: B 229 LEU cc_start: 0.9140 (mt) cc_final: 0.8609 (tp) REVERT: B 468 ILE cc_start: 0.9671 (OUTLIER) cc_final: 0.9284 (mp) REVERT: B 740 MET cc_start: 0.9007 (ttt) cc_final: 0.8698 (ttt) REVERT: C 427 ASP cc_start: 0.9210 (m-30) cc_final: 0.8866 (t0) REVERT: C 468 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7368 (mm) REVERT: C 571 ASP cc_start: 0.7840 (t70) cc_final: 0.7345 (t70) REVERT: C 740 MET cc_start: 0.9238 (tpp) cc_final: 0.8607 (tpp) REVERT: C 900 MET cc_start: 0.9029 (mtp) cc_final: 0.8741 (mtt) REVERT: C 957 GLN cc_start: 0.9267 (mt0) cc_final: 0.9027 (tt0) REVERT: D 73 ASP cc_start: 0.9234 (t0) cc_final: 0.8838 (p0) REVERT: D 117 TRP cc_start: 0.7358 (m-90) cc_final: 0.6554 (m-90) REVERT: E 108 ASP cc_start: 0.7337 (m-30) cc_final: 0.6989 (m-30) REVERT: F 46 GLU cc_start: 0.8217 (pm20) cc_final: 0.7872 (pm20) REVERT: F 81 LEU cc_start: 0.9166 (tp) cc_final: 0.8912 (tp) outliers start: 37 outliers final: 19 residues processed: 150 average time/residue: 0.1916 time to fit residues: 45.9048 Evaluate side-chains 131 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain E residue 112 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 331 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 290 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.055086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.034607 restraints weight = 190186.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.036105 restraints weight = 78864.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.037092 restraints weight = 46609.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.037749 restraints weight = 33087.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.038152 restraints weight = 26437.343| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27629 Z= 0.233 Angle : 0.590 9.573 37727 Z= 0.293 Chirality : 0.042 0.239 4440 Planarity : 0.003 0.038 4734 Dihedral : 4.831 55.587 4993 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.72 % Allowed : 8.97 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3296 helix: 2.28 (0.21), residues: 679 sheet: 0.35 (0.17), residues: 868 loop : -0.05 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 567 TYR 0.021 0.001 TYR E 104 PHE 0.013 0.001 PHE C 802 TRP 0.012 0.001 TRP F 53 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00496 (27521) covalent geometry : angle 0.57696 (37445) SS BOND : bond 0.00285 ( 42) SS BOND : angle 0.63843 ( 84) hydrogen bonds : bond 0.03922 ( 1177) hydrogen bonds : angle 5.17937 ( 3156) link_BETA1-4 : bond 0.00255 ( 20) link_BETA1-4 : angle 1.55298 ( 60) link_NAG-ASN : bond 0.00434 ( 46) link_NAG-ASN : angle 1.90482 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 99 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8023 (mmt90) REVERT: A 63 THR cc_start: 0.9410 (OUTLIER) cc_final: 0.9171 (m) REVERT: A 387 LEU cc_start: 0.9696 (mt) cc_final: 0.9426 (mt) REVERT: A 912 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.8894 (p) REVERT: A 979 ASP cc_start: 0.9254 (m-30) cc_final: 0.8741 (t0) REVERT: A 1017 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8527 (tm-30) REVERT: B 224 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8699 (pm20) REVERT: B 229 LEU cc_start: 0.9177 (mt) cc_final: 0.8704 (tp) REVERT: B 468 ILE cc_start: 0.9695 (OUTLIER) cc_final: 0.9339 (mp) REVERT: B 740 MET cc_start: 0.9017 (ttt) cc_final: 0.8775 (ttt) REVERT: C 468 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7645 (mm) REVERT: C 571 ASP cc_start: 0.7891 (t70) cc_final: 0.7410 (t70) REVERT: C 740 MET cc_start: 0.9192 (tpp) cc_final: 0.8943 (tpp) REVERT: C 900 MET cc_start: 0.9092 (mtp) cc_final: 0.8858 (mtt) REVERT: D 73 ASP cc_start: 0.9226 (t0) cc_final: 0.8831 (p0) REVERT: D 117 TRP cc_start: 0.7443 (m-90) cc_final: 0.6600 (m-90) REVERT: E 27 ARG cc_start: 0.8226 (ttt180) cc_final: 0.7810 (ptt180) REVERT: F 12 MET cc_start: 0.8626 (mmm) cc_final: 0.8329 (tpp) REVERT: F 81 LEU cc_start: 0.9155 (tp) cc_final: 0.8885 (tp) outliers start: 49 outliers final: 32 residues processed: 144 average time/residue: 0.1733 time to fit residues: 41.8153 Evaluate side-chains 130 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 259 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 323 optimal weight: 7.9990 chunk 296 optimal weight: 5.9990 chunk 322 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 519 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.054954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.034792 restraints weight = 172577.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.036250 restraints weight = 74404.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.037190 restraints weight = 44665.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.037736 restraints weight = 31987.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.038196 restraints weight = 26267.645| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27629 Z= 0.237 Angle : 0.582 10.269 37727 Z= 0.292 Chirality : 0.042 0.218 4440 Planarity : 0.003 0.037 4734 Dihedral : 4.763 54.980 4993 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.62 % Allowed : 9.64 % Favored : 88.74 % 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: 0.71 (0.15), residues: 3296 helix: 2.28 (0.21), residues: 679 sheet: 0.28 (0.17), residues: 868 loop : -0.09 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 567 TYR 0.018 0.001 TYR B 200 PHE 0.014 0.001 PHE C 802 TRP 0.013 0.001 TRP F 53 HIS 0.014 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00504 (27521) covalent geometry : angle 0.57044 (37445) SS BOND : bond 0.00421 ( 42) SS BOND : angle 0.69146 ( 84) hydrogen bonds : bond 0.03897 ( 1177) hydrogen bonds : angle 5.19532 ( 3156) link_BETA1-4 : bond 0.00170 ( 20) link_BETA1-4 : angle 1.31253 ( 60) link_NAG-ASN : bond 0.00349 ( 46) link_NAG-ASN : angle 1.76493 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 95 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9144 (p) REVERT: A 387 LEU cc_start: 0.9659 (mt) cc_final: 0.9439 (mt) REVERT: A 912 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.8951 (p) REVERT: A 979 ASP cc_start: 0.9204 (m-30) cc_final: 0.8848 (t0) REVERT: B 224 GLU cc_start: 0.9284 (OUTLIER) cc_final: 0.8696 (pm20) REVERT: B 229 LEU cc_start: 0.9211 (mt) cc_final: 0.8721 (tp) REVERT: B 468 ILE cc_start: 0.9713 (OUTLIER) cc_final: 0.9385 (mp) REVERT: C 468 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.7811 (mm) REVERT: C 571 ASP cc_start: 0.7922 (t70) cc_final: 0.7500 (t70) REVERT: C 900 MET cc_start: 0.9094 (mtp) cc_final: 0.8844 (mtt) REVERT: D 73 ASP cc_start: 0.9225 (t0) cc_final: 0.8814 (p0) REVERT: D 117 TRP cc_start: 0.7308 (m-90) cc_final: 0.6453 (m-90) REVERT: F 12 MET cc_start: 0.8735 (mmm) cc_final: 0.8470 (tpp) REVERT: F 81 LEU cc_start: 0.9135 (tp) cc_final: 0.8842 (tt) outliers start: 46 outliers final: 31 residues processed: 135 average time/residue: 0.1660 time to fit residues: 37.1046 Evaluate side-chains 125 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain D residue 108 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 19 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 234 optimal weight: 30.0000 chunk 186 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 319 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.055000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.034168 restraints weight = 258491.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.035860 restraints weight = 91940.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.036941 restraints weight = 51006.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.037665 restraints weight = 34853.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.038110 restraints weight = 27176.851| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27629 Z= 0.179 Angle : 0.551 11.483 37727 Z= 0.277 Chirality : 0.042 0.217 4440 Planarity : 0.003 0.037 4734 Dihedral : 4.609 55.125 4993 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.44 % Allowed : 10.13 % Favored : 88.43 % 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: 0.75 (0.15), residues: 3296 helix: 2.35 (0.21), residues: 680 sheet: 0.27 (0.16), residues: 874 loop : -0.06 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 567 TYR 0.018 0.001 TYR F 88 PHE 0.012 0.001 PHE B 329 TRP 0.010 0.001 TRP D 117 HIS 0.025 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00383 (27521) covalent geometry : angle 0.54017 (37445) SS BOND : bond 0.00247 ( 42) SS BOND : angle 0.64239 ( 84) hydrogen bonds : bond 0.03748 ( 1177) hydrogen bonds : angle 5.07846 ( 3156) link_BETA1-4 : bond 0.00177 ( 20) link_BETA1-4 : angle 1.28789 ( 60) link_NAG-ASN : bond 0.00261 ( 46) link_NAG-ASN : angle 1.67570 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 1.024 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 34 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8031 (mmt90) REVERT: A 63 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9142 (p) REVERT: A 387 LEU cc_start: 0.9643 (mt) cc_final: 0.9357 (mt) REVERT: A 869 MET cc_start: 0.9458 (mtp) cc_final: 0.9244 (mtm) REVERT: A 912 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.8948 (p) REVERT: A 979 ASP cc_start: 0.9192 (m-30) cc_final: 0.8811 (t0) REVERT: A 1017 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8523 (tm-30) REVERT: B 224 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8868 (mp0) REVERT: B 229 LEU cc_start: 0.9221 (mt) cc_final: 0.8714 (tp) REVERT: B 468 ILE cc_start: 0.9720 (OUTLIER) cc_final: 0.9405 (mp) REVERT: B 869 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8970 (mtm) REVERT: C 468 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.7856 (mm) REVERT: C 571 ASP cc_start: 0.7914 (t70) cc_final: 0.7500 (t70) REVERT: C 725 GLU cc_start: 0.8507 (tt0) cc_final: 0.8047 (tt0) REVERT: C 900 MET cc_start: 0.9084 (mtp) cc_final: 0.8827 (mtt) REVERT: C 933 LYS cc_start: 0.9743 (OUTLIER) cc_final: 0.9421 (mtmm) REVERT: D 12 MET cc_start: 0.2178 (pmm) cc_final: 0.1804 (ptp) REVERT: D 117 TRP cc_start: 0.7301 (m-90) cc_final: 0.6493 (m-90) REVERT: E 27 ARG cc_start: 0.8290 (ttt180) cc_final: 0.7870 (ptt90) REVERT: F 12 MET cc_start: 0.8757 (mmm) cc_final: 0.8201 (tpp) REVERT: F 81 LEU cc_start: 0.9176 (tp) cc_final: 0.8884 (tt) outliers start: 41 outliers final: 27 residues processed: 130 average time/residue: 0.1543 time to fit residues: 33.6110 Evaluate side-chains 125 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain F residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 68 optimal weight: 0.9980 chunk 309 optimal weight: 30.0000 chunk 151 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 237 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 191 optimal weight: 7.9990 chunk 260 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 243 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.054960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.034637 restraints weight = 186814.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.036143 restraints weight = 77716.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.037141 restraints weight = 45848.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.037797 restraints weight = 32487.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.038228 restraints weight = 25956.795| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 : 0.004 0.043 27629 Z= 0.178 Angle : 0.549 11.873 37727 Z= 0.275 Chirality : 0.042 0.218 4440 Planarity : 0.003 0.037 4734 Dihedral : 4.512 55.228 4993 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.51 % Allowed : 10.27 % Favored : 88.22 % 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: 0.77 (0.15), residues: 3296 helix: 2.35 (0.20), residues: 680 sheet: 0.26 (0.16), residues: 873 loop : -0.03 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 567 TYR 0.016 0.001 TYR B 200 PHE 0.011 0.001 PHE B 329 TRP 0.011 0.001 TRP D 117 HIS 0.017 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00381 (27521) covalent geometry : angle 0.53908 (37445) SS BOND : bond 0.00238 ( 42) SS BOND : angle 0.61093 ( 84) hydrogen bonds : bond 0.03701 ( 1177) hydrogen bonds : angle 5.03449 ( 3156) link_BETA1-4 : bond 0.00156 ( 20) link_BETA1-4 : angle 1.25330 ( 60) link_NAG-ASN : bond 0.00246 ( 46) link_NAG-ASN : angle 1.63911 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 0.770 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 34 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8070 (mmt90) REVERT: A 63 THR cc_start: 0.9391 (OUTLIER) cc_final: 0.9141 (p) REVERT: A 387 LEU cc_start: 0.9631 (mt) cc_final: 0.9344 (mt) REVERT: A 900 MET cc_start: 0.9414 (mmm) cc_final: 0.9030 (mtt) REVERT: A 912 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.8946 (p) REVERT: A 979 ASP cc_start: 0.9193 (m-30) cc_final: 0.8838 (t70) REVERT: A 1017 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8525 (tm-30) REVERT: B 224 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.8862 (mp0) REVERT: B 229 LEU cc_start: 0.9240 (mt) cc_final: 0.8699 (tp) REVERT: B 468 ILE cc_start: 0.9721 (OUTLIER) cc_final: 0.9413 (mp) REVERT: B 869 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8970 (mtm) REVERT: B 957 GLN cc_start: 0.8875 (mt0) cc_final: 0.8571 (tt0) REVERT: C 468 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.7929 (mm) REVERT: C 571 ASP cc_start: 0.7902 (t70) cc_final: 0.7486 (t70) REVERT: C 725 GLU cc_start: 0.8497 (tt0) cc_final: 0.8033 (tt0) REVERT: C 900 MET cc_start: 0.9073 (mtp) cc_final: 0.8823 (mtt) REVERT: C 933 LYS cc_start: 0.9743 (OUTLIER) cc_final: 0.9414 (mtmm) REVERT: D 12 MET cc_start: 0.2094 (pmm) cc_final: 0.1638 (ptp) REVERT: D 117 TRP cc_start: 0.7256 (m-90) cc_final: 0.6442 (m-90) REVERT: F 12 MET cc_start: 0.8679 (mmm) cc_final: 0.7981 (tpt) REVERT: F 81 LEU cc_start: 0.9209 (tp) cc_final: 0.8923 (tt) outliers start: 43 outliers final: 29 residues processed: 132 average time/residue: 0.1652 time to fit residues: 36.0178 Evaluate side-chains 127 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 251 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A1135 ASN C 762 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.054078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.033803 restraints weight = 184055.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.035231 restraints weight = 78897.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.036179 restraints weight = 47397.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.036793 restraints weight = 34023.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.037221 restraints weight = 27443.799| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 27629 Z= 0.312 Angle : 0.666 12.411 37727 Z= 0.328 Chirality : 0.043 0.298 4440 Planarity : 0.004 0.040 4734 Dihedral : 4.850 55.748 4993 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.44 % Allowed : 10.34 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3296 helix: 2.18 (0.20), residues: 679 sheet: 0.04 (0.16), residues: 903 loop : -0.17 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 27 TYR 0.020 0.001 TYR B 200 PHE 0.013 0.001 PHE B 718 TRP 0.020 0.002 TRP F 53 HIS 0.019 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00662 (27521) covalent geometry : angle 0.65433 (37445) SS BOND : bond 0.00344 ( 42) SS BOND : angle 0.83340 ( 84) hydrogen bonds : bond 0.04096 ( 1177) hydrogen bonds : angle 5.29938 ( 3156) link_BETA1-4 : bond 0.00352 ( 20) link_BETA1-4 : angle 1.53154 ( 60) link_NAG-ASN : bond 0.00536 ( 46) link_NAG-ASN : angle 1.91040 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 91 time to evaluate : 1.008 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 34 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7973 (mmt90) REVERT: A 63 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.9164 (p) REVERT: A 387 LEU cc_start: 0.9627 (mt) cc_final: 0.9339 (mt) REVERT: A 900 MET cc_start: 0.9367 (mmm) cc_final: 0.9058 (mtt) REVERT: A 912 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.8946 (p) REVERT: A 979 ASP cc_start: 0.9187 (m-30) cc_final: 0.8859 (t0) REVERT: A 1017 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8592 (tm-30) REVERT: B 224 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.8711 (pm20) REVERT: B 229 LEU cc_start: 0.9275 (mt) cc_final: 0.8752 (tp) REVERT: B 468 ILE cc_start: 0.9730 (OUTLIER) cc_final: 0.9429 (mp) REVERT: B 869 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.9008 (mtm) REVERT: C 468 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8070 (mm) REVERT: C 571 ASP cc_start: 0.7970 (t70) cc_final: 0.7572 (t70) REVERT: C 900 MET cc_start: 0.9126 (mtp) cc_final: 0.8885 (mtt) REVERT: D 12 MET cc_start: 0.2060 (pmm) cc_final: 0.1620 (ptp) REVERT: D 117 TRP cc_start: 0.7192 (m-90) cc_final: 0.6294 (m-90) REVERT: E 1 GLN cc_start: 0.8794 (pp30) cc_final: 0.8462 (tm-30) REVERT: F 12 MET cc_start: 0.8629 (mmm) cc_final: 0.8012 (tpt) REVERT: F 81 LEU cc_start: 0.9170 (tp) cc_final: 0.8875 (tt) outliers start: 41 outliers final: 31 residues processed: 126 average time/residue: 0.1569 time to fit residues: 33.4222 Evaluate side-chains 127 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 253 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 308 optimal weight: 7.9990 chunk 251 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 chunk 295 optimal weight: 0.0980 chunk 277 optimal weight: 0.9990 chunk 313 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS B 762 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.055530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.035324 restraints weight = 224815.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.037633 restraints weight = 86095.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.038331 restraints weight = 39658.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.038853 restraints weight = 26774.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.039015 restraints weight = 24020.221| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27629 Z= 0.109 Angle : 0.525 12.233 37727 Z= 0.266 Chirality : 0.043 0.250 4440 Planarity : 0.003 0.037 4734 Dihedral : 4.408 54.617 4993 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.06 % Allowed : 10.83 % Favored : 88.11 % 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: 0.76 (0.15), residues: 3296 helix: 2.35 (0.20), residues: 680 sheet: 0.26 (0.17), residues: 873 loop : -0.04 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 567 TYR 0.017 0.001 TYR C 369 PHE 0.013 0.001 PHE B 329 TRP 0.013 0.001 TRP D 117 HIS 0.019 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00233 (27521) covalent geometry : angle 0.51699 (37445) SS BOND : bond 0.00191 ( 42) SS BOND : angle 0.53857 ( 84) hydrogen bonds : bond 0.03578 ( 1177) hydrogen bonds : angle 4.94866 ( 3156) link_BETA1-4 : bond 0.00282 ( 20) link_BETA1-4 : angle 1.09958 ( 60) link_NAG-ASN : bond 0.00195 ( 46) link_NAG-ASN : angle 1.49052 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5138.02 seconds wall clock time: 89 minutes 11.35 seconds (5351.35 seconds total)