Starting phenix.real_space_refine on Sun Jul 5 10:43:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z9q_14575/07_2026/7z9q_14575.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z9q_14575/07_2026/7z9q_14575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7z9q_14575/07_2026/7z9q_14575.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z9q_14575/07_2026/7z9q_14575.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z9q_14575/07_2026/7z9q_14575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z9q_14575/07_2026/7z9q_14575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z9q_14575/07_2026/7z9q_14575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z9q_14575/07_2026/7z9q_14575.map" } resolution = 3.6 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 17225 2.51 5 N 4462 2.21 5 O 5261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27065 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: 1053 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Conformer: "B" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} bond proxies already assigned to first conformer: 1073 Chain: "E" Number of atoms: 1053 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Conformer: "B" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} bond proxies already assigned to first conformer: 1073 Chain: "F" Number of atoms: 1053 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Conformer: "B" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} bond proxies already assigned to first conformer: 1073 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 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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 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 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 chiralities: 8 Time building chain proxies: 7.06, per 1000 atoms: 0.26 Number of scatterers: 27065 At special positions: 0 Unit cell: (131.44, 137.8, 227.9, 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 5261 8.00 N 4462 7.00 C 17225 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=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 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=2.03 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 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=2.00 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.00 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.00 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 A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " 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 B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 234 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " 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: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6290 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 54 sheets defined 24.6% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.964A 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: 4.261A 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: 3.646A 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: 4.098A 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: 3.674A 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: 3.668A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.407A 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: 4.028A 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: 4.262A 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: 3.644A 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: 4.112A 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: 3.695A 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: 3.637A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.411A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.091A 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: 4.022A 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: 4.280A 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: 3.642A 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: 4.106A 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: 3.664A 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: 3.637A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.332A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.086A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'E' and resid 105 through 111 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: 5.634A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.891A 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: 8.820A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.994A 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: 3.564A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.856A 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: 3.571A 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: 6.555A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.565A 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: 6.660A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.980A 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: 6.497A 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: 6.561A 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: 3.863A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.444A 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: 6.969A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.785A 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: 4.195A 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: 5.705A 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: 4.376A 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: 8.035A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.957A 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: 3.571A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.865A 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 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.588A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.473A 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: 4.130A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.623A 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: 6.482A 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: 6.556A 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: 3.860A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.435A 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: 6.978A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.195A 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: 5.788A 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: 4.378A 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: 8.069A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.179A 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: 6.831A 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: 7.057A 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: 3.876A 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 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.583A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.499A 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: 4.133A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.038A 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: 6.493A 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 653 through 655 removed outlier: 6.561A 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: 3.864A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.462A 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: 6.968A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.308A 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: 4.188A 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: 4.379A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA D 33 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.392A 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: 6.198A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA E 33 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.392A 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: 6.198A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.198A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER F 126 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA F 33 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.392A 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: 6.198A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER F 126 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) 1172 hydrogen bonds defined for protein. 3129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.58 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4489 1.32 - 1.44: 7761 1.44 - 1.57: 15271 1.57 - 1.69: 0 1.69 - 1.82: 150 Bond restraints: 27671 Sorted by residual: bond pdb=" C TRP F 117 " pdb=" O TRP F 117 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.22e-02 6.72e+03 2.13e+01 bond pdb=" C TRP D 117 " pdb=" O TRP D 117 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.22e-02 6.72e+03 2.11e+01 bond pdb=" C TRP E 117 " pdb=" O TRP E 117 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.22e-02 6.72e+03 2.09e+01 bond pdb=" C VAL D 125 " pdb=" O VAL D 125 " ideal model delta sigma weight residual 1.237 1.192 0.046 1.10e-02 8.26e+03 1.71e+01 bond pdb=" C VAL F 125 " pdb=" O VAL F 125 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.10e-02 8.26e+03 1.70e+01 ... (remaining 27666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 31220 2.03 - 4.06: 5781 4.06 - 6.08: 576 6.08 - 8.11: 59 8.11 - 10.14: 10 Bond angle restraints: 37646 Sorted by residual: angle pdb=" C LYS A 113 " pdb=" CA LYS A 113 " pdb=" CB LYS A 113 " ideal model delta sigma weight residual 109.83 116.61 -6.78 9.90e-01 1.02e+00 4.69e+01 angle pdb=" C PRO C 600 " pdb=" CA PRO C 600 " pdb=" CB PRO C 600 " ideal model delta sigma weight residual 111.44 102.60 8.84 1.51e+00 4.39e-01 3.42e+01 angle pdb=" CA ASP F 115 " pdb=" CB ASP F 115 " pdb=" CG ASP F 115 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.37e+01 angle pdb=" CA ASP D 115 " pdb=" CB ASP D 115 " pdb=" CG ASP D 115 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" CA ASP E 115 " pdb=" CB ASP E 115 " pdb=" CG ASP E 115 " ideal model delta sigma weight residual 112.60 118.38 -5.78 1.00e+00 1.00e+00 3.34e+01 ... (remaining 37641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 14623 17.53 - 35.05: 968 35.05 - 52.58: 202 52.58 - 70.10: 39 70.10 - 87.63: 26 Dihedral angle restraints: 15858 sinusoidal: 6065 harmonic: 9793 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 -179.37 -87.63 1 1.00e+01 1.00e-02 9.20e+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 -179.68 -87.32 1 1.00e+01 1.00e-02 9.15e+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 -179.76 -87.24 1 1.00e+01 1.00e-02 9.14e+01 ... (remaining 15855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 3869 0.126 - 0.252: 560 0.252 - 0.378: 23 0.378 - 0.504: 2 0.504 - 0.630: 1 Chirality restraints: 4455 Sorted by residual: 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 -2.31 -0.09 2.00e-02 2.50e+03 1.93e+01 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.92e+00 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 -2.34 -0.06 2.00e-02 2.50e+03 9.92e+00 ... (remaining 4452 not shown) Planarity restraints: 4810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 80 " 0.044 2.00e-02 2.50e+03 4.00e-02 3.20e+01 pdb=" CG TYR D 80 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 80 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR D 80 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR D 80 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR D 80 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR D 80 " 0.053 2.00e-02 2.50e+03 pdb=" OH TYR D 80 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 80 " 0.045 2.00e-02 2.50e+03 3.99e-02 3.18e+01 pdb=" CG TYR F 80 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR F 80 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR F 80 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR F 80 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR F 80 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR F 80 " 0.052 2.00e-02 2.50e+03 pdb=" OH TYR F 80 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 80 " -0.044 2.00e-02 2.50e+03 3.99e-02 3.18e+01 pdb=" CG TYR E 80 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR E 80 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR E 80 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR E 80 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR E 80 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 80 " -0.052 2.00e-02 2.50e+03 pdb=" OH TYR E 80 " 0.014 2.00e-02 2.50e+03 ... (remaining 4807 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 80 2.56 - 3.14: 21144 3.14 - 3.73: 40222 3.73 - 4.31: 60934 4.31 - 4.90: 97995 Nonbonded interactions: 220375 Sorted by model distance: nonbonded pdb=" O ASN A 81 " pdb=" NE2 GLN A 239 " model vdw 1.974 3.120 nonbonded pdb=" NH1 ARG C 328 " pdb=" OD2 ASP C 578 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR B 200 " pdb=" OE1 GLU C 516 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 200 " pdb=" OH TYR C 396 " model vdw 2.215 3.040 nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.279 3.120 ... (remaining 220370 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 1308)) 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 1408 \ )) } ncs_group { reference = (chain 'D' and (resid 1 through 4 or resid 6 through 134)) selection = (chain 'E' and (resid 1 through 4 or resid 6 through 134)) selection = (chain 'F' and (resid 1 through 4 or resid 6 through 134)) } 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 28.320 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4532 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 : 0.010 0.056 27779 Z= 0.688 Angle : 1.560 12.064 37928 Z= 1.048 Chirality : 0.087 0.630 4455 Planarity : 0.007 0.053 4764 Dihedral : 12.891 85.484 9442 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.44 % Favored : 96.25 % Rotamer: Outliers : 0.88 % Allowed : 5.15 % Favored : 93.98 % Cbeta Deviations : 0.29 % 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: -1.07 (0.13), residues: 3314 helix: -0.61 (0.18), residues: 671 sheet: 0.11 (0.17), residues: 799 loop : -1.11 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG B 328 TYR 0.075 0.008 TYR E 80 PHE 0.036 0.006 PHE B 565 TRP 0.054 0.007 TRP F 112 HIS 0.062 0.003 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.01024 / 0.69 (27671) covalent geometry : angle 1.54249 / 1.05 (37646) SS BOND : bond 0.01450 / 0.91 ( 42) SS BOND : angle 3.18534 / 1.94 ( 84) hydrogen bonds : bond 0.13091 / 8.58 ( 1160) hydrogen bonds : angle 7.25311 / 4.93 ( 3129) link_BETA1-4 : bond 0.00524 / 0.33 ( 20) link_BETA1-4 : angle 3.23685 / 2.07 ( 60) link_NAG-ASN : bond 0.00926 / 0.57 ( 46) link_NAG-ASN : angle 2.94367 / 1.93 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 625 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.5015 (t70) cc_final: 0.4799 (t-170) REVERT: A 64 TRP cc_start: 0.5818 (t60) cc_final: 0.5548 (t60) REVERT: A 218 GLN cc_start: 0.7287 (tt0) cc_final: 0.6901 (tm-30) REVERT: A 307 THR cc_start: 0.7977 (m) cc_final: 0.7653 (t) REVERT: A 316 SER cc_start: 0.4937 (t) cc_final: 0.4424 (p) REVERT: A 369 TYR cc_start: 0.6862 (p90) cc_final: 0.6219 (p90) REVERT: A 554 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7983 (mp0) REVERT: A 568 ASP cc_start: 0.6020 (t0) cc_final: 0.5685 (m-30) REVERT: A 591 SER cc_start: 0.6413 (t) cc_final: 0.6170 (p) REVERT: A 666 ILE cc_start: 0.7531 (mt) cc_final: 0.7188 (mp) REVERT: A 693 ILE cc_start: 0.6297 (pt) cc_final: 0.5857 (pt) REVERT: A 702 GLU cc_start: 0.7713 (pt0) cc_final: 0.7306 (mp0) REVERT: A 758 SER cc_start: 0.5122 (m) cc_final: 0.4845 (t) REVERT: A 804 GLN cc_start: 0.6830 (mm-40) cc_final: 0.6506 (mt0) REVERT: A 968 SER cc_start: 0.7296 (m) cc_final: 0.6792 (t) REVERT: B 54 LEU cc_start: 0.7836 (mt) cc_final: 0.7610 (mt) REVERT: B 290 ASP cc_start: 0.5856 (t0) cc_final: 0.5651 (t0) REVERT: B 320 VAL cc_start: 0.5679 (t) cc_final: 0.4743 (m) REVERT: B 358 ILE cc_start: 0.6547 (mm) cc_final: 0.6239 (mp) REVERT: B 359 SER cc_start: 0.6548 (p) cc_final: 0.6291 (t) REVERT: B 389 ASP cc_start: 0.8250 (m-30) cc_final: 0.7515 (t70) REVERT: B 400 PHE cc_start: 0.5291 (p90) cc_final: 0.4962 (p90) REVERT: B 409 GLN cc_start: 0.4909 (mt0) cc_final: 0.4680 (mt0) REVERT: B 465 GLU cc_start: 0.4787 (tt0) cc_final: 0.4399 (tt0) REVERT: B 468 ILE cc_start: 0.5543 (pp) cc_final: 0.5153 (mp) REVERT: B 492 LEU cc_start: 0.3638 (mt) cc_final: 0.3327 (mt) REVERT: B 497 PHE cc_start: 0.3858 (m-80) cc_final: 0.3638 (m-80) REVERT: B 508 TYR cc_start: 0.6093 (m-80) cc_final: 0.5485 (m-80) REVERT: B 534 VAL cc_start: 0.6403 (t) cc_final: 0.6102 (p) REVERT: B 574 ASP cc_start: 0.6189 (OUTLIER) cc_final: 0.5980 (p0) REVERT: B 646 ARG cc_start: 0.6710 (tpp80) cc_final: 0.5906 (tpt90) REVERT: B 671 CYS cc_start: 0.6008 (m) cc_final: 0.5640 (m) REVERT: B 912 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7171 (p) REVERT: B 973 ILE cc_start: 0.6821 (pt) cc_final: 0.6506 (pt) REVERT: B 977 LEU cc_start: 0.5435 (tp) cc_final: 0.5233 (tp) REVERT: B 990 GLU cc_start: 0.5034 (mt-10) cc_final: 0.4829 (tt0) REVERT: C 48 LEU cc_start: 0.6680 (mt) cc_final: 0.6082 (mt) REVERT: C 65 PHE cc_start: 0.5665 (m-80) cc_final: 0.5125 (m-80) REVERT: C 189 LEU cc_start: 0.5832 (tp) cc_final: 0.5132 (tp) REVERT: C 191 GLU cc_start: 0.5942 (mt-10) cc_final: 0.5610 (mp0) REVERT: C 306 PHE cc_start: 0.3737 (m-80) cc_final: 0.2833 (m-80) REVERT: C 314 GLN cc_start: 0.7042 (tt0) cc_final: 0.6835 (tm-30) REVERT: C 317 ASN cc_start: 0.6428 (m-40) cc_final: 0.6006 (t0) REVERT: C 319 ARG cc_start: 0.5623 (mtp85) cc_final: 0.5366 (mtp85) REVERT: C 385 THR cc_start: 0.6944 (p) cc_final: 0.6705 (p) REVERT: C 605 SER cc_start: 0.6048 (t) cc_final: 0.5565 (p) REVERT: C 607 GLN cc_start: 0.6725 (tt0) cc_final: 0.6206 (pt0) REVERT: C 740 MET cc_start: 0.6916 (ttt) cc_final: 0.6515 (ttm) REVERT: C 751 ASN cc_start: 0.7638 (m-40) cc_final: 0.7426 (m110) REVERT: C 791 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7522 (t) REVERT: C 973 ILE cc_start: 0.7384 (tt) cc_final: 0.6968 (pt) REVERT: C 1017 GLU cc_start: 0.6721 (tt0) cc_final: 0.6472 (tm-30) REVERT: C 1045 LYS cc_start: 0.7222 (tttt) cc_final: 0.6838 (tttt) REVERT: C 1125 ASN cc_start: 0.6483 (p0) cc_final: 0.6263 (p0) REVERT: C 1144 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6572 (mp0) REVERT: F 51 ILE cc_start: 0.3968 (tt) cc_final: 0.1185 (tt) REVERT: F 71 SER cc_start: 0.5285 (p) cc_final: 0.5052 (t) REVERT: F 78 THR cc_start: 0.4483 (m) cc_final: 0.4113 (m) REVERT: F 83 MET cc_start: 0.2778 (mtp) cc_final: 0.1958 (ptp) outliers start: 25 outliers final: 3 residues processed: 645 average time/residue: 0.1618 time to fit residues: 165.8309 Evaluate side-chains 311 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 305 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 784 GLN A 804 GLN A 935 GLN A 955 ASN A 957 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 607 GLN B 675 GLN B 978 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 506 GLN C 607 GLN C 784 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1023 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.177401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.131211 restraints weight = 53629.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131251 restraints weight = 46324.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.128668 restraints weight = 25251.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.127893 restraints weight = 19655.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128232 restraints weight = 20727.885| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27779 Z= 0.155 Angle : 0.668 10.764 37928 Z= 0.338 Chirality : 0.046 0.272 4455 Planarity : 0.004 0.033 4764 Dihedral : 5.429 62.305 3632 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.03 % Allowed : 10.61 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.04 (0.14), residues: 3314 helix: 0.96 (0.20), residues: 689 sheet: 0.24 (0.17), residues: 818 loop : -0.49 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 319 TYR 0.029 0.002 TYR D 116 PHE 0.025 0.002 PHE C 135 TRP 0.019 0.001 TRP B 436 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (27671) covalent geometry : angle 0.64943 / 0.33 (37646) SS BOND : bond 0.00555 / 0.40 ( 42) SS BOND : angle 1.55874 / 0.93 ( 84) hydrogen bonds : bond 0.04808 / 3.12 ( 1160) hydrogen bonds : angle 5.76828 / 3.98 ( 3129) link_BETA1-4 : bond 0.00450 / 0.33 ( 20) link_BETA1-4 : angle 1.42832 / 0.94 ( 60) link_NAG-ASN : bond 0.00470 / 0.26 ( 46) link_NAG-ASN : angle 2.30033 / 1.52 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 366 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7987 (m) REVERT: A 129 LYS cc_start: 0.7930 (pttt) cc_final: 0.7444 (ptpp) REVERT: A 551 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8955 (m) REVERT: A 567 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6627 (mmt180) REVERT: A 1107 ARG cc_start: 0.7793 (mtm180) cc_final: 0.7394 (mtm-85) REVERT: B 54 LEU cc_start: 0.8300 (mt) cc_final: 0.7992 (mt) REVERT: B 389 ASP cc_start: 0.7600 (m-30) cc_final: 0.7380 (t70) REVERT: B 409 GLN cc_start: 0.6118 (mt0) cc_final: 0.5447 (mt0) REVERT: B 535 LYS cc_start: 0.7918 (ttpt) cc_final: 0.6912 (mtmt) REVERT: B 977 LEU cc_start: 0.8870 (tp) cc_final: 0.8644 (tp) REVERT: C 61 ASN cc_start: 0.5218 (m-40) cc_final: 0.4710 (m110) REVERT: C 189 LEU cc_start: 0.6668 (tp) cc_final: 0.6304 (tp) REVERT: C 278 LYS cc_start: 0.8429 (tttt) cc_final: 0.8101 (tttp) REVERT: C 540 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7636 (t0) REVERT: C 740 MET cc_start: 0.7813 (ttt) cc_final: 0.7484 (ttm) REVERT: C 856 ASN cc_start: 0.6966 (OUTLIER) cc_final: 0.6521 (m110) REVERT: C 938 LEU cc_start: 0.7137 (mt) cc_final: 0.6749 (mp) REVERT: C 1144 GLU cc_start: 0.6689 (mm-30) cc_final: 0.6458 (mp0) REVERT: F 34 MET cc_start: 0.2500 (ptt) cc_final: 0.2197 (ptp) REVERT: F 47 PHE cc_start: 0.3730 (t80) cc_final: 0.3184 (t80) REVERT: F 83 MET cc_start: 0.1740 (mtp) cc_final: 0.0874 (ptp) outliers start: 58 outliers final: 28 residues processed: 410 average time/residue: 0.1506 time to fit residues: 100.2140 Evaluate side-chains 289 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 256 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 303 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 281 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS A 207 HIS A 450 ASN A 644 GLN A 655 HIS A 762 GLN A 901 GLN A1048 HIS A1071 GLN B 30 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 655 HIS B 675 GLN B 901 GLN B1048 HIS C 125 ASN C 450 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1048 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.167807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.110501 restraints weight = 65909.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112454 restraints weight = 37404.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113540 restraints weight = 24276.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114173 restraints weight = 19689.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114380 restraints weight = 17690.140| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (13 function evaluations) r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 27779 Z= 0.330 Angle : 0.819 12.405 37928 Z= 0.411 Chirality : 0.052 0.360 4455 Planarity : 0.005 0.042 4764 Dihedral : 5.622 57.443 3627 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.78 % Allowed : 11.94 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.43 (0.14), residues: 3314 helix: 0.65 (0.19), residues: 690 sheet: 0.20 (0.17), residues: 827 loop : -0.87 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 765 TYR 0.038 0.003 TYR C 904 PHE 0.044 0.003 PHE C 135 TRP 0.028 0.002 TRP A 64 HIS 0.015 0.002 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00770 / 0.33 (27671) covalent geometry : angle 0.79485 / 0.40 (37646) SS BOND : bond 0.00558 / 0.33 ( 42) SS BOND : angle 2.28654 / 1.38 ( 84) hydrogen bonds : bond 0.05529 / 3.61 ( 1160) hydrogen bonds : angle 6.06834 / 4.23 ( 3129) link_BETA1-4 : bond 0.00469 / 0.26 ( 20) link_BETA1-4 : angle 1.58008 / 1.05 ( 60) link_NAG-ASN : bond 0.00599 / 0.37 ( 46) link_NAG-ASN : angle 2.80881 / 1.89 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 272 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8701 (m) REVERT: A 102 ARG cc_start: 0.6844 (mmt90) cc_final: 0.6488 (mmt-90) REVERT: A 129 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7525 (pttp) REVERT: A 567 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6694 (mtt180) REVERT: A 773 GLU cc_start: 0.7514 (tt0) cc_final: 0.7109 (tt0) REVERT: A 957 GLN cc_start: 0.8350 (tm-30) cc_final: 0.7955 (tm-30) REVERT: A 1107 ARG cc_start: 0.7776 (mtm180) cc_final: 0.7352 (mtm180) REVERT: A 1118 ASP cc_start: 0.7406 (m-30) cc_final: 0.7175 (m-30) REVERT: B 54 LEU cc_start: 0.8465 (mt) cc_final: 0.8044 (mt) REVERT: B 278 LYS cc_start: 0.8126 (tttt) cc_final: 0.7821 (ptmt) REVERT: B 387 LEU cc_start: 0.8336 (mt) cc_final: 0.8063 (mt) REVERT: B 409 GLN cc_start: 0.6396 (mt0) cc_final: 0.5767 (mt0) REVERT: B 983 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7186 (ttp-170) REVERT: C 61 ASN cc_start: 0.5744 (m-40) cc_final: 0.5194 (m-40) REVERT: C 237 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6816 (ttp80) REVERT: C 388 ASN cc_start: 0.7754 (m110) cc_final: 0.7510 (m110) REVERT: C 452 LEU cc_start: 0.4690 (OUTLIER) cc_final: 0.4471 (mp) REVERT: C 938 LEU cc_start: 0.7104 (mt) cc_final: 0.6844 (mp) REVERT: C 1144 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6651 (mp0) REVERT: F 34 MET cc_start: 0.2889 (OUTLIER) cc_final: 0.2413 (ptp) outliers start: 105 outliers final: 68 residues processed: 360 average time/residue: 0.1550 time to fit residues: 91.7465 Evaluate side-chains 300 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 225 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 54 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 274 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 331 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 312 optimal weight: 20.0000 chunk 264 optimal weight: 0.5980 chunk 258 optimal weight: 2.9990 chunk 326 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 207 HIS A 644 GLN A 913 GLN B 196 ASN B 474 GLN B 613 GLN B 675 GLN B 955 ASN C 99 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1106 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.172207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116082 restraints weight = 66604.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118741 restraints weight = 33590.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.119177 restraints weight = 20127.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120117 restraints weight = 17766.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120180 restraints weight = 16126.766| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27779 Z= 0.122 Angle : 0.611 12.780 37928 Z= 0.307 Chirality : 0.045 0.306 4455 Planarity : 0.004 0.049 4764 Dihedral : 4.924 57.549 3626 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.66 % Allowed : 14.19 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.02 (0.14), residues: 3314 helix: 1.50 (0.20), residues: 672 sheet: 0.18 (0.17), residues: 824 loop : -0.61 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 905 TYR 0.025 0.001 TYR C 904 PHE 0.027 0.001 PHE B 541 TRP 0.019 0.001 TRP C 104 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (27671) covalent geometry : angle 0.59364 / 0.30 (37646) SS BOND : bond 0.00464 / 0.29 ( 42) SS BOND : angle 1.96698 / 1.18 ( 84) hydrogen bonds : bond 0.04142 / 2.67 ( 1160) hydrogen bonds : angle 5.56978 / 3.89 ( 3129) link_BETA1-4 : bond 0.00369 / 0.21 ( 20) link_BETA1-4 : angle 1.14744 / 0.77 ( 60) link_NAG-ASN : bond 0.00250 / 0.16 ( 46) link_NAG-ASN : angle 1.90919 / 1.33 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 294 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6847 (mmt90) cc_final: 0.6218 (mmt-90) REVERT: A 129 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7538 (pttp) REVERT: A 567 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6780 (mtt180) REVERT: A 902 MET cc_start: 0.9159 (tpt) cc_final: 0.8835 (tpt) REVERT: A 957 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7470 (tt0) REVERT: B 278 LYS cc_start: 0.8121 (tttt) cc_final: 0.7817 (ptmt) REVERT: B 409 GLN cc_start: 0.6306 (mt0) cc_final: 0.5797 (mt0) REVERT: B 421 TYR cc_start: 0.7510 (m-10) cc_final: 0.7263 (m-80) REVERT: B 643 PHE cc_start: 0.7467 (t80) cc_final: 0.7203 (t80) REVERT: B 983 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7142 (ttp-170) REVERT: C 61 ASN cc_start: 0.5707 (m-40) cc_final: 0.5225 (m-40) REVERT: C 237 ARG cc_start: 0.6997 (ttp-170) cc_final: 0.6596 (ttp80) REVERT: C 388 ASN cc_start: 0.7739 (m110) cc_final: 0.7419 (m110) REVERT: C 396 TYR cc_start: 0.7540 (m-80) cc_final: 0.7328 (m-10) REVERT: C 452 LEU cc_start: 0.4667 (OUTLIER) cc_final: 0.4401 (mp) REVERT: C 468 ILE cc_start: 0.2784 (OUTLIER) cc_final: 0.2437 (pp) REVERT: C 516 GLU cc_start: 0.6450 (tt0) cc_final: 0.6135 (tt0) REVERT: C 564 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: C 791 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8229 (m) REVERT: C 938 LEU cc_start: 0.7037 (mt) cc_final: 0.6701 (mp) REVERT: C 1144 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6623 (mp0) REVERT: F 34 MET cc_start: 0.2788 (ptt) cc_final: 0.2334 (ptp) outliers start: 73 outliers final: 42 residues processed: 348 average time/residue: 0.1542 time to fit residues: 87.7384 Evaluate side-chains 301 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 20 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 78 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 334 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 207 HIS A 913 GLN A 955 ASN B 414 GLN B 675 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.166012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.110167 restraints weight = 69057.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112464 restraints weight = 37728.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.111300 restraints weight = 28163.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.111735 restraints weight = 25676.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112016 restraints weight = 22221.051| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 27779 Z= 0.309 Angle : 0.774 11.709 37928 Z= 0.385 Chirality : 0.050 0.316 4455 Planarity : 0.005 0.062 4764 Dihedral : 5.337 57.196 3626 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.89 % Allowed : 14.29 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.51 (0.14), residues: 3314 helix: 0.88 (0.20), residues: 687 sheet: -0.06 (0.17), residues: 864 loop : -0.95 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 765 TYR 0.030 0.002 TYR C 904 PHE 0.035 0.002 PHE B 140 TRP 0.020 0.002 TRP A 64 HIS 0.010 0.002 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.31 (27671) covalent geometry : angle 0.75043 / 0.38 (37646) SS BOND : bond 0.00679 / 0.45 ( 42) SS BOND : angle 2.36813 / 1.43 ( 84) hydrogen bonds : bond 0.05284 / 3.43 ( 1160) hydrogen bonds : angle 5.93639 / 4.13 ( 3129) link_BETA1-4 : bond 0.00445 / 0.21 ( 20) link_BETA1-4 : angle 1.43242 / 0.94 ( 60) link_NAG-ASN : bond 0.00574 / 0.35 ( 46) link_NAG-ASN : angle 2.58180 / 1.76 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 248 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8641 (m) REVERT: A 102 ARG cc_start: 0.6698 (mmt90) cc_final: 0.6288 (mmt-90) REVERT: A 129 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7560 (pttp) REVERT: A 773 GLU cc_start: 0.7456 (tt0) cc_final: 0.7172 (tt0) REVERT: A 779 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7511 (tp40) REVERT: B 138 ASP cc_start: 0.7967 (t0) cc_final: 0.6871 (m-30) REVERT: B 278 LYS cc_start: 0.8226 (tttt) cc_final: 0.7906 (ptmt) REVERT: B 409 GLN cc_start: 0.6482 (mt0) cc_final: 0.6041 (mt0) REVERT: B 505 TYR cc_start: 0.6731 (m-80) cc_final: 0.6317 (m-80) REVERT: B 643 PHE cc_start: 0.7694 (t80) cc_final: 0.7438 (t80) REVERT: B 983 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7304 (ttm170) REVERT: B 988 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6961 (pt0) REVERT: C 237 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6748 (ttp80) REVERT: C 388 ASN cc_start: 0.7731 (m110) cc_final: 0.7383 (m110) REVERT: C 396 TYR cc_start: 0.7594 (m-80) cc_final: 0.7184 (m-10) REVERT: C 452 LEU cc_start: 0.4754 (OUTLIER) cc_final: 0.4477 (mp) REVERT: C 468 ILE cc_start: 0.2780 (OUTLIER) cc_final: 0.2490 (pp) REVERT: C 516 GLU cc_start: 0.6762 (tt0) cc_final: 0.6101 (tt0) REVERT: C 564 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7171 (tt0) REVERT: C 791 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8308 (m) REVERT: C 1144 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6785 (mp0) outliers start: 108 outliers final: 71 residues processed: 337 average time/residue: 0.1474 time to fit residues: 82.3363 Evaluate side-chains 304 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 223 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 258 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 156 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 263 optimal weight: 0.0670 chunk 267 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 957 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 935 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 = 0.4133 r_free = 0.4133 target = 0.170648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115132 restraints weight = 61035.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.117840 restraints weight = 32934.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.117829 restraints weight = 19628.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118486 restraints weight = 20238.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118456 restraints weight = 18703.354| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27779 Z= 0.130 Angle : 0.602 10.247 37928 Z= 0.302 Chirality : 0.044 0.266 4455 Planarity : 0.004 0.051 4764 Dihedral : 4.838 55.756 3626 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.38 % Allowed : 16.29 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.15 (0.14), residues: 3314 helix: 1.47 (0.20), residues: 675 sheet: 0.01 (0.17), residues: 842 loop : -0.74 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 103 TYR 0.023 0.001 TYR B 200 PHE 0.027 0.001 PHE B 541 TRP 0.018 0.001 TRP A 64 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (27671) covalent geometry : angle 0.58375 / 0.30 (37646) SS BOND : bond 0.00349 / 0.23 ( 42) SS BOND : angle 2.02591 / 1.12 ( 84) hydrogen bonds : bond 0.04092 / 2.66 ( 1160) hydrogen bonds : angle 5.54585 / 3.88 ( 3129) link_BETA1-4 : bond 0.00346 / 0.19 ( 20) link_BETA1-4 : angle 1.09089 / 0.73 ( 60) link_NAG-ASN : bond 0.00221 / 0.14 ( 46) link_NAG-ASN : angle 1.89585 / 1.32 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 263 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8555 (m) REVERT: A 102 ARG cc_start: 0.6596 (mmt90) cc_final: 0.4538 (mtp180) REVERT: A 129 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7438 (pttp) REVERT: A 654 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6790 (mp0) REVERT: B 138 ASP cc_start: 0.7854 (t0) cc_final: 0.6878 (m-30) REVERT: B 200 TYR cc_start: 0.3570 (m-10) cc_final: 0.3360 (m-10) REVERT: B 278 LYS cc_start: 0.8172 (tttt) cc_final: 0.7857 (ptmt) REVERT: B 505 TYR cc_start: 0.6604 (m-80) cc_final: 0.6337 (m-80) REVERT: B 740 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7210 (mtp) REVERT: B 977 LEU cc_start: 0.8816 (tt) cc_final: 0.8443 (tt) REVERT: B 988 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6891 (pt0) REVERT: C 237 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6776 (ttp80) REVERT: C 388 ASN cc_start: 0.7796 (m110) cc_final: 0.7433 (m110) REVERT: C 452 LEU cc_start: 0.4680 (OUTLIER) cc_final: 0.4426 (mp) REVERT: C 468 ILE cc_start: 0.3134 (OUTLIER) cc_final: 0.2826 (pp) REVERT: C 564 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: C 791 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8276 (m) REVERT: C 938 LEU cc_start: 0.7192 (mt) cc_final: 0.6873 (mp) REVERT: C 1141 LEU cc_start: 0.8019 (mt) cc_final: 0.7671 (tp) REVERT: C 1144 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6619 (mp0) outliers start: 65 outliers final: 39 residues processed: 307 average time/residue: 0.1482 time to fit residues: 74.8739 Evaluate side-chains 293 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 224 optimal weight: 0.4980 chunk 167 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 268 optimal weight: 0.7980 chunk 289 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 228 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 171 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 207 HIS ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 30 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 935 GLN C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.177127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121271 restraints weight = 72492.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123916 restraints weight = 36395.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123885 restraints weight = 24024.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125011 restraints weight = 20166.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125138 restraints weight = 18693.497| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27779 Z= 0.125 Angle : 0.579 10.464 37928 Z= 0.290 Chirality : 0.044 0.274 4455 Planarity : 0.004 0.053 4764 Dihedral : 4.612 55.031 3626 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.94 % Allowed : 16.15 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.02 (0.14), residues: 3314 helix: 1.66 (0.21), residues: 680 sheet: 0.06 (0.17), residues: 846 loop : -0.63 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 103 TYR 0.023 0.001 TYR A 369 PHE 0.027 0.001 PHE B 541 TRP 0.015 0.001 TRP A 64 HIS 0.008 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (27671) covalent geometry : angle 0.56334 / 0.29 (37646) SS BOND : bond 0.00368 / 0.25 ( 42) SS BOND : angle 1.73381 / 0.96 ( 84) hydrogen bonds : bond 0.03933 / 2.56 ( 1160) hydrogen bonds : angle 5.39518 / 3.78 ( 3129) link_BETA1-4 : bond 0.00277 / 0.15 ( 20) link_BETA1-4 : angle 1.06535 / 0.71 ( 60) link_NAG-ASN : bond 0.00193 / 0.12 ( 46) link_NAG-ASN : angle 1.78927 / 1.25 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 269 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8502 (m) REVERT: A 102 ARG cc_start: 0.6573 (mmt90) cc_final: 0.6022 (mmp80) REVERT: A 129 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7336 (pttp) REVERT: A 403 ARG cc_start: 0.7197 (mtt180) cc_final: 0.6893 (mtt90) REVERT: B 138 ASP cc_start: 0.7854 (t0) cc_final: 0.6919 (m-30) REVERT: B 237 ARG cc_start: 0.7400 (mtp85) cc_final: 0.7028 (mtp85) REVERT: B 278 LYS cc_start: 0.8199 (tttt) cc_final: 0.7890 (ptmt) REVERT: B 421 TYR cc_start: 0.8105 (m-80) cc_final: 0.7769 (m-80) REVERT: B 505 TYR cc_start: 0.6557 (m-80) cc_final: 0.6285 (m-80) REVERT: B 740 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7247 (mtp) REVERT: B 988 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6894 (pt0) REVERT: C 52 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7631 (tm-30) REVERT: C 237 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6707 (ttp80) REVERT: C 388 ASN cc_start: 0.7869 (m110) cc_final: 0.6965 (t0) REVERT: C 452 LEU cc_start: 0.4645 (OUTLIER) cc_final: 0.4387 (mp) REVERT: C 468 ILE cc_start: 0.2897 (OUTLIER) cc_final: 0.2609 (pt) REVERT: C 564 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.6897 (tt0) REVERT: C 791 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8271 (m) REVERT: C 938 LEU cc_start: 0.7269 (mt) cc_final: 0.6937 (mp) REVERT: C 1141 LEU cc_start: 0.7990 (mt) cc_final: 0.7671 (tp) REVERT: C 1144 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6561 (mp0) outliers start: 81 outliers final: 50 residues processed: 327 average time/residue: 0.1520 time to fit residues: 82.5988 Evaluate side-chains 305 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 246 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 108 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 259 optimal weight: 3.9990 chunk 139 optimal weight: 0.4980 chunk 161 optimal weight: 0.8980 chunk 266 optimal weight: 4.9990 chunk 192 optimal weight: 0.0270 chunk 218 optimal weight: 0.0570 chunk 96 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.170218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115052 restraints weight = 58677.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116825 restraints weight = 35576.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117776 restraints weight = 21264.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118209 restraints weight = 18300.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118681 restraints weight = 16780.288| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27779 Z= 0.117 Angle : 0.572 11.212 37928 Z= 0.287 Chirality : 0.044 0.271 4455 Planarity : 0.004 0.054 4764 Dihedral : 4.483 53.695 3626 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.52 % Allowed : 16.81 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.12 (0.14), residues: 3314 helix: 1.71 (0.20), residues: 686 sheet: 0.12 (0.17), residues: 836 loop : -0.55 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 103 TYR 0.036 0.001 TYR B 200 PHE 0.030 0.001 PHE C 65 TRP 0.024 0.001 TRP A 64 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (27671) covalent geometry : angle 0.55900 / 0.28 (37646) SS BOND : bond 0.00324 / 0.22 ( 42) SS BOND : angle 1.54013 / 0.86 ( 84) hydrogen bonds : bond 0.03824 / 2.49 ( 1160) hydrogen bonds : angle 5.31216 / 3.74 ( 3129) link_BETA1-4 : bond 0.00318 / 0.18 ( 20) link_BETA1-4 : angle 1.04679 / 0.70 ( 60) link_NAG-ASN : bond 0.00187 / 0.12 ( 46) link_NAG-ASN : angle 1.68389 / 1.17 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 259 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8492 (m) REVERT: A 102 ARG cc_start: 0.6746 (mmt90) cc_final: 0.6304 (mmt-90) REVERT: A 129 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7331 (pttp) REVERT: A 957 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7126 (tm-30) REVERT: A 1050 MET cc_start: 0.8425 (ptm) cc_final: 0.8203 (ptm) REVERT: B 138 ASP cc_start: 0.7875 (t0) cc_final: 0.7113 (m-30) REVERT: B 278 LYS cc_start: 0.8167 (tttt) cc_final: 0.7811 (ptmt) REVERT: B 505 TYR cc_start: 0.6548 (m-80) cc_final: 0.6291 (m-80) REVERT: B 643 PHE cc_start: 0.7593 (t80) cc_final: 0.7359 (t80) REVERT: B 740 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7260 (mtp) REVERT: B 817 PHE cc_start: 0.7416 (t80) cc_final: 0.7063 (t80) REVERT: B 988 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6910 (pt0) REVERT: C 195 LYS cc_start: 0.7362 (pttt) cc_final: 0.7054 (mtmm) REVERT: C 237 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6748 (ttp80) REVERT: C 388 ASN cc_start: 0.7880 (m110) cc_final: 0.6975 (t0) REVERT: C 452 LEU cc_start: 0.4605 (OUTLIER) cc_final: 0.4387 (mp) REVERT: C 468 ILE cc_start: 0.2835 (OUTLIER) cc_final: 0.2538 (pt) REVERT: C 564 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.6816 (tt0) REVERT: C 791 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8283 (m) REVERT: C 1141 LEU cc_start: 0.7950 (mt) cc_final: 0.7697 (tp) REVERT: C 1144 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6563 (mp0) outliers start: 69 outliers final: 51 residues processed: 306 average time/residue: 0.1587 time to fit residues: 79.1930 Evaluate side-chains 302 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 261 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 266 optimal weight: 4.9990 chunk 181 optimal weight: 0.0980 chunk 240 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 257 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.172272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.118403 restraints weight = 63717.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120498 restraints weight = 33491.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120140 restraints weight = 21700.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120698 restraints weight = 22067.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120774 restraints weight = 20235.296| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27779 Z= 0.140 Angle : 0.584 10.607 37928 Z= 0.293 Chirality : 0.044 0.271 4455 Planarity : 0.004 0.053 4764 Dihedral : 4.445 52.611 3626 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.63 % Allowed : 16.78 % Favored : 80.60 % Cbeta Deviations : 0.00 % 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: 0.13 (0.14), residues: 3314 helix: 1.65 (0.20), residues: 687 sheet: 0.24 (0.17), residues: 819 loop : -0.58 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 103 TYR 0.026 0.001 TYR A 369 PHE 0.027 0.001 PHE B 541 TRP 0.026 0.001 TRP C 104 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (27671) covalent geometry : angle 0.57066 / 0.29 (37646) SS BOND : bond 0.00361 / 0.25 ( 42) SS BOND : angle 1.57210 / 0.88 ( 84) hydrogen bonds : bond 0.03939 / 2.57 ( 1160) hydrogen bonds : angle 5.31165 / 3.74 ( 3129) link_BETA1-4 : bond 0.00302 / 0.16 ( 20) link_BETA1-4 : angle 1.05902 / 0.70 ( 60) link_NAG-ASN : bond 0.00203 / 0.13 ( 46) link_NAG-ASN : angle 1.73238 / 1.19 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 256 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8530 (m) REVERT: A 102 ARG cc_start: 0.6718 (mmt90) cc_final: 0.6327 (mmt-90) REVERT: A 129 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7185 (pttp) REVERT: A 773 GLU cc_start: 0.7251 (tt0) cc_final: 0.6819 (tt0) REVERT: B 138 ASP cc_start: 0.7967 (t0) cc_final: 0.7206 (m-30) REVERT: B 237 ARG cc_start: 0.7358 (mtp85) cc_final: 0.6884 (mtm110) REVERT: B 278 LYS cc_start: 0.8145 (tttt) cc_final: 0.7837 (ptmt) REVERT: B 505 TYR cc_start: 0.6759 (m-80) cc_final: 0.6471 (m-80) REVERT: B 643 PHE cc_start: 0.7579 (t80) cc_final: 0.7354 (t80) REVERT: B 740 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7320 (mtp) REVERT: B 817 PHE cc_start: 0.7452 (t80) cc_final: 0.7096 (t80) REVERT: B 988 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6977 (pt0) REVERT: C 237 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6803 (ttp80) REVERT: C 351 TYR cc_start: 0.5306 (p90) cc_final: 0.4856 (p90) REVERT: C 388 ASN cc_start: 0.7932 (m110) cc_final: 0.6985 (t0) REVERT: C 468 ILE cc_start: 0.2911 (OUTLIER) cc_final: 0.2650 (pt) REVERT: C 564 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.6740 (tt0) REVERT: C 791 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8203 (m) REVERT: C 1141 LEU cc_start: 0.7918 (mt) cc_final: 0.7655 (tp) REVERT: C 1144 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6624 (mp0) outliers start: 72 outliers final: 54 residues processed: 306 average time/residue: 0.1472 time to fit residues: 74.3404 Evaluate side-chains 304 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 242 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 151 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 216 optimal weight: 0.9990 chunk 130 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 51 optimal weight: 0.0870 chunk 278 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.173989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118976 restraints weight = 75831.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121947 restraints weight = 37277.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121885 restraints weight = 22303.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.122510 restraints weight = 22693.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122548 restraints weight = 21159.135| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27779 Z= 0.112 Angle : 0.563 10.836 37928 Z= 0.282 Chirality : 0.043 0.269 4455 Planarity : 0.004 0.054 4764 Dihedral : 4.320 51.498 3626 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.35 % Allowed : 17.16 % Favored : 80.49 % Cbeta Deviations : 0.00 % 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: 0.26 (0.14), residues: 3314 helix: 1.79 (0.20), residues: 688 sheet: 0.25 (0.17), residues: 819 loop : -0.48 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 765 TYR 0.025 0.001 TYR A 369 PHE 0.031 0.001 PHE B 168 TRP 0.022 0.001 TRP C 104 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (27671) covalent geometry : angle 0.55190 / 0.28 (37646) SS BOND : bond 0.00313 / 0.22 ( 42) SS BOND : angle 1.34910 / 0.75 ( 84) hydrogen bonds : bond 0.03685 / 2.41 ( 1160) hydrogen bonds : angle 5.19420 / 3.66 ( 3129) link_BETA1-4 : bond 0.00328 / 0.18 ( 20) link_BETA1-4 : angle 1.02663 / 0.69 ( 60) link_NAG-ASN : bond 0.00179 / 0.11 ( 46) link_NAG-ASN : angle 1.58093 / 1.10 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6628 Ramachandran restraints generated. 3314 Oldfield, 0 Emsley, 3314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 266 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8485 (m) REVERT: A 102 ARG cc_start: 0.6795 (mmt90) cc_final: 0.6357 (mmt-90) REVERT: A 129 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7216 (pttp) REVERT: A 957 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7968 (tt0) REVERT: B 117 LEU cc_start: 0.8060 (tt) cc_final: 0.7684 (tp) REVERT: B 138 ASP cc_start: 0.7917 (t0) cc_final: 0.7179 (m-30) REVERT: B 237 ARG cc_start: 0.7379 (mtp85) cc_final: 0.6932 (mtm110) REVERT: B 278 LYS cc_start: 0.8097 (tttt) cc_final: 0.7800 (ptmt) REVERT: B 492 LEU cc_start: 0.7842 (mp) cc_final: 0.7292 (tp) REVERT: B 505 TYR cc_start: 0.6752 (m-80) cc_final: 0.6453 (m-80) REVERT: B 528 LYS cc_start: 0.7931 (tppt) cc_final: 0.7368 (mmmm) REVERT: B 740 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7295 (mtp) REVERT: B 817 PHE cc_start: 0.7315 (t80) cc_final: 0.6984 (t80) REVERT: B 977 LEU cc_start: 0.8802 (tt) cc_final: 0.8447 (tt) REVERT: B 988 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7059 (pt0) REVERT: C 65 PHE cc_start: 0.7053 (m-80) cc_final: 0.6748 (m-10) REVERT: C 351 TYR cc_start: 0.5246 (p90) cc_final: 0.4892 (p90) REVERT: C 388 ASN cc_start: 0.7916 (m110) cc_final: 0.6984 (t0) REVERT: C 465 GLU cc_start: 0.4896 (tt0) cc_final: 0.3536 (mm-30) REVERT: C 468 ILE cc_start: 0.2958 (OUTLIER) cc_final: 0.2690 (pt) REVERT: C 564 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6685 (tt0) REVERT: C 791 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8258 (m) REVERT: C 1141 LEU cc_start: 0.7881 (mt) cc_final: 0.7653 (tp) REVERT: C 1144 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6594 (mp0) outliers start: 64 outliers final: 51 residues processed: 310 average time/residue: 0.1649 time to fit residues: 84.0362 Evaluate side-chains 310 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 107 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 104 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 166 optimal weight: 0.0000 chunk 261 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 221 optimal weight: 0.5980 chunk 202 optimal weight: 10.0000 chunk 43 optimal weight: 0.2980 chunk 138 optimal weight: 7.9990 chunk 311 optimal weight: 20.0000 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.177809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123317 restraints weight = 58521.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125401 restraints weight = 33958.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126151 restraints weight = 20334.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126762 restraints weight = 18663.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126922 restraints weight = 16423.138| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27779 Z= 0.119 Angle : 0.561 10.441 37928 Z= 0.282 Chirality : 0.043 0.268 4455 Planarity : 0.004 0.052 4764 Dihedral : 4.243 50.520 3626 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.17 % Allowed : 17.76 % Favored : 80.07 % Cbeta Deviations : 0.00 % 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: 0.30 (0.15), residues: 3314 helix: 1.83 (0.20), residues: 686 sheet: 0.26 (0.17), residues: 820 loop : -0.43 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 765 TYR 0.025 0.001 TYR A 369 PHE 0.028 0.001 PHE B 541 TRP 0.025 0.001 TRP C 104 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (27671) covalent geometry : angle 0.54983 / 0.28 (37646) SS BOND : bond 0.00308 / 0.21 ( 42) SS BOND : angle 1.38181 / 0.77 ( 84) hydrogen bonds : bond 0.03701 / 2.42 ( 1160) hydrogen bonds : angle 5.14371 / 3.62 ( 3129) link_BETA1-4 : bond 0.00302 / 0.16 ( 20) link_BETA1-4 : angle 1.03703 / 0.69 ( 60) link_NAG-ASN : bond 0.00174 / 0.11 ( 46) link_NAG-ASN : angle 1.58800 / 1.09 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4864.96 seconds wall clock time: 84 minutes 37.91 seconds (5077.91 seconds total)