Starting phenix.real_space_refine on Fri Mar 6 09:47:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nd4_12275/03_2026/7nd4_12275.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nd4_12275/03_2026/7nd4_12275.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 { model { file = "/net/cci-nas-00/data/ceres_data/7nd4_12275/03_2026/7nd4_12275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nd4_12275/03_2026/7nd4_12275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nd4_12275/03_2026/7nd4_12275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nd4_12275/03_2026/7nd4_12275.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= 0.002 sd= 0.021 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 126 5.16 5 C 18918 2.51 5 N 4884 2.21 5 O 5920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29848 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 832 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 105} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Chain: "E" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 832 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 105} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 832 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 105} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.97, per 1000 atoms: 0.23 Number of scatterers: 29848 At special positions: 0 Unit cell: (141.04, 139.4, 227.96, 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 126 16.00 O 5920 8.00 N 4884 7.00 C 18918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA Y 3 " - " MAN Y 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 165 " " 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 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C 165 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " " NAG Y 1 " - " ASN H 35 " " NAG Z 1 " - " ASN D 35 " " NAG a 1 " - " ASN F 35 " Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6930 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 60 sheets defined 21.9% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.563A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.248A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.363A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 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 759 removed outlier: 7.053A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.595A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.772A 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: 4.070A 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: 3.898A 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.602A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.563A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.248A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.362A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 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 759 removed outlier: 7.054A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.595A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.773A 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: 4.069A 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: 3.898A 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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.602A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.563A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.247A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.363A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 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 759 removed outlier: 7.054A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.596A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.772A 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: 4.069A 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: 3.898A 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.602A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.526A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.526A pdb=" N GLU E 84 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 66 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.527A pdb=" N GLU G 84 " --> pdb=" O SER G 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.747A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.588A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.331A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.892A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.386A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.645A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.954A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.380A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.380A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.560A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.492A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.589A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.330A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.892A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.168A 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: 4.386A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.646A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.955A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.381A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.381A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.559A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.491A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.589A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.331A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 316 removed outlier: 6.893A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.645A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.954A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.380A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.380A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.559A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.491A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.480A pdb=" N TRP H 36 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.488A pdb=" N VAL H 116 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N CYS H 101 " --> pdb=" O MET H 114 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET H 114 " --> pdb=" O CYS H 101 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.869A pdb=" N GLU L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.869A pdb=" N GLU L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL L 98 " --> pdb=" O ASP L 93 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.564A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.480A pdb=" N TRP D 36 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG D 52 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP D 38 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.487A pdb=" N VAL D 116 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N CYS D 101 " --> pdb=" O MET D 114 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET D 114 " --> pdb=" O CYS D 101 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.870A pdb=" N GLU E 12 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.870A pdb=" N GLU E 12 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 98 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 17 through 23 removed outlier: 3.564A pdb=" N VAL E 18 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.481A pdb=" N TRP F 36 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG F 52 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP F 38 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.488A pdb=" N VAL F 116 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N CYS F 101 " --> pdb=" O MET F 114 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET F 114 " --> pdb=" O CYS F 101 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.869A pdb=" N GLU G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.869A pdb=" N GLU G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL G 98 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 17 through 23 removed outlier: 3.565A pdb=" N VAL G 18 " --> pdb=" O ILE G 76 " (cutoff:3.500A) 1253 hydrogen bonds defined for protein. 3390 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: 8.17 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9474 1.35 - 1.47: 7747 1.47 - 1.59: 13122 1.59 - 1.71: 0 1.71 - 1.83: 153 Bond restraints: 30496 Sorted by residual: bond pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sigma weight residual 1.417 1.492 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 BMA Y 3 " pdb=" O5 BMA Y 3 " ideal model delta sigma weight residual 1.417 1.492 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 BMA Z 3 " pdb=" O5 BMA Z 3 " ideal model delta sigma weight residual 1.417 1.492 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C4 BMA Y 3 " pdb=" C5 BMA Y 3 " ideal model delta sigma weight residual 1.528 1.575 -0.047 2.00e-02 2.50e+03 5.46e+00 bond pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " ideal model delta sigma weight residual 1.528 1.574 -0.046 2.00e-02 2.50e+03 5.37e+00 ... (remaining 30491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 40546 1.86 - 3.72: 869 3.72 - 5.58: 57 5.58 - 7.44: 27 7.44 - 9.30: 6 Bond angle restraints: 41505 Sorted by residual: angle pdb=" C SER A 698 " pdb=" N LEU A 699 " pdb=" CA LEU A 699 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C SER B 698 " pdb=" N LEU B 699 " pdb=" CA LEU B 699 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C SER C 698 " pdb=" N LEU C 699 " pdb=" CA LEU C 699 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.36e+01 angle pdb=" CA PRO B 527 " pdb=" N PRO B 527 " pdb=" CD PRO B 527 " ideal model delta sigma weight residual 112.00 106.73 5.27 1.40e+00 5.10e-01 1.42e+01 angle pdb=" CA PRO C 527 " pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 112.00 106.73 5.27 1.40e+00 5.10e-01 1.42e+01 ... (remaining 41500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 18050 17.45 - 34.91: 701 34.91 - 52.36: 187 52.36 - 69.81: 78 69.81 - 87.26: 45 Dihedral angle restraints: 19061 sinusoidal: 8261 harmonic: 10800 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -163.35 77.35 1 1.00e+01 1.00e-02 7.50e+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 -86.00 -163.35 77.35 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -163.34 77.34 1 1.00e+01 1.00e-02 7.50e+01 ... (remaining 19058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4456 0.088 - 0.176: 452 0.176 - 0.265: 10 0.265 - 0.353: 3 0.353 - 0.441: 3 Chirality restraints: 4924 Sorted by residual: chirality pdb=" CA ASN B 331 " pdb=" N ASN B 331 " pdb=" C ASN B 331 " pdb=" CB ASN B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA ASN A 331 " pdb=" N ASN A 331 " pdb=" C ASN A 331 " pdb=" CB ASN A 331 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CA ASN C 331 " pdb=" N ASN C 331 " pdb=" C ASN C 331 " pdb=" CB ASN C 331 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 ... (remaining 4921 not shown) Planarity restraints: 5313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.092 5.00e-02 4.00e+02 1.38e-01 3.03e+01 pdb=" N PRO A 527 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " 0.092 5.00e-02 4.00e+02 1.37e-01 3.02e+01 pdb=" N PRO C 527 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " -0.092 5.00e-02 4.00e+02 1.37e-01 3.02e+01 pdb=" N PRO B 527 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.072 5.00e-02 4.00e+02 ... (remaining 5310 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4509 2.77 - 3.30: 27386 3.30 - 3.83: 49230 3.83 - 4.37: 58642 4.37 - 4.90: 101735 Nonbonded interactions: 241502 Sorted by model distance: nonbonded pdb=" O PHE B 565 " pdb=" N PHE C 43 " model vdw 2.233 3.120 nonbonded pdb=" O ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.279 3.040 nonbonded pdb=" O ASP E 83 " pdb=" OH TYR E 87 " model vdw 2.279 3.040 nonbonded pdb=" NZ LYS B 417 " pdb=" OH TYR G 51 " model vdw 2.280 3.120 nonbonded pdb=" O ASP G 83 " pdb=" OH TYR G 87 " model vdw 2.280 3.040 ... (remaining 241497 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' 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' } ncs_group { reference = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.290 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.004 0.081 30615 Z= 0.185 Angle : 0.642 9.301 41814 Z= 0.325 Chirality : 0.048 0.441 4924 Planarity : 0.005 0.138 5265 Dihedral : 11.679 87.262 11987 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 0.28 % Allowed : 2.51 % Favored : 97.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 3669 helix: 0.66 (0.19), residues: 660 sheet: 0.36 (0.15), residues: 990 loop : -0.50 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1000 TYR 0.014 0.001 TYR C 904 PHE 0.016 0.001 PHE C 55 TRP 0.018 0.001 TRP A 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00392 (30496) covalent geometry : angle 0.62023 (41505) SS BOND : bond 0.00250 ( 48) SS BOND : angle 1.11231 ( 96) hydrogen bonds : bond 0.20123 ( 1187) hydrogen bonds : angle 8.26819 ( 3390) link_ALPHA1-3 : bond 0.00770 ( 1) link_ALPHA1-3 : angle 5.60254 ( 3) link_ALPHA1-6 : bond 0.00675 ( 1) link_ALPHA1-6 : angle 0.87223 ( 3) link_BETA1-4 : bond 0.00414 ( 21) link_BETA1-4 : angle 1.13542 ( 63) link_NAG-ASN : bond 0.00222 ( 48) link_NAG-ASN : angle 2.58819 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 343 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 THR cc_start: 0.8921 (m) cc_final: 0.8705 (t) REVERT: A 675 GLN cc_start: 0.7367 (mt0) cc_final: 0.7104 (mt0) REVERT: B 307 THR cc_start: 0.8952 (m) cc_final: 0.8690 (t) REVERT: B 562 PHE cc_start: 0.7905 (p90) cc_final: 0.7672 (p90) REVERT: B 675 GLN cc_start: 0.7369 (mt0) cc_final: 0.7128 (mt0) REVERT: B 975 SER cc_start: 0.8684 (p) cc_final: 0.8402 (t) REVERT: C 239 GLN cc_start: 0.6904 (tt0) cc_final: 0.6342 (mt0) REVERT: C 307 THR cc_start: 0.8973 (m) cc_final: 0.8742 (t) REVERT: C 562 PHE cc_start: 0.7861 (p90) cc_final: 0.7383 (p90) outliers start: 9 outliers final: 1 residues processed: 352 average time/residue: 0.1990 time to fit residues: 112.5876 Evaluate side-chains 166 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 907 ASN A 935 GLN A 949 GLN B 317 ASN B 762 GLN B 935 GLN B 949 GLN C 87 ASN C 317 ASN C 762 GLN C 907 ASN C 935 GLN C 949 GLN C1002 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.204212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.191532 restraints weight = 42282.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.189909 restraints weight = 88851.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.188299 restraints weight = 98039.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.175464 restraints weight = 88885.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.169049 restraints weight = 69323.556| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30615 Z= 0.133 Angle : 0.567 9.107 41814 Z= 0.296 Chirality : 0.046 0.329 4924 Planarity : 0.004 0.079 5265 Dihedral : 6.605 63.712 5473 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.80 % Favored : 98.12 % Rotamer: Outliers : 1.39 % Allowed : 5.42 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.13), residues: 3669 helix: 2.06 (0.20), residues: 642 sheet: 0.58 (0.15), residues: 957 loop : -0.46 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 646 TYR 0.020 0.001 TYR B1067 PHE 0.014 0.001 PHE C 65 TRP 0.010 0.001 TRP A 886 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00298 (30496) covalent geometry : angle 0.54932 (41505) SS BOND : bond 0.00244 ( 48) SS BOND : angle 0.91894 ( 96) hydrogen bonds : bond 0.04127 ( 1187) hydrogen bonds : angle 5.99891 ( 3390) link_ALPHA1-3 : bond 0.00597 ( 1) link_ALPHA1-3 : angle 5.48731 ( 3) link_ALPHA1-6 : bond 0.00669 ( 1) link_ALPHA1-6 : angle 1.46232 ( 3) link_BETA1-4 : bond 0.00425 ( 21) link_BETA1-4 : angle 1.48525 ( 63) link_NAG-ASN : bond 0.00376 ( 48) link_NAG-ASN : angle 2.04049 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 1100 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8221 (m) REVERT: C 562 PHE cc_start: 0.7945 (p90) cc_final: 0.7441 (p90) REVERT: C 1050 MET cc_start: 0.8316 (ptm) cc_final: 0.8110 (ptm) outliers start: 45 outliers final: 22 residues processed: 207 average time/residue: 0.1678 time to fit residues: 59.7036 Evaluate side-chains 170 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 299 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 134 optimal weight: 50.0000 chunk 303 optimal weight: 9.9990 chunk 178 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 chunk 301 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 762 GLN A 907 ASN A1002 GLN B 207 HIS B 762 GLN B 949 GLN C 949 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.201152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159886 restraints weight = 42191.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160727 restraints weight = 89986.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.160194 restraints weight = 38022.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.160504 restraints weight = 35721.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.160516 restraints weight = 26192.156| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30615 Z= 0.195 Angle : 0.564 9.633 41814 Z= 0.293 Chirality : 0.046 0.310 4924 Planarity : 0.004 0.039 5265 Dihedral : 5.559 53.580 5471 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.61 % Allowed : 6.66 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.13), residues: 3669 helix: 1.92 (0.21), residues: 639 sheet: 0.61 (0.15), residues: 969 loop : -0.45 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.019 0.001 TYR B1067 PHE 0.022 0.002 PHE A 168 TRP 0.012 0.001 TRP A 886 HIS 0.008 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00466 (30496) covalent geometry : angle 0.54692 (41505) SS BOND : bond 0.00328 ( 48) SS BOND : angle 0.91788 ( 96) hydrogen bonds : bond 0.04270 ( 1187) hydrogen bonds : angle 5.67789 ( 3390) link_ALPHA1-3 : bond 0.00594 ( 1) link_ALPHA1-3 : angle 5.88599 ( 3) link_ALPHA1-6 : bond 0.00578 ( 1) link_ALPHA1-6 : angle 1.40002 ( 3) link_BETA1-4 : bond 0.00419 ( 21) link_BETA1-4 : angle 1.44914 ( 63) link_NAG-ASN : bond 0.00314 ( 48) link_NAG-ASN : angle 1.96160 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8911 (p) REVERT: A 1100 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8471 (m) REVERT: C 562 PHE cc_start: 0.7956 (p90) cc_final: 0.7563 (p90) outliers start: 52 outliers final: 31 residues processed: 198 average time/residue: 0.1637 time to fit residues: 56.8168 Evaluate side-chains 176 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 347 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 172 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 259 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 901 GLN A 907 ASN B 762 GLN B 949 GLN C 935 GLN C 949 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.200310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.158595 restraints weight = 41834.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.159349 restraints weight = 93302.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158907 restraints weight = 32894.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.159256 restraints weight = 39609.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.159274 restraints weight = 27122.211| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30615 Z= 0.200 Angle : 0.555 13.060 41814 Z= 0.286 Chirality : 0.045 0.269 4924 Planarity : 0.004 0.042 5265 Dihedral : 5.251 53.814 5471 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.47 % Rotamer: Outliers : 1.46 % Allowed : 8.27 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.13), residues: 3669 helix: 1.71 (0.21), residues: 657 sheet: 0.55 (0.15), residues: 966 loop : -0.47 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 905 TYR 0.018 0.001 TYR B1067 PHE 0.018 0.002 PHE C 643 TRP 0.010 0.001 TRP B 886 HIS 0.006 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00480 (30496) covalent geometry : angle 0.53838 (41505) SS BOND : bond 0.00354 ( 48) SS BOND : angle 0.90412 ( 96) hydrogen bonds : bond 0.04018 ( 1187) hydrogen bonds : angle 5.56261 ( 3390) link_ALPHA1-3 : bond 0.01069 ( 1) link_ALPHA1-3 : angle 5.94559 ( 3) link_ALPHA1-6 : bond 0.00521 ( 1) link_ALPHA1-6 : angle 1.39781 ( 3) link_BETA1-4 : bond 0.00345 ( 21) link_BETA1-4 : angle 1.40100 ( 63) link_NAG-ASN : bond 0.00279 ( 48) link_NAG-ASN : angle 1.89824 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1100 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8486 (m) outliers start: 47 outliers final: 37 residues processed: 191 average time/residue: 0.1494 time to fit residues: 51.3660 Evaluate side-chains 183 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 237 optimal weight: 4.9990 chunk 355 optimal weight: 8.9990 chunk 234 optimal weight: 40.0000 chunk 272 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 274 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1002 GLN B 901 GLN B 935 GLN B 949 GLN C 949 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.201605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.173525 restraints weight = 41995.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.171821 restraints weight = 91166.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.168372 restraints weight = 84818.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.165978 restraints weight = 92911.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.163492 restraints weight = 81820.457| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30615 Z= 0.120 Angle : 0.492 10.319 41814 Z= 0.254 Chirality : 0.043 0.197 4924 Planarity : 0.004 0.042 5265 Dihedral : 4.701 53.494 5471 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.40 % Favored : 97.55 % Rotamer: Outliers : 1.15 % Allowed : 8.80 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 3669 helix: 1.93 (0.21), residues: 660 sheet: 0.69 (0.16), residues: 975 loop : -0.45 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.018 0.001 TYR A1067 PHE 0.019 0.001 PHE C 643 TRP 0.008 0.001 TRP H 36 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00278 (30496) covalent geometry : angle 0.47738 (41505) SS BOND : bond 0.00214 ( 48) SS BOND : angle 0.71542 ( 96) hydrogen bonds : bond 0.03453 ( 1187) hydrogen bonds : angle 5.20593 ( 3390) link_ALPHA1-3 : bond 0.01370 ( 1) link_ALPHA1-3 : angle 5.65728 ( 3) link_ALPHA1-6 : bond 0.00456 ( 1) link_ALPHA1-6 : angle 1.47559 ( 3) link_BETA1-4 : bond 0.00395 ( 21) link_BETA1-4 : angle 1.25808 ( 63) link_NAG-ASN : bond 0.00262 ( 48) link_NAG-ASN : angle 1.66572 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 PHE cc_start: 0.7689 (m-80) cc_final: 0.7480 (m-80) outliers start: 37 outliers final: 32 residues processed: 182 average time/residue: 0.1559 time to fit residues: 50.1172 Evaluate side-chains 176 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 194 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 357 optimal weight: 50.0000 chunk 149 optimal weight: 0.7980 chunk 249 optimal weight: 0.3980 chunk 24 optimal weight: 5.9990 chunk 239 optimal weight: 50.0000 chunk 138 optimal weight: 50.0000 chunk 32 optimal weight: 50.0000 chunk 130 optimal weight: 40.0000 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.198553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.184986 restraints weight = 41620.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.183320 restraints weight = 96558.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.171366 restraints weight = 103477.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.165422 restraints weight = 99994.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.161870 restraints weight = 67611.711| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 30615 Z= 0.317 Angle : 0.616 9.562 41814 Z= 0.317 Chirality : 0.048 0.217 4924 Planarity : 0.004 0.047 5265 Dihedral : 4.995 53.766 5471 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 1.80 % Allowed : 8.77 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3669 helix: 1.42 (0.20), residues: 657 sheet: 0.32 (0.15), residues: 1005 loop : -0.55 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1014 TYR 0.018 0.001 TYR B1067 PHE 0.024 0.002 PHE C 643 TRP 0.014 0.001 TRP B 886 HIS 0.008 0.002 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00773 (30496) covalent geometry : angle 0.60095 (41505) SS BOND : bond 0.00560 ( 48) SS BOND : angle 1.01944 ( 96) hydrogen bonds : bond 0.04445 ( 1187) hydrogen bonds : angle 5.61712 ( 3390) link_ALPHA1-3 : bond 0.01373 ( 1) link_ALPHA1-3 : angle 5.06466 ( 3) link_ALPHA1-6 : bond 0.00417 ( 1) link_ALPHA1-6 : angle 1.52155 ( 3) link_BETA1-4 : bond 0.00286 ( 21) link_BETA1-4 : angle 1.40975 ( 63) link_NAG-ASN : bond 0.00356 ( 48) link_NAG-ASN : angle 1.97542 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.8931 (p) REVERT: A 1100 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8395 (m) REVERT: B 284 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.8941 (p) REVERT: B 735 SER cc_start: 0.8671 (t) cc_final: 0.8321 (m) REVERT: C 284 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.8943 (p) REVERT: C 735 SER cc_start: 0.8555 (t) cc_final: 0.8254 (m) outliers start: 58 outliers final: 39 residues processed: 203 average time/residue: 0.1606 time to fit residues: 57.0040 Evaluate side-chains 179 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 265 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 361 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 38 optimal weight: 40.0000 chunk 107 optimal weight: 0.1980 chunk 149 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 314 optimal weight: 50.0000 chunk 365 optimal weight: 50.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 949 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.200772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.173266 restraints weight = 41557.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.170297 restraints weight = 88266.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.167805 restraints weight = 89114.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.165615 restraints weight = 82591.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.164456 restraints weight = 87727.331| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30615 Z= 0.112 Angle : 0.503 9.064 41814 Z= 0.258 Chirality : 0.043 0.188 4924 Planarity : 0.004 0.046 5265 Dihedral : 4.644 53.615 5471 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % Rotamer: Outliers : 1.43 % Allowed : 9.67 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3669 helix: 1.88 (0.21), residues: 660 sheet: 0.59 (0.16), residues: 975 loop : -0.51 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 983 TYR 0.018 0.001 TYR A1067 PHE 0.018 0.001 PHE C 643 TRP 0.008 0.001 TRP H 36 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00252 (30496) covalent geometry : angle 0.48869 (41505) SS BOND : bond 0.00254 ( 48) SS BOND : angle 0.78358 ( 96) hydrogen bonds : bond 0.03487 ( 1187) hydrogen bonds : angle 5.19165 ( 3390) link_ALPHA1-3 : bond 0.01357 ( 1) link_ALPHA1-3 : angle 4.55377 ( 3) link_ALPHA1-6 : bond 0.00451 ( 1) link_ALPHA1-6 : angle 1.52837 ( 3) link_BETA1-4 : bond 0.00389 ( 21) link_BETA1-4 : angle 1.22049 ( 63) link_NAG-ASN : bond 0.00339 ( 48) link_NAG-ASN : angle 1.75472 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 735 SER cc_start: 0.8563 (t) cc_final: 0.8253 (m) REVERT: B 740 MET cc_start: 0.8331 (tpp) cc_final: 0.7806 (tpp) outliers start: 46 outliers final: 32 residues processed: 187 average time/residue: 0.1598 time to fit residues: 52.2836 Evaluate side-chains 179 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 313 optimal weight: 0.1980 chunk 69 optimal weight: 0.0270 chunk 235 optimal weight: 10.0000 chunk 330 optimal weight: 0.4980 chunk 344 optimal weight: 50.0000 chunk 28 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 35 optimal weight: 50.0000 chunk 221 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 949 GLN C 949 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.201675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.174855 restraints weight = 41756.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.171488 restraints weight = 83684.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.168789 restraints weight = 87351.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.166588 restraints weight = 79836.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.164248 restraints weight = 85846.805| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30615 Z= 0.099 Angle : 0.473 8.528 41814 Z= 0.244 Chirality : 0.043 0.182 4924 Planarity : 0.003 0.042 5265 Dihedral : 4.365 53.218 5471 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 1.18 % Allowed : 9.98 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3669 helix: 2.23 (0.21), residues: 642 sheet: 0.60 (0.16), residues: 987 loop : -0.45 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 646 TYR 0.018 0.001 TYR A1067 PHE 0.020 0.001 PHE C 643 TRP 0.009 0.001 TRP A 104 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00224 (30496) covalent geometry : angle 0.46073 (41505) SS BOND : bond 0.00180 ( 48) SS BOND : angle 0.73743 ( 96) hydrogen bonds : bond 0.03228 ( 1187) hydrogen bonds : angle 4.97942 ( 3390) link_ALPHA1-3 : bond 0.01275 ( 1) link_ALPHA1-3 : angle 3.85403 ( 3) link_ALPHA1-6 : bond 0.00484 ( 1) link_ALPHA1-6 : angle 1.50842 ( 3) link_BETA1-4 : bond 0.00400 ( 21) link_BETA1-4 : angle 1.16034 ( 63) link_NAG-ASN : bond 0.00353 ( 48) link_NAG-ASN : angle 1.56067 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 646 ARG cc_start: 0.7236 (tpt90) cc_final: 0.6940 (tpt90) REVERT: B 740 MET cc_start: 0.8341 (tpp) cc_final: 0.7828 (tpp) REVERT: B 754 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8774 (mt) REVERT: B 776 LYS cc_start: 0.8300 (tttt) cc_final: 0.8031 (tttm) REVERT: B 804 GLN cc_start: 0.8017 (mt0) cc_final: 0.7568 (mp10) REVERT: C 776 LYS cc_start: 0.8180 (tttt) cc_final: 0.7839 (tttm) outliers start: 38 outliers final: 27 residues processed: 191 average time/residue: 0.1694 time to fit residues: 55.4201 Evaluate side-chains 179 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 51 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 284 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 255 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 361 optimal weight: 40.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 949 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.200274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.172298 restraints weight = 41658.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.170476 restraints weight = 87820.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.167598 restraints weight = 86327.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.165129 restraints weight = 87896.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.163008 restraints weight = 86420.054| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30615 Z= 0.155 Angle : 0.498 8.309 41814 Z= 0.257 Chirality : 0.044 0.174 4924 Planarity : 0.004 0.041 5265 Dihedral : 4.395 53.815 5471 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.33 % Rotamer: Outliers : 1.15 % Allowed : 9.91 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3669 helix: 2.14 (0.21), residues: 642 sheet: 0.64 (0.16), residues: 969 loop : -0.46 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.018 0.001 TYR B1067 PHE 0.031 0.001 PHE C 643 TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00368 (30496) covalent geometry : angle 0.48636 (41505) SS BOND : bond 0.00290 ( 48) SS BOND : angle 0.78798 ( 96) hydrogen bonds : bond 0.03497 ( 1187) hydrogen bonds : angle 5.06274 ( 3390) link_ALPHA1-3 : bond 0.01630 ( 1) link_ALPHA1-3 : angle 3.41815 ( 3) link_ALPHA1-6 : bond 0.00454 ( 1) link_ALPHA1-6 : angle 1.47673 ( 3) link_BETA1-4 : bond 0.00362 ( 21) link_BETA1-4 : angle 1.19045 ( 63) link_NAG-ASN : bond 0.00234 ( 48) link_NAG-ASN : angle 1.62492 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 284 THR cc_start: 0.9389 (OUTLIER) cc_final: 0.8978 (p) REVERT: B 646 ARG cc_start: 0.7267 (tpt90) cc_final: 0.6904 (tpt90) REVERT: B 735 SER cc_start: 0.8554 (t) cc_final: 0.8270 (m) REVERT: B 740 MET cc_start: 0.8354 (tpp) cc_final: 0.7831 (tpp) REVERT: B 754 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8802 (mp) REVERT: B 804 GLN cc_start: 0.8041 (mt0) cc_final: 0.7639 (mp10) REVERT: C 735 SER cc_start: 0.8464 (t) cc_final: 0.8208 (m) outliers start: 37 outliers final: 30 residues processed: 183 average time/residue: 0.1559 time to fit residues: 50.1190 Evaluate side-chains 184 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 194 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 293 optimal weight: 0.7980 chunk 367 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 365 optimal weight: 50.0000 chunk 275 optimal weight: 0.5980 chunk 140 optimal weight: 50.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.200312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.172374 restraints weight = 41509.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.170503 restraints weight = 88623.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.167963 restraints weight = 84305.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.165454 restraints weight = 80629.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.162649 restraints weight = 88722.348| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30615 Z= 0.147 Angle : 0.497 8.214 41814 Z= 0.256 Chirality : 0.044 0.175 4924 Planarity : 0.004 0.041 5265 Dihedral : 4.365 53.886 5471 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.38 % Rotamer: Outliers : 1.15 % Allowed : 10.10 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3669 helix: 2.15 (0.21), residues: 639 sheet: 0.59 (0.16), residues: 987 loop : -0.45 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.018 0.001 TYR B1067 PHE 0.037 0.001 PHE C 643 TRP 0.011 0.001 TRP A 104 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00350 (30496) covalent geometry : angle 0.48539 (41505) SS BOND : bond 0.00271 ( 48) SS BOND : angle 0.78004 ( 96) hydrogen bonds : bond 0.03459 ( 1187) hydrogen bonds : angle 5.04591 ( 3390) link_ALPHA1-3 : bond 0.01299 ( 1) link_ALPHA1-3 : angle 3.23945 ( 3) link_ALPHA1-6 : bond 0.00483 ( 1) link_ALPHA1-6 : angle 1.48313 ( 3) link_BETA1-4 : bond 0.00376 ( 21) link_BETA1-4 : angle 1.18459 ( 63) link_NAG-ASN : bond 0.00232 ( 48) link_NAG-ASN : angle 1.60837 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7338 Ramachandran restraints generated. 3669 Oldfield, 0 Emsley, 3669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1100 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8327 (m) REVERT: B 284 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.8965 (p) REVERT: B 646 ARG cc_start: 0.7263 (tpt90) cc_final: 0.6884 (tpt90) REVERT: B 735 SER cc_start: 0.8541 (t) cc_final: 0.8266 (m) REVERT: B 740 MET cc_start: 0.8350 (tpp) cc_final: 0.7858 (tpp) REVERT: B 804 GLN cc_start: 0.8051 (mt0) cc_final: 0.7647 (mp10) REVERT: C 735 SER cc_start: 0.8454 (t) cc_final: 0.8231 (m) outliers start: 37 outliers final: 29 residues processed: 181 average time/residue: 0.1528 time to fit residues: 49.1965 Evaluate side-chains 181 residues out of total 3231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain G residue 51 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 111 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 288 optimal weight: 0.2980 chunk 102 optimal weight: 0.0980 chunk 121 optimal weight: 0.5980 chunk 354 optimal weight: 30.0000 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 949 GLN B1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.201583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.172284 restraints weight = 41993.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.171248 restraints weight = 96035.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.169221 restraints weight = 85845.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.166483 restraints weight = 92722.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.164934 restraints weight = 85196.304| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30615 Z= 0.100 Angle : 0.478 10.217 41814 Z= 0.245 Chirality : 0.043 0.172 4924 Planarity : 0.003 0.039 5265 Dihedral : 4.216 53.634 5471 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 0.96 % Allowed : 10.56 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3669 helix: 2.31 (0.21), residues: 639 sheet: 0.66 (0.16), residues: 990 loop : -0.39 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.018 0.001 TYR A1067 PHE 0.035 0.001 PHE C 643 TRP 0.008 0.001 TRP B 104 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00226 (30496) covalent geometry : angle 0.46716 (41505) SS BOND : bond 0.00202 ( 48) SS BOND : angle 0.72617 ( 96) hydrogen bonds : bond 0.03203 ( 1187) hydrogen bonds : angle 4.90558 ( 3390) link_ALPHA1-3 : bond 0.01592 ( 1) link_ALPHA1-3 : angle 2.94293 ( 3) link_ALPHA1-6 : bond 0.00507 ( 1) link_ALPHA1-6 : angle 1.45979 ( 3) link_BETA1-4 : bond 0.00396 ( 21) link_BETA1-4 : angle 1.13745 ( 63) link_NAG-ASN : bond 0.00246 ( 48) link_NAG-ASN : angle 1.51373 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3898.20 seconds wall clock time: 69 minutes 12.48 seconds (4152.48 seconds total)