Starting phenix.real_space_refine on Sun Jul 5 09:35:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n1y_24127/07_2026/7n1y_24127.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n1y_24127/07_2026/7n1y_24127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n1y_24127/07_2026/7n1y_24127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n1y_24127/07_2026/7n1y_24127.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7n1y_24127/07_2026/7n1y_24127.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n1y_24127/07_2026/7n1y_24127.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n1y_24127/07_2026/7n1y_24127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n1y_24127/07_2026/7n1y_24127.map" } resolution = 4.3 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= 0.005 sd= 0.052 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 114 5.16 5 C 16930 2.51 5 N 4314 2.21 5 O 5278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 139 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26636 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 8441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8441 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 52, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 8517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8517 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 52, 'TRANS': 1034} Chain breaks: 5 Chain: "C" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8434 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 52, 'TRANS': 1024} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.99, per 1000 atoms: 0.22 Number of scatterers: 26636 At special positions: 0 Unit cell: (153.462, 152.637, 216.168, 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 114 16.00 O 5278 8.00 N 4314 7.00 C 16930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.00 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=1.99 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.00 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.00 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 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=1.99 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.05 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.07 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 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=1, symmetry=0 Links applied ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG S 2 " - " MAN S 3 " " NAG T 2 " - " MAN T 3 " " NAG a 2 " - " MAN a 3 " " NAG b 2 " - " MAN b 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 3 " " NAG Z 1 " - " FUC Z 3 " NAG-ASN " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1405 " - " ASN A 234 " " NAG A1406 " - " ASN A 282 " " NAG A1407 " - " ASN A 343 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 657 " " NAG A1410 " - " ASN A 709 " " NAG A1411 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 331 " " NAG B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG B1410 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1403 " - " ASN C 149 " " NAG C1404 " - " ASN C 165 " " NAG C1406 " - " ASN C 282 " " NAG C1407 " - " ASN C 343 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 657 " " NAG C1410 " - " ASN C 709 " " NAG C1411 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 282 " " NAG O 1 " - " ASN B 616 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1074 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 17 " " NAG V 1 " - " ASN C 331 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.0 seconds 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6074 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 47 sheets defined 25.2% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.502A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.742A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.052A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.762A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.603A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.685A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.781A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.895A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) 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: 4.258A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.516A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 993 Processing helix chain 'A' and resid 993 through 1033 removed outlier: 3.843A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.947A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.548A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.483A 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 438 through 443 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.601A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.214A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.712A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.846A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.584A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.572A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.727A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.555A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (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 978 through 983 Processing helix chain 'B' and resid 987 through 1033 removed outlier: 4.173A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1159 removed outlier: 3.911A pdb=" N GLU B1151 " --> pdb=" O SER B1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.557A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.123A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.615A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 623 removed outlier: 3.835A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 737 through 743 removed outlier: 4.042A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.539A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.696A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 4.152A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.529A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.584A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.854A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) 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 966 removed outlier: 3.661A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 989 through 1032 removed outlier: 4.280A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 3.553A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 9.006A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.760A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N SER A 221 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ARG A 34 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N LEU A 223 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.687A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.564A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.705A 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: 6.538A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.596A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.046A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.254A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.128A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.660A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.485A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.745A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.493A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.493A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.035A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.029A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.893A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.627A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 6.786A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.242A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.688A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 318 removed outlier: 3.727A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.967A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.450A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.253A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.170A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.527A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.745A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.745A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.252A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.504A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 9.733A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.722A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.360A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.523A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.503A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.843A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.007A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.576A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.892A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.216A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.155A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.609A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 2928 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.23 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4416 1.31 - 1.44: 7414 1.44 - 1.58: 15250 1.58 - 1.72: 0 1.72 - 1.85: 144 Bond restraints: 27224 Sorted by residual: bond pdb=" CA ASP C 985 " pdb=" C ASP C 985 " ideal model delta sigma weight residual 1.517 1.565 -0.048 6.30e-03 2.52e+04 5.77e+01 bond pdb=" CA PRO C 792 " pdb=" C PRO C 792 " ideal model delta sigma weight residual 1.514 1.548 -0.033 5.50e-03 3.31e+04 3.66e+01 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.522 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" CA ARG C 995 " pdb=" C ARG C 995 " ideal model delta sigma weight residual 1.525 1.458 0.067 1.25e-02 6.40e+03 2.86e+01 bond pdb=" C5 NAG A1410 " pdb=" O5 NAG A1410 " ideal model delta sigma weight residual 1.413 1.514 -0.101 2.00e-02 2.50e+03 2.54e+01 ... (remaining 27219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 30416 2.78 - 5.55: 6080 5.55 - 8.33: 503 8.33 - 11.10: 25 11.10 - 13.88: 3 Bond angle restraints: 37027 Sorted by residual: angle pdb=" N ARG C1091 " pdb=" CA ARG C1091 " pdb=" C ARG C1091 " ideal model delta sigma weight residual 111.03 97.92 13.11 1.11e+00 8.12e-01 1.39e+02 angle pdb=" N PHE B 374 " pdb=" CA PHE B 374 " pdb=" C PHE B 374 " ideal model delta sigma weight residual 109.96 123.84 -13.88 1.49e+00 4.50e-01 8.67e+01 angle pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " pdb=" CG PHE A 559 " ideal model delta sigma weight residual 113.80 122.70 -8.90 1.00e+00 1.00e+00 7.92e+01 angle pdb=" N ARG A1091 " pdb=" CA ARG A1091 " pdb=" C ARG A1091 " ideal model delta sigma weight residual 111.14 101.70 9.44 1.08e+00 8.57e-01 7.63e+01 angle pdb=" OD1 ASN A 149 " pdb=" CG ASN A 149 " pdb=" ND2 ASN A 149 " ideal model delta sigma weight residual 122.60 114.25 8.35 1.00e+00 1.00e+00 6.97e+01 ... (remaining 37022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13949 17.95 - 35.89: 1244 35.89 - 53.84: 200 53.84 - 71.78: 66 71.78 - 89.73: 40 Dihedral angle restraints: 15499 sinusoidal: 6059 harmonic: 9440 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -174.36 88.36 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 159.74 -66.74 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 156.88 -63.88 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 15496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.680: 4432 0.680 - 1.360: 5 1.360 - 2.039: 3 2.039 - 2.719: 1 2.719 - 3.399: 2 Chirality restraints: 4443 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 1.00 -3.40 2.00e-01 2.50e+01 2.89e+02 chirality pdb=" C1 NAG A1407 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1407 " pdb=" O5 NAG A1407 " both_signs ideal model delta sigma weight residual False -2.40 0.67 -3.07 2.00e-01 2.50e+01 2.35e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.71 0.31 2.00e-02 2.50e+03 2.35e+02 ... (remaining 4440 not shown) Planarity restraints: 4714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " 0.202 2.00e-02 2.50e+03 2.22e-01 6.14e+02 pdb=" CG ASN C 165 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " -0.370 2.00e-02 2.50e+03 pdb=" C1 NAG C1404 " 0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 17 " 0.164 2.00e-02 2.50e+03 1.78e-01 3.95e+02 pdb=" CG ASN C 17 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN C 17 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN C 17 " -0.284 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1098 " 0.183 2.00e-02 2.50e+03 1.72e-01 3.70e+02 pdb=" CG ASN A1098 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN A1098 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN A1098 " -0.270 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.190 2.00e-02 2.50e+03 ... (remaining 4711 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 8 1.86 - 2.62: 191 2.62 - 3.38: 34780 3.38 - 4.14: 65438 4.14 - 4.90: 111177 Nonbonded interactions: 211594 Sorted by model distance: nonbonded pdb=" CD ARG B1107 " pdb=" CE1 TYR C 904 " model vdw 1.099 3.740 nonbonded pdb=" NH1 ARG C 21 " pdb=" O PHE C 79 " model vdw 1.301 3.120 nonbonded pdb=" NE ARG B1107 " pdb=" CE1 TYR C 904 " model vdw 1.314 3.420 nonbonded pdb=" O PRO A 337 " pdb=" OE2 GLU A 340 " model vdw 1.382 3.040 nonbonded pdb=" CB TYR C 453 " pdb=" OH TYR C 495 " model vdw 1.452 3.440 ... (remaining 211589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 826 or resid 854 through 1410)) selection = (chain 'B' and (resid 14 through 623 or resid 641 through 826 or resid 854 throu \ gh 1410)) selection = (chain 'C' and (resid 14 through 826 or resid 854 through 1410)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) } 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: 7.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 27.350 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 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 : 0.018 0.502 27351 Z= 1.026 Angle : 2.222 39.650 37363 Z= 1.399 Chirality : 0.154 3.399 4443 Planarity : 0.015 0.114 4664 Dihedral : 14.945 89.729 9299 Min Nonbonded Distance : 1.099 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.55 % Favored : 90.83 % Rotamer: Outliers : 1.91 % Allowed : 7.16 % Favored : 90.93 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.13), residues: 3206 helix: -2.14 (0.16), residues: 680 sheet: -0.56 (0.21), residues: 499 loop : -2.23 (0.12), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.002 ARG C1039 TYR 0.117 0.022 TYR A 91 PHE 0.094 0.019 PHE C 898 TRP 0.123 0.027 TRP A 886 HIS 0.034 0.008 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.01610 / 0.94 (27224) covalent geometry : angle 2.10881 / 1.38 (37027) SS BOND : bond 0.01799 / 1.33 ( 42) SS BOND : angle 2.84694 / 1.95 ( 84) hydrogen bonds : bond 0.16785 / 10.95 ( 1030) hydrogen bonds : angle 9.58036 / 6.52 ( 2928) Misc. bond : bond 0.33256 / 17.50 ( 1) link_ALPHA1-4 : bond 0.03580 / 1.84 ( 6) link_ALPHA1-4 : angle 5.16023 / 3.01 ( 18) link_BETA1-4 : bond 0.02522 / 1.74 ( 25) link_BETA1-4 : angle 4.16341 / 2.71 ( 75) link_BETA1-6 : bond 0.03372 / 1.70 ( 3) link_BETA1-6 : angle 3.56731 / 2.25 ( 9) link_NAG-ASN : bond 0.16939 / 7.86 ( 50) link_NAG-ASN : angle 10.71153 / 7.63 ( 150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 727 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.5901 (t80) cc_final: 0.5365 (t80) REVERT: A 51 THR cc_start: 0.7019 (t) cc_final: 0.6809 (m) REVERT: A 196 ASN cc_start: 0.6556 (p0) cc_final: 0.6129 (p0) REVERT: A 223 LEU cc_start: 0.7515 (mp) cc_final: 0.7272 (mp) REVERT: A 298 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7038 (pp20) REVERT: A 468 ILE cc_start: 0.8003 (mm) cc_final: 0.7776 (pt) REVERT: A 515 PHE cc_start: 0.5431 (p90) cc_final: 0.5202 (p90) REVERT: A 695 TYR cc_start: 0.7211 (p90) cc_final: 0.6481 (p90) REVERT: A 705 VAL cc_start: 0.7713 (t) cc_final: 0.7333 (p) REVERT: A 737 ASP cc_start: 0.7404 (t0) cc_final: 0.6482 (t0) REVERT: A 759 PHE cc_start: 0.7447 (p90) cc_final: 0.7061 (p90) REVERT: A 773 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6762 (tp30) REVERT: A 789 TYR cc_start: 0.8357 (m-80) cc_final: 0.7960 (m-10) REVERT: A 795 LYS cc_start: 0.6623 (mmtp) cc_final: 0.6387 (mmtt) REVERT: A 858 LEU cc_start: 0.7372 (pp) cc_final: 0.6607 (mt) REVERT: A 865 LEU cc_start: 0.8598 (mt) cc_final: 0.7963 (pp) REVERT: A 894 LEU cc_start: 0.8451 (mm) cc_final: 0.8201 (mm) REVERT: A 900 MET cc_start: 0.7789 (tpp) cc_final: 0.7582 (tpp) REVERT: A 906 PHE cc_start: 0.8467 (m-80) cc_final: 0.8110 (m-80) REVERT: A 907 ASN cc_start: 0.7371 (m-40) cc_final: 0.6750 (m-40) REVERT: A 913 GLN cc_start: 0.8784 (pm20) cc_final: 0.8162 (pm20) REVERT: A 954 GLN cc_start: 0.7672 (pt0) cc_final: 0.7373 (pt0) REVERT: A 1050 MET cc_start: 0.5949 (ptm) cc_final: 0.5313 (ptm) REVERT: A 1108 ASN cc_start: 0.8581 (m110) cc_final: 0.8364 (m110) REVERT: A 1115 ILE cc_start: 0.8590 (mp) cc_final: 0.8353 (mt) REVERT: A 1121 PHE cc_start: 0.7733 (p90) cc_final: 0.7500 (p90) REVERT: B 33 THR cc_start: 0.6407 (p) cc_final: 0.5283 (m) REVERT: B 58 PHE cc_start: 0.8019 (m-10) cc_final: 0.7554 (m-80) REVERT: B 64 TRP cc_start: 0.5074 (t60) cc_final: 0.4577 (t60) REVERT: B 80 ASP cc_start: 0.4983 (t0) cc_final: 0.4112 (p0) REVERT: B 81 ASN cc_start: 0.6136 (p0) cc_final: 0.5814 (m-40) REVERT: B 157 PHE cc_start: 0.4001 (t80) cc_final: 0.3381 (t80) REVERT: B 201 PHE cc_start: 0.7595 (t80) cc_final: 0.7388 (t80) REVERT: B 228 ASP cc_start: 0.7291 (t70) cc_final: 0.6983 (t70) REVERT: B 270 LEU cc_start: 0.8417 (tp) cc_final: 0.8046 (tp) REVERT: B 451 TYR cc_start: 0.5381 (m-80) cc_final: 0.4905 (m-10) REVERT: B 455 LEU cc_start: 0.6667 (tp) cc_final: 0.6409 (tp) REVERT: B 541 PHE cc_start: 0.7116 (p90) cc_final: 0.6899 (p90) REVERT: B 573 THR cc_start: 0.7506 (m) cc_final: 0.7131 (m) REVERT: B 675 GLN cc_start: 0.7888 (mt0) cc_final: 0.7485 (tt0) REVERT: B 693 ILE cc_start: 0.8251 (mt) cc_final: 0.7794 (mp) REVERT: B 707 TYR cc_start: 0.7018 (t80) cc_final: 0.6242 (t80) REVERT: B 725 GLU cc_start: 0.7843 (tp30) cc_final: 0.7631 (tp30) REVERT: B 731 MET cc_start: 0.7362 (ptt) cc_final: 0.6923 (ptt) REVERT: B 773 GLU cc_start: 0.7482 (pt0) cc_final: 0.7113 (pp20) REVERT: B 780 GLU cc_start: 0.7247 (mt-10) cc_final: 0.7035 (mt-10) REVERT: B 815 ARG cc_start: 0.6458 (ttp-170) cc_final: 0.5609 (ttp-170) REVERT: B 819 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7134 (mt-10) REVERT: B 882 ILE cc_start: 0.8789 (tt) cc_final: 0.8546 (mm) REVERT: B 900 MET cc_start: 0.8451 (mmp) cc_final: 0.8100 (mmm) REVERT: B 921 LYS cc_start: 0.8094 (mmmm) cc_final: 0.7640 (mmmm) REVERT: B 950 ASP cc_start: 0.7848 (t70) cc_final: 0.7145 (t0) REVERT: B 1028 LYS cc_start: 0.7563 (ttmm) cc_final: 0.7177 (ttmm) REVERT: B 1031 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6839 (tt0) REVERT: B 1037 SER cc_start: 0.6949 (OUTLIER) cc_final: 0.6109 (t) REVERT: B 1088 HIS cc_start: 0.7390 (m170) cc_final: 0.7024 (m170) REVERT: B 1111 GLU cc_start: 0.7538 (tm-30) cc_final: 0.6329 (tm-30) REVERT: C 41 LYS cc_start: 0.7752 (tttt) cc_final: 0.7338 (tttp) REVERT: C 133 PHE cc_start: 0.7258 (m-80) cc_final: 0.6948 (m-80) REVERT: C 206 LYS cc_start: 0.7310 (ttpp) cc_final: 0.6979 (ttpp) REVERT: C 343 ASN cc_start: 0.5033 (OUTLIER) cc_final: 0.4331 (p0) REVERT: C 387 LEU cc_start: 0.8235 (tp) cc_final: 0.7745 (pp) REVERT: C 540 ASN cc_start: 0.7570 (m-40) cc_final: 0.7098 (m110) REVERT: C 654 GLU cc_start: 0.6994 (mp0) cc_final: 0.6707 (mp0) REVERT: C 664 ILE cc_start: 0.7633 (mm) cc_final: 0.7421 (mm) REVERT: C 720 ILE cc_start: 0.8148 (mm) cc_final: 0.7737 (tt) REVERT: C 736 VAL cc_start: 0.7963 (t) cc_final: 0.7526 (p) REVERT: C 742 ILE cc_start: 0.8248 (mm) cc_final: 0.7676 (tt) REVERT: C 814 LYS cc_start: 0.7561 (mmtt) cc_final: 0.7303 (mmmt) REVERT: C 898 PHE cc_start: 0.7652 (t80) cc_final: 0.7022 (t80) REVERT: C 907 ASN cc_start: 0.8701 (t0) cc_final: 0.8488 (t0) REVERT: C 919 ASN cc_start: 0.8423 (t0) cc_final: 0.7744 (t0) REVERT: C 973 ILE cc_start: 0.7878 (pt) cc_final: 0.7598 (pt) REVERT: C 975 SER cc_start: 0.7915 (p) cc_final: 0.7612 (m) REVERT: C 1001 LEU cc_start: 0.8261 (tp) cc_final: 0.7958 (tp) outliers start: 54 outliers final: 16 residues processed: 771 average time/residue: 0.1819 time to fit residues: 220.8469 Evaluate side-chains 557 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 537 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 872 GLN A 919 ASN A1106 GLN A1113 GLN B 115 GLN B 239 GLN B 321 GLN B 856 ASN B 872 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1048 HIS B1088 HIS C 115 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 655 HIS C 675 GLN C 907 ASN C 919 ASN C 926 GLN C 957 GLN C1058 HIS C1083 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.077867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.065350 restraints weight = 137670.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.067261 restraints weight = 83858.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.068611 restraints weight = 56741.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.069544 restraints weight = 41657.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.070193 restraints weight = 32870.968| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27351 Z= 0.182 Angle : 0.938 21.925 37363 Z= 0.454 Chirality : 0.056 0.681 4443 Planarity : 0.005 0.065 4664 Dihedral : 7.079 30.486 3472 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 0.14 % Allowed : 4.76 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.13), residues: 3206 helix: -0.50 (0.18), residues: 691 sheet: -0.40 (0.20), residues: 543 loop : -1.79 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 815 TYR 0.042 0.003 TYR C 505 PHE 0.041 0.002 PHE A 58 TRP 0.042 0.003 TRP A 64 HIS 0.012 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (27224) covalent geometry : angle 0.84892 / 0.43 (37027) SS BOND : bond 0.00424 / 0.28 ( 42) SS BOND : angle 1.99385 / 1.28 ( 84) hydrogen bonds : bond 0.05006 / 3.34 ( 1030) hydrogen bonds : angle 7.15009 / 4.86 ( 2928) Misc. bond : bond 0.00291 / 0.15 ( 1) link_ALPHA1-4 : bond 0.01125 / 0.61 ( 6) link_ALPHA1-4 : angle 3.09106 / 1.77 ( 18) link_BETA1-4 : bond 0.00560 / 0.39 ( 25) link_BETA1-4 : angle 2.10517 / 1.37 ( 75) link_BETA1-6 : bond 0.00532 / 0.27 ( 3) link_BETA1-6 : angle 1.68958 / 0.90 ( 9) link_NAG-ASN : bond 0.01051 / 0.65 ( 50) link_NAG-ASN : angle 5.97080 / 3.94 ( 150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 638 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.5785 (t80) cc_final: 0.5349 (t80) REVERT: A 106 PHE cc_start: 0.7039 (m-80) cc_final: 0.6801 (m-80) REVERT: A 118 LEU cc_start: 0.7940 (tt) cc_final: 0.7716 (tt) REVERT: A 270 LEU cc_start: 0.8220 (mt) cc_final: 0.7988 (mt) REVERT: A 300 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7800 (mttm) REVERT: A 309 GLU cc_start: 0.7676 (pm20) cc_final: 0.7453 (pm20) REVERT: A 532 ASN cc_start: 0.7576 (m110) cc_final: 0.7103 (p0) REVERT: A 553 THR cc_start: 0.7612 (m) cc_final: 0.7345 (m) REVERT: A 654 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6488 (mm-30) REVERT: A 695 TYR cc_start: 0.7204 (p90) cc_final: 0.6170 (p90) REVERT: A 737 ASP cc_start: 0.7083 (t0) cc_final: 0.6430 (t70) REVERT: A 759 PHE cc_start: 0.7364 (p90) cc_final: 0.7123 (p90) REVERT: A 773 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6676 (tp30) REVERT: A 818 ILE cc_start: 0.8525 (mm) cc_final: 0.8262 (mm) REVERT: A 901 GLN cc_start: 0.7507 (tm-30) cc_final: 0.7161 (tm-30) REVERT: A 906 PHE cc_start: 0.8526 (m-80) cc_final: 0.8097 (m-80) REVERT: A 916 LEU cc_start: 0.8316 (tp) cc_final: 0.7870 (tp) REVERT: A 934 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7816 (mm) REVERT: A 951 VAL cc_start: 0.8070 (t) cc_final: 0.7785 (t) REVERT: A 1034 LEU cc_start: 0.8629 (mp) cc_final: 0.8392 (mp) REVERT: A 1041 ASP cc_start: 0.7976 (t0) cc_final: 0.7730 (t0) REVERT: B 33 THR cc_start: 0.6710 (p) cc_final: 0.5843 (m) REVERT: B 58 PHE cc_start: 0.8069 (m-10) cc_final: 0.7358 (m-80) REVERT: B 64 TRP cc_start: 0.4973 (t60) cc_final: 0.3598 (t60) REVERT: B 80 ASP cc_start: 0.4877 (t0) cc_final: 0.4121 (p0) REVERT: B 81 ASN cc_start: 0.6048 (p0) cc_final: 0.5702 (m-40) REVERT: B 92 PHE cc_start: 0.6696 (t80) cc_final: 0.6308 (t80) REVERT: B 270 LEU cc_start: 0.8085 (tp) cc_final: 0.7835 (tp) REVERT: B 495 TYR cc_start: 0.6076 (m-80) cc_final: 0.5701 (m-80) REVERT: B 693 ILE cc_start: 0.8092 (mt) cc_final: 0.7818 (mp) REVERT: B 710 ASN cc_start: 0.8126 (p0) cc_final: 0.7212 (t0) REVERT: B 731 MET cc_start: 0.7070 (ptt) cc_final: 0.6612 (ptt) REVERT: B 741 TYR cc_start: 0.8407 (t80) cc_final: 0.7945 (t80) REVERT: B 773 GLU cc_start: 0.7221 (pt0) cc_final: 0.6946 (pp20) REVERT: B 815 ARG cc_start: 0.6335 (ttp-170) cc_final: 0.5777 (ttp-170) REVERT: B 820 ASP cc_start: 0.7296 (m-30) cc_final: 0.6687 (m-30) REVERT: B 900 MET cc_start: 0.8629 (mmp) cc_final: 0.8109 (mmp) REVERT: B 901 GLN cc_start: 0.7556 (tm-30) cc_final: 0.7194 (tm-30) REVERT: B 902 MET cc_start: 0.8291 (tpp) cc_final: 0.8013 (tpt) REVERT: B 921 LYS cc_start: 0.8034 (mmmm) cc_final: 0.7737 (mmmt) REVERT: B 950 ASP cc_start: 0.7879 (t70) cc_final: 0.7279 (t0) REVERT: B 960 ASN cc_start: 0.7777 (t0) cc_final: 0.7464 (t0) REVERT: B 1028 LYS cc_start: 0.7702 (ttmm) cc_final: 0.7476 (ttmm) REVERT: B 1037 SER cc_start: 0.6722 (p) cc_final: 0.6379 (m) REVERT: B 1088 HIS cc_start: 0.7422 (m-70) cc_final: 0.6927 (m-70) REVERT: B 1105 THR cc_start: 0.6536 (m) cc_final: 0.5941 (t) REVERT: B 1111 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6156 (tm-30) REVERT: B 1113 GLN cc_start: 0.6382 (mp10) cc_final: 0.5760 (mp10) REVERT: B 1121 PHE cc_start: 0.6408 (p90) cc_final: 0.5999 (p90) REVERT: C 228 ASP cc_start: 0.7029 (t0) cc_final: 0.6764 (t70) REVERT: C 296 LEU cc_start: 0.7642 (tt) cc_final: 0.7350 (tt) REVERT: C 387 LEU cc_start: 0.8104 (tp) cc_final: 0.7792 (pp) REVERT: C 646 ARG cc_start: 0.8225 (mmt90) cc_final: 0.7547 (mmm-85) REVERT: C 664 ILE cc_start: 0.7444 (mm) cc_final: 0.6667 (mm) REVERT: C 720 ILE cc_start: 0.7916 (mm) cc_final: 0.7401 (tt) REVERT: C 814 LYS cc_start: 0.7338 (mmtt) cc_final: 0.6979 (mmmt) REVERT: C 900 MET cc_start: 0.8540 (mmp) cc_final: 0.7667 (mmp) REVERT: C 904 TYR cc_start: 0.7948 (m-80) cc_final: 0.7431 (m-80) REVERT: C 917 TYR cc_start: 0.8051 (m-80) cc_final: 0.7466 (m-80) REVERT: C 919 ASN cc_start: 0.8451 (t0) cc_final: 0.7776 (t0) REVERT: C 922 LEU cc_start: 0.8212 (tt) cc_final: 0.7886 (tt) REVERT: C 923 ILE cc_start: 0.8481 (mt) cc_final: 0.8184 (mt) REVERT: C 926 GLN cc_start: 0.7825 (pt0) cc_final: 0.7597 (pt0) REVERT: C 973 ILE cc_start: 0.7875 (pt) cc_final: 0.7647 (pt) REVERT: C 1001 LEU cc_start: 0.8094 (tp) cc_final: 0.7807 (tp) REVERT: C 1005 GLN cc_start: 0.7340 (mm-40) cc_final: 0.7110 (mm-40) REVERT: C 1033 VAL cc_start: 0.8857 (t) cc_final: 0.8474 (t) REVERT: C 1039 ARG cc_start: 0.6721 (mtm180) cc_final: 0.6505 (mtm-85) REVERT: C 1061 VAL cc_start: 0.8231 (t) cc_final: 0.7939 (m) REVERT: C 1062 PHE cc_start: 0.7174 (m-80) cc_final: 0.6753 (m-80) REVERT: C 1110 TYR cc_start: 0.6770 (t80) cc_final: 0.6569 (t80) REVERT: C 1138 TYR cc_start: 0.7331 (t80) cc_final: 0.7105 (t80) outliers start: 4 outliers final: 0 residues processed: 640 average time/residue: 0.1774 time to fit residues: 181.2641 Evaluate side-chains 496 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 495 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 93 optimal weight: 0.6980 chunk 321 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 230 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 254 optimal weight: 0.0970 chunk 222 optimal weight: 5.9990 chunk 280 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 225 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 895 GLN B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 675 GLN C1125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.077999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.065381 restraints weight = 136981.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.067272 restraints weight = 83320.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.068610 restraints weight = 56474.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.069567 restraints weight = 41595.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.070177 restraints weight = 32824.822| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27351 Z= 0.147 Angle : 0.804 20.109 37363 Z= 0.389 Chirality : 0.051 0.589 4443 Planarity : 0.005 0.063 4664 Dihedral : 6.280 28.129 3472 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.14), residues: 3206 helix: 0.19 (0.20), residues: 689 sheet: -0.40 (0.21), residues: 519 loop : -1.62 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 214 TYR 0.027 0.002 TYR A 453 PHE 0.042 0.002 PHE C1156 TRP 0.026 0.002 TRP A 64 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (27224) covalent geometry : angle 0.74182 / 0.38 (37027) SS BOND : bond 0.00568 / 0.43 ( 42) SS BOND : angle 1.72218 / 1.12 ( 84) hydrogen bonds : bond 0.04290 / 2.83 ( 1030) hydrogen bonds : angle 6.59780 / 4.49 ( 2928) Misc. bond : bond 0.00343 / 0.18 ( 1) link_ALPHA1-4 : bond 0.01070 / 0.60 ( 6) link_ALPHA1-4 : angle 2.61128 / 1.51 ( 18) link_BETA1-4 : bond 0.00517 / 0.35 ( 25) link_BETA1-4 : angle 1.78034 / 1.14 ( 75) link_BETA1-6 : bond 0.00580 / 0.30 ( 3) link_BETA1-6 : angle 1.08823 / 0.60 ( 9) link_NAG-ASN : bond 0.00745 / 0.47 ( 50) link_NAG-ASN : angle 4.56752 / 2.94 ( 150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 602 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8409 (m-30) cc_final: 0.8032 (p0) REVERT: A 140 PHE cc_start: 0.6241 (p90) cc_final: 0.6039 (p90) REVERT: A 201 PHE cc_start: 0.7479 (t80) cc_final: 0.7072 (t80) REVERT: A 207 HIS cc_start: 0.6341 (t-90) cc_final: 0.6053 (t-170) REVERT: A 208 THR cc_start: 0.7406 (p) cc_final: 0.6916 (t) REVERT: A 270 LEU cc_start: 0.8242 (mt) cc_final: 0.8008 (mt) REVERT: A 296 LEU cc_start: 0.8805 (tp) cc_final: 0.8552 (tp) REVERT: A 300 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7740 (mttm) REVERT: A 468 ILE cc_start: 0.7678 (mm) cc_final: 0.7401 (pt) REVERT: A 532 ASN cc_start: 0.7679 (m110) cc_final: 0.7190 (p0) REVERT: A 553 THR cc_start: 0.7625 (m) cc_final: 0.7386 (m) REVERT: A 695 TYR cc_start: 0.7379 (p90) cc_final: 0.6392 (p90) REVERT: A 697 MET cc_start: 0.6785 (ptp) cc_final: 0.6282 (ptm) REVERT: A 699 LEU cc_start: 0.8213 (mm) cc_final: 0.7910 (mp) REVERT: A 707 TYR cc_start: 0.6874 (t80) cc_final: 0.6477 (t80) REVERT: A 737 ASP cc_start: 0.7067 (t0) cc_final: 0.6529 (t0) REVERT: A 740 MET cc_start: 0.6991 (tpt) cc_final: 0.6781 (tpt) REVERT: A 759 PHE cc_start: 0.7277 (p90) cc_final: 0.6980 (p90) REVERT: A 773 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6571 (tp30) REVERT: A 815 ARG cc_start: 0.5998 (mtm110) cc_final: 0.5566 (mtm110) REVERT: A 818 ILE cc_start: 0.8475 (mm) cc_final: 0.8201 (mm) REVERT: A 900 MET cc_start: 0.7735 (tpp) cc_final: 0.7464 (mmm) REVERT: A 901 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7249 (tm-30) REVERT: A 905 ARG cc_start: 0.7291 (mtt-85) cc_final: 0.7036 (mtt-85) REVERT: A 906 PHE cc_start: 0.8532 (m-80) cc_final: 0.8122 (m-80) REVERT: A 916 LEU cc_start: 0.8302 (tp) cc_final: 0.7670 (tp) REVERT: A 934 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7713 (mm) REVERT: A 1017 GLU cc_start: 0.7772 (mp0) cc_final: 0.7391 (mp0) REVERT: A 1047 TYR cc_start: 0.7903 (m-80) cc_final: 0.7408 (m-80) REVERT: B 33 THR cc_start: 0.6757 (p) cc_final: 0.5816 (m) REVERT: B 58 PHE cc_start: 0.8095 (m-10) cc_final: 0.7353 (m-80) REVERT: B 80 ASP cc_start: 0.4905 (t0) cc_final: 0.4291 (p0) REVERT: B 92 PHE cc_start: 0.6590 (t80) cc_final: 0.6104 (t80) REVERT: B 158 ARG cc_start: 0.4691 (mpt180) cc_final: 0.4376 (mmt-90) REVERT: B 201 PHE cc_start: 0.7710 (t80) cc_final: 0.7460 (t80) REVERT: B 270 LEU cc_start: 0.8020 (tp) cc_final: 0.7761 (tp) REVERT: B 309 GLU cc_start: 0.7514 (mp0) cc_final: 0.7302 (mp0) REVERT: B 338 PHE cc_start: 0.5384 (m-10) cc_final: 0.4964 (m-80) REVERT: B 351 TYR cc_start: 0.6132 (p90) cc_final: 0.5827 (p90) REVERT: B 495 TYR cc_start: 0.6077 (m-80) cc_final: 0.5564 (m-80) REVERT: B 557 LYS cc_start: 0.6801 (mtmt) cc_final: 0.6414 (mttp) REVERT: B 573 THR cc_start: 0.8108 (p) cc_final: 0.7827 (p) REVERT: B 613 GLN cc_start: 0.6465 (OUTLIER) cc_final: 0.6255 (mp10) REVERT: B 693 ILE cc_start: 0.7899 (mt) cc_final: 0.7621 (mp) REVERT: B 710 ASN cc_start: 0.8089 (p0) cc_final: 0.7203 (t0) REVERT: B 725 GLU cc_start: 0.8006 (tp30) cc_final: 0.7693 (tp30) REVERT: B 731 MET cc_start: 0.7013 (ptt) cc_final: 0.6712 (ptt) REVERT: B 733 LYS cc_start: 0.7515 (mtpt) cc_final: 0.7270 (mtpp) REVERT: B 741 TYR cc_start: 0.8428 (t80) cc_final: 0.7950 (t80) REVERT: B 755 GLN cc_start: 0.7939 (mm110) cc_final: 0.7525 (mm-40) REVERT: B 872 GLN cc_start: 0.8061 (mp10) cc_final: 0.7769 (mm-40) REVERT: B 882 ILE cc_start: 0.8959 (mm) cc_final: 0.8741 (tt) REVERT: B 900 MET cc_start: 0.8362 (mmp) cc_final: 0.7963 (mmp) REVERT: B 902 MET cc_start: 0.8348 (tpp) cc_final: 0.8125 (tpp) REVERT: B 921 LYS cc_start: 0.8104 (mmmm) cc_final: 0.7854 (mmmt) REVERT: B 960 ASN cc_start: 0.7859 (t0) cc_final: 0.7528 (t0) REVERT: B 1017 GLU cc_start: 0.7573 (tt0) cc_final: 0.7334 (tt0) REVERT: B 1028 LYS cc_start: 0.7733 (ttmm) cc_final: 0.7476 (ttmm) REVERT: B 1034 LEU cc_start: 0.8441 (mp) cc_final: 0.8200 (mp) REVERT: B 1037 SER cc_start: 0.6845 (p) cc_final: 0.6538 (m) REVERT: B 1050 MET cc_start: 0.7357 (ptm) cc_final: 0.7138 (ptm) REVERT: B 1088 HIS cc_start: 0.7504 (m-70) cc_final: 0.6988 (m170) REVERT: B 1105 THR cc_start: 0.6386 (m) cc_final: 0.5793 (t) REVERT: C 40 ASP cc_start: 0.8031 (p0) cc_final: 0.7813 (p0) REVERT: C 65 PHE cc_start: 0.7530 (m-80) cc_final: 0.7162 (m-80) REVERT: C 153 MET cc_start: 0.3756 (mtm) cc_final: 0.3282 (ttm) REVERT: C 228 ASP cc_start: 0.6924 (t0) cc_final: 0.6656 (t70) REVERT: C 720 ILE cc_start: 0.7766 (mm) cc_final: 0.7287 (tt) REVERT: C 742 ILE cc_start: 0.8219 (mm) cc_final: 0.7503 (tt) REVERT: C 814 LYS cc_start: 0.7260 (mmtt) cc_final: 0.6841 (mmmt) REVERT: C 886 TRP cc_start: 0.7280 (p90) cc_final: 0.7010 (p90) REVERT: C 898 PHE cc_start: 0.7308 (t80) cc_final: 0.7047 (t80) REVERT: C 900 MET cc_start: 0.8513 (mmp) cc_final: 0.7230 (mmp) REVERT: C 902 MET cc_start: 0.8405 (mmm) cc_final: 0.7826 (mmm) REVERT: C 919 ASN cc_start: 0.8305 (t0) cc_final: 0.7738 (t0) REVERT: C 922 LEU cc_start: 0.8199 (tt) cc_final: 0.7934 (tt) REVERT: C 1013 ILE cc_start: 0.7548 (tp) cc_final: 0.7235 (tt) REVERT: C 1019 ARG cc_start: 0.7180 (ttm170) cc_final: 0.6966 (ttm170) REVERT: C 1061 VAL cc_start: 0.8206 (t) cc_final: 0.7872 (m) REVERT: C 1110 TYR cc_start: 0.6716 (t80) cc_final: 0.6455 (t80) REVERT: C 1125 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.7050 (p0) REVERT: C 1138 TYR cc_start: 0.7349 (t80) cc_final: 0.7127 (t80) outliers start: 4 outliers final: 0 residues processed: 605 average time/residue: 0.1765 time to fit residues: 170.5505 Evaluate side-chains 482 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 479 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 290 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 134 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 239 GLN C 926 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.077504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.064735 restraints weight = 139846.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.066609 restraints weight = 86120.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.067982 restraints weight = 58810.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.068925 restraints weight = 43362.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.069611 restraints weight = 34308.449| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27351 Z= 0.156 Angle : 0.794 19.795 37363 Z= 0.383 Chirality : 0.050 0.504 4443 Planarity : 0.005 0.160 4664 Dihedral : 6.134 27.378 3472 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.14), residues: 3206 helix: 0.44 (0.20), residues: 681 sheet: -0.44 (0.21), residues: 559 loop : -1.57 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 815 TYR 0.023 0.002 TYR C 741 PHE 0.033 0.002 PHE C 135 TRP 0.045 0.002 TRP A 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (27224) covalent geometry : angle 0.73069 / 0.37 (37027) SS BOND : bond 0.00618 / 0.37 ( 42) SS BOND : angle 1.78365 / 1.13 ( 84) hydrogen bonds : bond 0.04122 / 2.73 ( 1030) hydrogen bonds : angle 6.47996 / 4.41 ( 2928) Misc. bond : bond 0.00309 / 0.16 ( 1) link_ALPHA1-4 : bond 0.00933 / 0.48 ( 6) link_ALPHA1-4 : angle 2.18615 / 1.24 ( 18) link_BETA1-4 : bond 0.00473 / 0.31 ( 25) link_BETA1-4 : angle 1.71469 / 1.10 ( 75) link_BETA1-6 : bond 0.00532 / 0.27 ( 3) link_BETA1-6 : angle 1.07236 / 0.59 ( 9) link_NAG-ASN : bond 0.00697 / 0.44 ( 50) link_NAG-ASN : angle 4.62997 / 3.07 ( 150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 573 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8421 (m-30) cc_final: 0.8028 (p0) REVERT: A 140 PHE cc_start: 0.6287 (p90) cc_final: 0.5999 (p90) REVERT: A 191 GLU cc_start: 0.6825 (pm20) cc_final: 0.6601 (pm20) REVERT: A 296 LEU cc_start: 0.8805 (tp) cc_final: 0.8534 (tp) REVERT: A 300 LYS cc_start: 0.8145 (mtpt) cc_final: 0.7727 (mttm) REVERT: A 468 ILE cc_start: 0.7635 (mm) cc_final: 0.7337 (pt) REVERT: A 517 LEU cc_start: 0.5248 (tp) cc_final: 0.5021 (tt) REVERT: A 532 ASN cc_start: 0.7835 (m110) cc_final: 0.7321 (p0) REVERT: A 553 THR cc_start: 0.7742 (m) cc_final: 0.7368 (m) REVERT: A 695 TYR cc_start: 0.7514 (p90) cc_final: 0.6560 (p90) REVERT: A 697 MET cc_start: 0.6895 (ptp) cc_final: 0.6150 (ptm) REVERT: A 699 LEU cc_start: 0.8274 (mm) cc_final: 0.8018 (mt) REVERT: A 707 TYR cc_start: 0.6930 (t80) cc_final: 0.6618 (t80) REVERT: A 737 ASP cc_start: 0.7083 (t0) cc_final: 0.6511 (t0) REVERT: A 773 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6687 (tp30) REVERT: A 815 ARG cc_start: 0.5891 (mtm110) cc_final: 0.5652 (mtm180) REVERT: A 818 ILE cc_start: 0.8498 (mm) cc_final: 0.8159 (mm) REVERT: A 901 GLN cc_start: 0.7470 (tm-30) cc_final: 0.6663 (tm-30) REVERT: A 905 ARG cc_start: 0.7281 (mtt-85) cc_final: 0.7009 (mtt-85) REVERT: A 906 PHE cc_start: 0.8530 (m-80) cc_final: 0.8125 (m-80) REVERT: A 916 LEU cc_start: 0.8161 (tp) cc_final: 0.7835 (tp) REVERT: A 934 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7713 (mm) REVERT: A 1017 GLU cc_start: 0.7707 (mp0) cc_final: 0.7154 (mp0) REVERT: A 1041 ASP cc_start: 0.7868 (t70) cc_final: 0.7544 (t0) REVERT: B 33 THR cc_start: 0.6804 (p) cc_final: 0.5439 (m) REVERT: B 58 PHE cc_start: 0.8027 (m-10) cc_final: 0.7354 (m-80) REVERT: B 88 ASP cc_start: 0.6974 (m-30) cc_final: 0.6681 (p0) REVERT: B 92 PHE cc_start: 0.6377 (t80) cc_final: 0.6158 (t80) REVERT: B 115 GLN cc_start: 0.7437 (mt0) cc_final: 0.7213 (mp10) REVERT: B 201 PHE cc_start: 0.7783 (t80) cc_final: 0.7578 (t80) REVERT: B 204 TYR cc_start: 0.6582 (m-80) cc_final: 0.6107 (m-80) REVERT: B 270 LEU cc_start: 0.8070 (tp) cc_final: 0.7302 (tp) REVERT: B 309 GLU cc_start: 0.7557 (mp0) cc_final: 0.7310 (mp0) REVERT: B 351 TYR cc_start: 0.6109 (p90) cc_final: 0.5789 (p90) REVERT: B 557 LYS cc_start: 0.6781 (mtmt) cc_final: 0.6354 (mttp) REVERT: B 570 ASP cc_start: 0.7300 (t70) cc_final: 0.6983 (t0) REVERT: B 573 THR cc_start: 0.8136 (p) cc_final: 0.7857 (p) REVERT: B 693 ILE cc_start: 0.7878 (mt) cc_final: 0.7632 (mp) REVERT: B 697 MET cc_start: 0.6707 (ttp) cc_final: 0.6337 (ttp) REVERT: B 710 ASN cc_start: 0.8137 (p0) cc_final: 0.7219 (t0) REVERT: B 731 MET cc_start: 0.7051 (ptt) cc_final: 0.6743 (ptt) REVERT: B 741 TYR cc_start: 0.8446 (t80) cc_final: 0.7847 (t80) REVERT: B 755 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7482 (mm-40) REVERT: B 872 GLN cc_start: 0.8022 (mp10) cc_final: 0.7774 (mm-40) REVERT: B 900 MET cc_start: 0.8349 (mmp) cc_final: 0.8093 (mmp) REVERT: B 902 MET cc_start: 0.8394 (tpp) cc_final: 0.8075 (tpp) REVERT: B 921 LYS cc_start: 0.8142 (mmmm) cc_final: 0.7859 (mmmt) REVERT: B 949 GLN cc_start: 0.8138 (mm110) cc_final: 0.7872 (mm110) REVERT: B 960 ASN cc_start: 0.7907 (t0) cc_final: 0.7586 (t0) REVERT: B 1028 LYS cc_start: 0.7758 (ttmm) cc_final: 0.7511 (ttmm) REVERT: B 1034 LEU cc_start: 0.8425 (mp) cc_final: 0.8190 (mp) REVERT: B 1037 SER cc_start: 0.6963 (p) cc_final: 0.6606 (m) REVERT: B 1088 HIS cc_start: 0.7501 (m-70) cc_final: 0.7196 (m-70) REVERT: B 1105 THR cc_start: 0.6468 (m) cc_final: 0.5929 (t) REVERT: C 65 PHE cc_start: 0.7470 (m-80) cc_final: 0.7020 (m-80) REVERT: C 133 PHE cc_start: 0.6445 (m-80) cc_final: 0.6141 (m-10) REVERT: C 153 MET cc_start: 0.3829 (mtm) cc_final: 0.3400 (ttm) REVERT: C 189 LEU cc_start: 0.7948 (tp) cc_final: 0.7508 (tp) REVERT: C 190 ARG cc_start: 0.6051 (mmm-85) cc_final: 0.4811 (tpp80) REVERT: C 228 ASP cc_start: 0.6960 (t0) cc_final: 0.6710 (t70) REVERT: C 720 ILE cc_start: 0.7722 (mm) cc_final: 0.7260 (tt) REVERT: C 742 ILE cc_start: 0.8310 (mm) cc_final: 0.7607 (tt) REVERT: C 814 LYS cc_start: 0.7382 (mmtt) cc_final: 0.7000 (mmmt) REVERT: C 900 MET cc_start: 0.8437 (mmp) cc_final: 0.7526 (mmp) REVERT: C 919 ASN cc_start: 0.8296 (t0) cc_final: 0.7646 (t0) REVERT: C 922 LEU cc_start: 0.8195 (tt) cc_final: 0.7875 (tt) REVERT: C 973 ILE cc_start: 0.7777 (pt) cc_final: 0.7555 (pt) REVERT: C 1013 ILE cc_start: 0.7529 (tp) cc_final: 0.7300 (tp) REVERT: C 1061 VAL cc_start: 0.8245 (t) cc_final: 0.7848 (m) REVERT: C 1110 TYR cc_start: 0.6739 (t80) cc_final: 0.6359 (t80) REVERT: C 1138 TYR cc_start: 0.7354 (t80) cc_final: 0.7088 (t80) outliers start: 2 outliers final: 0 residues processed: 574 average time/residue: 0.1724 time to fit residues: 160.1669 Evaluate side-chains 472 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 471 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 212 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 282 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 225 optimal weight: 0.0040 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.077700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.064935 restraints weight = 140169.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066827 restraints weight = 85136.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.068190 restraints weight = 57872.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.069150 restraints weight = 42639.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.069755 restraints weight = 33744.105| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27351 Z= 0.139 Angle : 0.746 19.784 37363 Z= 0.361 Chirality : 0.049 0.499 4443 Planarity : 0.005 0.109 4664 Dihedral : 5.888 27.323 3472 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.04 % Allowed : 2.51 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3206 helix: 0.60 (0.20), residues: 681 sheet: -0.40 (0.20), residues: 577 loop : -1.56 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 815 TYR 0.028 0.002 TYR B 636 PHE 0.040 0.002 PHE B 157 TRP 0.024 0.002 TRP A 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (27224) covalent geometry : angle 0.69548 / 0.35 (37027) SS BOND : bond 0.00443 / 0.29 ( 42) SS BOND : angle 1.67260 / 1.11 ( 84) hydrogen bonds : bond 0.03928 / 2.60 ( 1030) hydrogen bonds : angle 6.33569 / 4.30 ( 2928) Misc. bond : bond 0.00400 / 0.21 ( 1) link_ALPHA1-4 : bond 0.00958 / 0.52 ( 6) link_ALPHA1-4 : angle 2.19254 / 1.29 ( 18) link_BETA1-4 : bond 0.00475 / 0.31 ( 25) link_BETA1-4 : angle 1.57012 / 1.01 ( 75) link_BETA1-6 : bond 0.00626 / 0.32 ( 3) link_BETA1-6 : angle 1.15738 / 0.63 ( 9) link_NAG-ASN : bond 0.00629 / 0.38 ( 50) link_NAG-ASN : angle 3.99164 / 2.59 ( 150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 587 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8483 (m-30) cc_final: 0.8026 (p0) REVERT: A 140 PHE cc_start: 0.6382 (p90) cc_final: 0.6030 (p90) REVERT: A 191 GLU cc_start: 0.6830 (pm20) cc_final: 0.6267 (pm20) REVERT: A 275 PHE cc_start: 0.6921 (m-10) cc_final: 0.6678 (m-80) REVERT: A 296 LEU cc_start: 0.8819 (tp) cc_final: 0.8530 (tp) REVERT: A 300 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7668 (mttm) REVERT: A 466 ARG cc_start: 0.5799 (mmt90) cc_final: 0.4820 (mmm160) REVERT: A 468 ILE cc_start: 0.7595 (mm) cc_final: 0.7339 (pt) REVERT: A 532 ASN cc_start: 0.7866 (m110) cc_final: 0.7335 (p0) REVERT: A 553 THR cc_start: 0.7711 (m) cc_final: 0.7337 (m) REVERT: A 695 TYR cc_start: 0.7539 (p90) cc_final: 0.6561 (p90) REVERT: A 699 LEU cc_start: 0.8236 (mm) cc_final: 0.7965 (mt) REVERT: A 702 GLU cc_start: 0.7802 (tt0) cc_final: 0.7458 (mp0) REVERT: A 707 TYR cc_start: 0.6852 (t80) cc_final: 0.6601 (t80) REVERT: A 737 ASP cc_start: 0.7101 (t0) cc_final: 0.6436 (t0) REVERT: A 773 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6727 (tp30) REVERT: A 815 ARG cc_start: 0.5917 (mtm110) cc_final: 0.5490 (mtm110) REVERT: A 901 GLN cc_start: 0.7696 (tm-30) cc_final: 0.6613 (tm-30) REVERT: A 905 ARG cc_start: 0.7308 (mtt-85) cc_final: 0.7082 (mtt-85) REVERT: A 907 ASN cc_start: 0.8110 (p0) cc_final: 0.7906 (p0) REVERT: A 1017 GLU cc_start: 0.7685 (mp0) cc_final: 0.7162 (mp0) REVERT: A 1041 ASP cc_start: 0.7873 (t70) cc_final: 0.7512 (t0) REVERT: B 33 THR cc_start: 0.6699 (p) cc_final: 0.5365 (m) REVERT: B 48 LEU cc_start: 0.8434 (mp) cc_final: 0.7994 (mt) REVERT: B 58 PHE cc_start: 0.8074 (m-10) cc_final: 0.7376 (m-80) REVERT: B 61 ASN cc_start: 0.3779 (t0) cc_final: 0.3138 (p0) REVERT: B 64 TRP cc_start: 0.4168 (t60) cc_final: 0.2764 (t60) REVERT: B 88 ASP cc_start: 0.6900 (m-30) cc_final: 0.6590 (p0) REVERT: B 92 PHE cc_start: 0.6480 (t80) cc_final: 0.6191 (t80) REVERT: B 198 ASP cc_start: 0.6311 (m-30) cc_final: 0.5860 (m-30) REVERT: B 201 PHE cc_start: 0.7854 (t80) cc_final: 0.7580 (t80) REVERT: B 204 TYR cc_start: 0.6604 (m-80) cc_final: 0.6036 (m-80) REVERT: B 270 LEU cc_start: 0.8128 (tp) cc_final: 0.7330 (tp) REVERT: B 309 GLU cc_start: 0.7576 (mp0) cc_final: 0.7309 (mp0) REVERT: B 351 TYR cc_start: 0.6124 (p90) cc_final: 0.5874 (p90) REVERT: B 495 TYR cc_start: 0.5829 (m-80) cc_final: 0.5438 (m-80) REVERT: B 557 LYS cc_start: 0.6790 (mtmt) cc_final: 0.6342 (mttp) REVERT: B 570 ASP cc_start: 0.7342 (t70) cc_final: 0.7057 (t0) REVERT: B 573 THR cc_start: 0.8150 (p) cc_final: 0.7904 (p) REVERT: B 693 ILE cc_start: 0.7806 (mt) cc_final: 0.7564 (mp) REVERT: B 697 MET cc_start: 0.6509 (ttp) cc_final: 0.6234 (ttp) REVERT: B 710 ASN cc_start: 0.8127 (p0) cc_final: 0.7232 (t0) REVERT: B 725 GLU cc_start: 0.8121 (tp30) cc_final: 0.7768 (tp30) REVERT: B 731 MET cc_start: 0.7068 (ptt) cc_final: 0.6751 (ptt) REVERT: B 741 TYR cc_start: 0.8476 (t80) cc_final: 0.7854 (t80) REVERT: B 755 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7417 (mm-40) REVERT: B 872 GLN cc_start: 0.8162 (mp10) cc_final: 0.7887 (mm-40) REVERT: B 900 MET cc_start: 0.8358 (mmp) cc_final: 0.8022 (mmp) REVERT: B 960 ASN cc_start: 0.7894 (t0) cc_final: 0.7601 (t0) REVERT: B 961 THR cc_start: 0.7387 (m) cc_final: 0.7169 (m) REVERT: B 1028 LYS cc_start: 0.7738 (ttmm) cc_final: 0.7449 (ttmm) REVERT: B 1037 SER cc_start: 0.6947 (p) cc_final: 0.6562 (m) REVERT: B 1088 HIS cc_start: 0.7520 (m-70) cc_final: 0.7265 (m-70) REVERT: B 1105 THR cc_start: 0.6301 (m) cc_final: 0.5797 (t) REVERT: C 40 ASP cc_start: 0.8073 (p0) cc_final: 0.7785 (p0) REVERT: C 65 PHE cc_start: 0.7532 (m-80) cc_final: 0.6954 (m-80) REVERT: C 96 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6765 (mt-10) REVERT: C 133 PHE cc_start: 0.6235 (m-80) cc_final: 0.5888 (m-10) REVERT: C 153 MET cc_start: 0.4008 (mtm) cc_final: 0.3639 (ttm) REVERT: C 177 MET cc_start: 0.4213 (mpp) cc_final: 0.3905 (mmt) REVERT: C 189 LEU cc_start: 0.7942 (tp) cc_final: 0.7668 (tp) REVERT: C 190 ARG cc_start: 0.6022 (mmm-85) cc_final: 0.5589 (tpp80) REVERT: C 228 ASP cc_start: 0.6979 (t0) cc_final: 0.6751 (t70) REVERT: C 720 ILE cc_start: 0.7657 (mm) cc_final: 0.7113 (tt) REVERT: C 782 PHE cc_start: 0.8211 (m-10) cc_final: 0.8006 (m-80) REVERT: C 814 LYS cc_start: 0.7412 (mmtt) cc_final: 0.6991 (mmmt) REVERT: C 821 LEU cc_start: 0.7105 (mm) cc_final: 0.6605 (mm) REVERT: C 886 TRP cc_start: 0.7202 (p90) cc_final: 0.6998 (p90) REVERT: C 900 MET cc_start: 0.8434 (mmp) cc_final: 0.7398 (mmp) REVERT: C 919 ASN cc_start: 0.8344 (t0) cc_final: 0.7684 (t0) REVERT: C 922 LEU cc_start: 0.8153 (tt) cc_final: 0.7765 (tt) REVERT: C 1013 ILE cc_start: 0.7513 (tp) cc_final: 0.7243 (tp) REVERT: C 1061 VAL cc_start: 0.8242 (t) cc_final: 0.7803 (m) REVERT: C 1110 TYR cc_start: 0.6661 (t80) cc_final: 0.6371 (t80) REVERT: C 1138 TYR cc_start: 0.7361 (t80) cc_final: 0.7141 (t80) REVERT: C 1141 LEU cc_start: 0.7935 (tp) cc_final: 0.7688 (mp) outliers start: 1 outliers final: 0 residues processed: 587 average time/residue: 0.1677 time to fit residues: 158.9099 Evaluate side-chains 485 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 220 optimal weight: 0.0870 chunk 240 optimal weight: 9.9990 chunk 108 optimal weight: 0.0170 chunk 57 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 183 optimal weight: 0.0670 overall best weight: 0.8336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 196 ASN A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 115 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.077618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.064944 restraints weight = 140458.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.066840 restraints weight = 85332.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.068199 restraints weight = 57969.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.069161 restraints weight = 42669.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.069848 restraints weight = 33696.636| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27351 Z= 0.145 Angle : 0.741 19.629 37363 Z= 0.359 Chirality : 0.049 0.489 4443 Planarity : 0.005 0.081 4664 Dihedral : 5.753 26.097 3472 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.07 % Allowed : 2.51 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.14), residues: 3206 helix: 0.57 (0.20), residues: 691 sheet: -0.52 (0.20), residues: 590 loop : -1.56 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 815 TYR 0.024 0.002 TYR C 741 PHE 0.064 0.002 PHE B 823 TRP 0.018 0.002 TRP A 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (27224) covalent geometry : angle 0.69409 / 0.35 (37027) SS BOND : bond 0.00484 / 0.35 ( 42) SS BOND : angle 1.79510 / 1.11 ( 84) hydrogen bonds : bond 0.03846 / 2.54 ( 1030) hydrogen bonds : angle 6.27932 / 4.26 ( 2928) Misc. bond : bond 0.00281 / 0.15 ( 1) link_ALPHA1-4 : bond 0.00968 / 0.53 ( 6) link_ALPHA1-4 : angle 2.09162 / 1.24 ( 18) link_BETA1-4 : bond 0.00453 / 0.29 ( 25) link_BETA1-4 : angle 1.50125 / 0.97 ( 75) link_BETA1-6 : bond 0.00533 / 0.27 ( 3) link_BETA1-6 : angle 1.10798 / 0.60 ( 9) link_NAG-ASN : bond 0.00621 / 0.37 ( 50) link_NAG-ASN : angle 3.79241 / 2.44 ( 150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 592 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8492 (m-30) cc_final: 0.8056 (p0) REVERT: A 140 PHE cc_start: 0.6347 (p90) cc_final: 0.5985 (p90) REVERT: A 191 GLU cc_start: 0.6873 (pm20) cc_final: 0.6274 (pm20) REVERT: A 201 PHE cc_start: 0.7841 (t80) cc_final: 0.7533 (t80) REVERT: A 275 PHE cc_start: 0.6972 (m-10) cc_final: 0.6732 (m-80) REVERT: A 296 LEU cc_start: 0.8839 (tp) cc_final: 0.8398 (tp) REVERT: A 300 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7680 (mttm) REVERT: A 313 TYR cc_start: 0.7642 (m-80) cc_final: 0.7433 (m-10) REVERT: A 468 ILE cc_start: 0.7656 (mm) cc_final: 0.7118 (tt) REVERT: A 532 ASN cc_start: 0.8010 (m110) cc_final: 0.7417 (p0) REVERT: A 553 THR cc_start: 0.7622 (m) cc_final: 0.7231 (m) REVERT: A 695 TYR cc_start: 0.7597 (p90) cc_final: 0.6565 (p90) REVERT: A 699 LEU cc_start: 0.8334 (mm) cc_final: 0.7999 (mt) REVERT: A 707 TYR cc_start: 0.6894 (t80) cc_final: 0.6254 (t80) REVERT: A 737 ASP cc_start: 0.7195 (t0) cc_final: 0.6883 (t0) REVERT: A 773 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6760 (tp30) REVERT: A 815 ARG cc_start: 0.5831 (mtm110) cc_final: 0.5369 (mtm-85) REVERT: A 934 ILE cc_start: 0.7942 (mm) cc_final: 0.7697 (mm) REVERT: A 1017 GLU cc_start: 0.7655 (mp0) cc_final: 0.7171 (mp0) REVERT: B 48 LEU cc_start: 0.8411 (mp) cc_final: 0.7970 (mt) REVERT: B 61 ASN cc_start: 0.3966 (t0) cc_final: 0.3290 (p0) REVERT: B 88 ASP cc_start: 0.6924 (m-30) cc_final: 0.6669 (p0) REVERT: B 92 PHE cc_start: 0.6501 (t80) cc_final: 0.5979 (t80) REVERT: B 201 PHE cc_start: 0.7801 (t80) cc_final: 0.7524 (t80) REVERT: B 204 TYR cc_start: 0.6590 (m-80) cc_final: 0.6038 (m-80) REVERT: B 270 LEU cc_start: 0.8028 (tp) cc_final: 0.7037 (tp) REVERT: B 309 GLU cc_start: 0.7580 (mp0) cc_final: 0.7320 (mp0) REVERT: B 351 TYR cc_start: 0.6198 (p90) cc_final: 0.5997 (p90) REVERT: B 495 TYR cc_start: 0.5908 (m-80) cc_final: 0.5380 (m-80) REVERT: B 557 LYS cc_start: 0.6808 (mtmt) cc_final: 0.6384 (mttp) REVERT: B 570 ASP cc_start: 0.7488 (t70) cc_final: 0.7194 (t0) REVERT: B 573 THR cc_start: 0.8113 (p) cc_final: 0.7875 (p) REVERT: B 693 ILE cc_start: 0.7851 (mt) cc_final: 0.7622 (mp) REVERT: B 697 MET cc_start: 0.6525 (ttp) cc_final: 0.6217 (ttp) REVERT: B 707 TYR cc_start: 0.7187 (t80) cc_final: 0.6463 (t80) REVERT: B 710 ASN cc_start: 0.8145 (p0) cc_final: 0.7263 (t0) REVERT: B 725 GLU cc_start: 0.8150 (tp30) cc_final: 0.7764 (tp30) REVERT: B 731 MET cc_start: 0.7031 (ptt) cc_final: 0.6709 (ptt) REVERT: B 741 TYR cc_start: 0.8479 (t80) cc_final: 0.7836 (t80) REVERT: B 755 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7323 (mm-40) REVERT: B 815 ARG cc_start: 0.6268 (ttp-170) cc_final: 0.6057 (ttp-170) REVERT: B 867 ASP cc_start: 0.7524 (p0) cc_final: 0.7245 (t0) REVERT: B 872 GLN cc_start: 0.8212 (mp10) cc_final: 0.7844 (mm-40) REVERT: B 882 ILE cc_start: 0.8942 (mm) cc_final: 0.8633 (tt) REVERT: B 902 MET cc_start: 0.8360 (tpp) cc_final: 0.8160 (tpp) REVERT: B 954 GLN cc_start: 0.7672 (mt0) cc_final: 0.7431 (tt0) REVERT: B 960 ASN cc_start: 0.7854 (t0) cc_final: 0.7576 (t0) REVERT: B 961 THR cc_start: 0.7428 (m) cc_final: 0.7145 (m) REVERT: B 1014 ARG cc_start: 0.6137 (ttm170) cc_final: 0.5573 (ttm170) REVERT: B 1028 LYS cc_start: 0.7774 (ttmm) cc_final: 0.7491 (ttmm) REVERT: B 1037 SER cc_start: 0.6944 (p) cc_final: 0.6544 (m) REVERT: B 1088 HIS cc_start: 0.7536 (m-70) cc_final: 0.7335 (m-70) REVERT: B 1105 THR cc_start: 0.6330 (m) cc_final: 0.6072 (m) REVERT: C 40 ASP cc_start: 0.8083 (p0) cc_final: 0.7793 (p0) REVERT: C 65 PHE cc_start: 0.7596 (m-80) cc_final: 0.7025 (m-80) REVERT: C 133 PHE cc_start: 0.6252 (m-80) cc_final: 0.5947 (m-10) REVERT: C 153 MET cc_start: 0.4126 (mtm) cc_final: 0.3794 (ttm) REVERT: C 190 ARG cc_start: 0.6137 (mmm-85) cc_final: 0.5788 (tpp80) REVERT: C 568 ASP cc_start: 0.8003 (t0) cc_final: 0.7789 (t70) REVERT: C 646 ARG cc_start: 0.8356 (mmt90) cc_final: 0.8084 (mmm-85) REVERT: C 720 ILE cc_start: 0.7601 (mm) cc_final: 0.7044 (tt) REVERT: C 742 ILE cc_start: 0.8173 (mm) cc_final: 0.7511 (tt) REVERT: C 782 PHE cc_start: 0.8208 (m-10) cc_final: 0.7994 (m-80) REVERT: C 814 LYS cc_start: 0.7470 (mmtt) cc_final: 0.7058 (mmmt) REVERT: C 898 PHE cc_start: 0.7349 (t80) cc_final: 0.7027 (t80) REVERT: C 900 MET cc_start: 0.8401 (mmp) cc_final: 0.7250 (mmp) REVERT: C 919 ASN cc_start: 0.8372 (t0) cc_final: 0.7736 (t0) REVERT: C 922 LEU cc_start: 0.8165 (tt) cc_final: 0.7743 (tt) REVERT: C 973 ILE cc_start: 0.7730 (pt) cc_final: 0.7493 (pt) REVERT: C 1013 ILE cc_start: 0.7463 (tp) cc_final: 0.7208 (tp) REVERT: C 1061 VAL cc_start: 0.8265 (t) cc_final: 0.7799 (m) REVERT: C 1110 TYR cc_start: 0.6749 (t80) cc_final: 0.6440 (t80) REVERT: C 1138 TYR cc_start: 0.7376 (t80) cc_final: 0.7112 (t80) outliers start: 2 outliers final: 0 residues processed: 592 average time/residue: 0.1671 time to fit residues: 159.4503 Evaluate side-chains 485 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 142 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 320 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 564 GLN C 895 GLN C 926 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.076991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.064376 restraints weight = 141036.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.066194 restraints weight = 86730.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.067531 restraints weight = 59457.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.068488 restraints weight = 44072.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.069100 restraints weight = 34897.363| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27351 Z= 0.171 Angle : 0.771 19.422 37363 Z= 0.375 Chirality : 0.050 0.481 4443 Planarity : 0.005 0.053 4664 Dihedral : 5.868 31.114 3472 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.14), residues: 3206 helix: 0.32 (0.19), residues: 707 sheet: -0.69 (0.20), residues: 606 loop : -1.61 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1019 TYR 0.022 0.002 TYR C 741 PHE 0.044 0.002 PHE B 823 TRP 0.052 0.003 TRP B 633 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (27224) covalent geometry : angle 0.72572 / 0.36 (37027) SS BOND : bond 0.00503 / 0.36 ( 42) SS BOND : angle 1.93206 / 1.31 ( 84) hydrogen bonds : bond 0.04035 / 2.67 ( 1030) hydrogen bonds : angle 6.38592 / 4.33 ( 2928) Misc. bond : bond 0.00236 / 0.12 ( 1) link_ALPHA1-4 : bond 0.01031 / 0.58 ( 6) link_ALPHA1-4 : angle 2.16494 / 1.28 ( 18) link_BETA1-4 : bond 0.00432 / 0.27 ( 25) link_BETA1-4 : angle 1.51602 / 0.99 ( 75) link_BETA1-6 : bond 0.00477 / 0.24 ( 3) link_BETA1-6 : angle 1.14295 / 0.62 ( 9) link_NAG-ASN : bond 0.00616 / 0.37 ( 50) link_NAG-ASN : angle 3.74643 / 2.42 ( 150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 565 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8480 (m-30) cc_final: 0.7994 (p0) REVERT: A 140 PHE cc_start: 0.6273 (p90) cc_final: 0.5863 (p90) REVERT: A 191 GLU cc_start: 0.6893 (pm20) cc_final: 0.6271 (pm20) REVERT: A 275 PHE cc_start: 0.7070 (m-10) cc_final: 0.6861 (m-80) REVERT: A 296 LEU cc_start: 0.8820 (tp) cc_final: 0.8416 (tp) REVERT: A 300 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7715 (mttm) REVERT: A 532 ASN cc_start: 0.8074 (m110) cc_final: 0.7464 (p0) REVERT: A 553 THR cc_start: 0.7618 (m) cc_final: 0.7232 (m) REVERT: A 697 MET cc_start: 0.7009 (ptm) cc_final: 0.6780 (ptm) REVERT: A 699 LEU cc_start: 0.8249 (mm) cc_final: 0.7927 (mt) REVERT: A 707 TYR cc_start: 0.6913 (t80) cc_final: 0.6648 (t80) REVERT: A 737 ASP cc_start: 0.6968 (t0) cc_final: 0.6684 (t0) REVERT: A 759 PHE cc_start: 0.7344 (p90) cc_final: 0.7067 (p90) REVERT: A 773 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6809 (tp30) REVERT: A 815 ARG cc_start: 0.5833 (mtm110) cc_final: 0.5343 (mtm-85) REVERT: A 934 ILE cc_start: 0.8013 (mm) cc_final: 0.7717 (mm) REVERT: B 48 LEU cc_start: 0.8427 (mp) cc_final: 0.7996 (mt) REVERT: B 61 ASN cc_start: 0.3947 (t0) cc_final: 0.3213 (p0) REVERT: B 88 ASP cc_start: 0.6948 (m-30) cc_final: 0.6662 (p0) REVERT: B 115 GLN cc_start: 0.7284 (mp-120) cc_final: 0.6682 (mp10) REVERT: B 158 ARG cc_start: 0.4277 (mmt-90) cc_final: 0.3869 (mmp80) REVERT: B 201 PHE cc_start: 0.7750 (t80) cc_final: 0.7494 (t80) REVERT: B 204 TYR cc_start: 0.6535 (m-80) cc_final: 0.5994 (m-80) REVERT: B 270 LEU cc_start: 0.8083 (tp) cc_final: 0.7195 (tp) REVERT: B 309 GLU cc_start: 0.7588 (mp0) cc_final: 0.7330 (mp0) REVERT: B 495 TYR cc_start: 0.5907 (m-80) cc_final: 0.5390 (m-80) REVERT: B 570 ASP cc_start: 0.7421 (t70) cc_final: 0.7169 (t0) REVERT: B 573 THR cc_start: 0.8210 (p) cc_final: 0.7975 (p) REVERT: B 595 VAL cc_start: 0.7774 (t) cc_final: 0.7284 (t) REVERT: B 613 GLN cc_start: 0.7368 (pm20) cc_final: 0.6728 (pm20) REVERT: B 693 ILE cc_start: 0.7880 (mt) cc_final: 0.7655 (mp) REVERT: B 707 TYR cc_start: 0.7162 (t80) cc_final: 0.6517 (t80) REVERT: B 710 ASN cc_start: 0.8183 (p0) cc_final: 0.7307 (t0) REVERT: B 725 GLU cc_start: 0.8139 (tp30) cc_final: 0.7778 (tp30) REVERT: B 731 MET cc_start: 0.7049 (ptt) cc_final: 0.6724 (ptt) REVERT: B 741 TYR cc_start: 0.8459 (t80) cc_final: 0.8088 (t80) REVERT: B 864 LEU cc_start: 0.7472 (tp) cc_final: 0.7227 (tp) REVERT: B 867 ASP cc_start: 0.7469 (p0) cc_final: 0.7227 (t0) REVERT: B 872 GLN cc_start: 0.8279 (mp10) cc_final: 0.7966 (mm-40) REVERT: B 882 ILE cc_start: 0.8939 (mm) cc_final: 0.8661 (tt) REVERT: B 900 MET cc_start: 0.8461 (mmp) cc_final: 0.7908 (mmp) REVERT: B 933 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7732 (mtmt) REVERT: B 957 GLN cc_start: 0.8252 (tp-100) cc_final: 0.7946 (tp40) REVERT: B 960 ASN cc_start: 0.7833 (t0) cc_final: 0.7579 (t0) REVERT: B 1014 ARG cc_start: 0.6080 (ttm170) cc_final: 0.5537 (ttm170) REVERT: B 1028 LYS cc_start: 0.7779 (ttmm) cc_final: 0.7556 (ttmm) REVERT: B 1034 LEU cc_start: 0.8446 (mp) cc_final: 0.8160 (mp) REVERT: B 1037 SER cc_start: 0.6943 (p) cc_final: 0.6521 (m) REVERT: C 65 PHE cc_start: 0.7623 (m-80) cc_final: 0.7054 (m-80) REVERT: C 133 PHE cc_start: 0.6477 (m-80) cc_final: 0.6035 (m-10) REVERT: C 153 MET cc_start: 0.4079 (mtm) cc_final: 0.3742 (ttm) REVERT: C 592 PHE cc_start: 0.5701 (p90) cc_final: 0.5454 (p90) REVERT: C 742 ILE cc_start: 0.8198 (mm) cc_final: 0.7542 (tt) REVERT: C 782 PHE cc_start: 0.8227 (m-10) cc_final: 0.7992 (m-80) REVERT: C 814 LYS cc_start: 0.7502 (mmtt) cc_final: 0.7108 (mmmt) REVERT: C 898 PHE cc_start: 0.7208 (t80) cc_final: 0.6810 (t80) REVERT: C 900 MET cc_start: 0.8373 (mmp) cc_final: 0.7279 (mmp) REVERT: C 919 ASN cc_start: 0.8281 (t0) cc_final: 0.7557 (t0) REVERT: C 922 LEU cc_start: 0.8129 (tt) cc_final: 0.7704 (tt) REVERT: C 973 ILE cc_start: 0.7713 (pt) cc_final: 0.7469 (pt) REVERT: C 1013 ILE cc_start: 0.7504 (tp) cc_final: 0.7149 (tt) REVERT: C 1061 VAL cc_start: 0.8235 (t) cc_final: 0.7740 (m) REVERT: C 1110 TYR cc_start: 0.6744 (t80) cc_final: 0.6502 (t80) REVERT: C 1138 TYR cc_start: 0.7383 (t80) cc_final: 0.7121 (t80) REVERT: C 1148 PHE cc_start: 0.4869 (t80) cc_final: 0.4660 (t80) outliers start: 1 outliers final: 0 residues processed: 565 average time/residue: 0.1741 time to fit residues: 157.8705 Evaluate side-chains 470 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 118 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 85 optimal weight: 0.0020 chunk 108 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS C 895 GLN C 926 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.077872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065257 restraints weight = 140171.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.067128 restraints weight = 85828.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.068496 restraints weight = 58365.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.069457 restraints weight = 42945.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.070093 restraints weight = 33832.598| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27351 Z= 0.133 Angle : 0.735 19.172 37363 Z= 0.356 Chirality : 0.049 0.481 4443 Planarity : 0.005 0.093 4664 Dihedral : 5.653 32.463 3472 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.11 % Allowed : 1.06 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 3206 helix: 0.50 (0.20), residues: 701 sheet: -0.60 (0.20), residues: 590 loop : -1.52 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 214 TYR 0.042 0.002 TYR B 421 PHE 0.037 0.002 PHE B 823 TRP 0.041 0.002 TRP B 633 HIS 0.011 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (27224) covalent geometry : angle 0.69020 / 0.35 (37027) SS BOND : bond 0.00399 / 0.28 ( 42) SS BOND : angle 1.76344 / 1.17 ( 84) hydrogen bonds : bond 0.03721 / 2.44 ( 1030) hydrogen bonds : angle 6.25005 / 4.24 ( 2928) Misc. bond : bond 0.00273 / 0.14 ( 1) link_ALPHA1-4 : bond 0.00925 / 0.51 ( 6) link_ALPHA1-4 : angle 1.96597 / 1.17 ( 18) link_BETA1-4 : bond 0.00456 / 0.30 ( 25) link_BETA1-4 : angle 1.43448 / 0.92 ( 75) link_BETA1-6 : bond 0.00547 / 0.28 ( 3) link_BETA1-6 : angle 1.14066 / 0.62 ( 9) link_NAG-ASN : bond 0.00616 / 0.37 ( 50) link_NAG-ASN : angle 3.70581 / 2.28 ( 150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 571 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8491 (m-30) cc_final: 0.8003 (p0) REVERT: A 66 HIS cc_start: 0.6382 (m90) cc_final: 0.6163 (t-90) REVERT: A 140 PHE cc_start: 0.6271 (p90) cc_final: 0.5877 (p90) REVERT: A 191 GLU cc_start: 0.6788 (pm20) cc_final: 0.6089 (pm20) REVERT: A 201 PHE cc_start: 0.7711 (t80) cc_final: 0.7415 (t80) REVERT: A 275 PHE cc_start: 0.7053 (m-10) cc_final: 0.6823 (m-80) REVERT: A 296 LEU cc_start: 0.8811 (tp) cc_final: 0.8401 (tp) REVERT: A 300 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7748 (mttm) REVERT: A 313 TYR cc_start: 0.7908 (m-80) cc_final: 0.7308 (m-10) REVERT: A 553 THR cc_start: 0.7259 (m) cc_final: 0.7009 (m) REVERT: A 613 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7500 (mt0) REVERT: A 699 LEU cc_start: 0.8192 (mm) cc_final: 0.7867 (mp) REVERT: A 707 TYR cc_start: 0.6941 (t80) cc_final: 0.6276 (t80) REVERT: A 718 PHE cc_start: 0.7448 (p90) cc_final: 0.7165 (p90) REVERT: A 737 ASP cc_start: 0.6882 (t0) cc_final: 0.6611 (t0) REVERT: A 773 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6874 (tp30) REVERT: A 792 PRO cc_start: 0.7313 (Cg_exo) cc_final: 0.7081 (Cg_endo) REVERT: A 815 ARG cc_start: 0.5904 (mtm110) cc_final: 0.5261 (mtm-85) REVERT: A 906 PHE cc_start: 0.8554 (m-80) cc_final: 0.8229 (m-80) REVERT: A 916 LEU cc_start: 0.8204 (tp) cc_final: 0.7948 (tp) REVERT: A 934 ILE cc_start: 0.7894 (mm) cc_final: 0.7656 (mm) REVERT: A 1061 VAL cc_start: 0.7422 (t) cc_final: 0.6807 (m) REVERT: B 48 LEU cc_start: 0.8365 (mp) cc_final: 0.7862 (mt) REVERT: B 61 ASN cc_start: 0.3820 (t0) cc_final: 0.3071 (p0) REVERT: B 88 ASP cc_start: 0.6911 (m-30) cc_final: 0.6569 (p0) REVERT: B 115 GLN cc_start: 0.7299 (mp-120) cc_final: 0.6678 (mp10) REVERT: B 133 PHE cc_start: 0.6360 (m-80) cc_final: 0.6018 (m-80) REVERT: B 158 ARG cc_start: 0.4261 (mmt-90) cc_final: 0.3901 (mmp80) REVERT: B 201 PHE cc_start: 0.7697 (t80) cc_final: 0.7437 (t80) REVERT: B 204 TYR cc_start: 0.6547 (m-80) cc_final: 0.5989 (m-80) REVERT: B 270 LEU cc_start: 0.8131 (tp) cc_final: 0.7115 (tp) REVERT: B 309 GLU cc_start: 0.7597 (mp0) cc_final: 0.7331 (mp0) REVERT: B 495 TYR cc_start: 0.5921 (m-80) cc_final: 0.5431 (m-80) REVERT: B 570 ASP cc_start: 0.7527 (t70) cc_final: 0.7238 (t0) REVERT: B 573 THR cc_start: 0.8133 (p) cc_final: 0.7883 (p) REVERT: B 707 TYR cc_start: 0.7234 (t80) cc_final: 0.6541 (t80) REVERT: B 710 ASN cc_start: 0.8213 (p0) cc_final: 0.7403 (t0) REVERT: B 725 GLU cc_start: 0.8089 (tp30) cc_final: 0.7752 (tp30) REVERT: B 741 TYR cc_start: 0.8467 (t80) cc_final: 0.8067 (t80) REVERT: B 755 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7439 (mt0) REVERT: B 867 ASP cc_start: 0.7593 (p0) cc_final: 0.7219 (t0) REVERT: B 882 ILE cc_start: 0.8953 (mm) cc_final: 0.8631 (tt) REVERT: B 900 MET cc_start: 0.8414 (mmp) cc_final: 0.7894 (mmp) REVERT: B 960 ASN cc_start: 0.7798 (t0) cc_final: 0.7575 (t0) REVERT: B 1028 LYS cc_start: 0.7752 (ttmm) cc_final: 0.7549 (ttmm) REVERT: B 1031 GLU cc_start: 0.7561 (mt-10) cc_final: 0.6879 (tt0) REVERT: B 1034 LEU cc_start: 0.8448 (mp) cc_final: 0.8163 (mp) REVERT: B 1037 SER cc_start: 0.6955 (p) cc_final: 0.5455 (p) REVERT: C 40 ASP cc_start: 0.8162 (p0) cc_final: 0.7884 (p0) REVERT: C 65 PHE cc_start: 0.7596 (m-80) cc_final: 0.7086 (m-80) REVERT: C 133 PHE cc_start: 0.6474 (m-80) cc_final: 0.6016 (m-80) REVERT: C 153 MET cc_start: 0.4130 (mtm) cc_final: 0.3806 (ttm) REVERT: C 188 ASN cc_start: 0.4390 (OUTLIER) cc_final: 0.3835 (p0) REVERT: C 568 ASP cc_start: 0.7656 (t70) cc_final: 0.7185 (t70) REVERT: C 742 ILE cc_start: 0.8223 (mm) cc_final: 0.7569 (tt) REVERT: C 773 GLU cc_start: 0.8046 (tt0) cc_final: 0.7003 (tp30) REVERT: C 784 GLN cc_start: 0.7684 (tp40) cc_final: 0.7265 (tp-100) REVERT: C 814 LYS cc_start: 0.7471 (mmtt) cc_final: 0.7117 (mmmt) REVERT: C 898 PHE cc_start: 0.7252 (t80) cc_final: 0.6757 (t80) REVERT: C 900 MET cc_start: 0.8343 (mmp) cc_final: 0.7249 (mmp) REVERT: C 902 MET cc_start: 0.8339 (mmm) cc_final: 0.7920 (mmm) REVERT: C 919 ASN cc_start: 0.8457 (t0) cc_final: 0.8182 (t0) REVERT: C 973 ILE cc_start: 0.7706 (pt) cc_final: 0.7459 (pt) REVERT: C 1029 MET cc_start: 0.8338 (tpp) cc_final: 0.7829 (tpp) REVERT: C 1061 VAL cc_start: 0.8227 (t) cc_final: 0.7741 (m) REVERT: C 1110 TYR cc_start: 0.6739 (t80) cc_final: 0.6479 (t80) REVERT: C 1141 LEU cc_start: 0.7851 (tp) cc_final: 0.7624 (mp) REVERT: C 1148 PHE cc_start: 0.4849 (t80) cc_final: 0.4581 (t80) outliers start: 3 outliers final: 0 residues processed: 571 average time/residue: 0.1686 time to fit residues: 154.4527 Evaluate side-chains 468 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 466 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 185 optimal weight: 0.0770 chunk 200 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 311 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 257 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 45 optimal weight: 0.0570 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN B 957 GLN C 207 HIS C 564 GLN C 895 GLN C 926 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.077957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.065096 restraints weight = 137375.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.067052 restraints weight = 83608.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.068457 restraints weight = 56834.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.069454 restraints weight = 41818.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.070176 restraints weight = 32903.153| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27351 Z= 0.131 Angle : 0.730 18.968 37363 Z= 0.354 Chirality : 0.049 0.480 4443 Planarity : 0.004 0.055 4664 Dihedral : 5.551 32.506 3472 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.07 % Allowed : 0.88 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.14), residues: 3206 helix: 0.58 (0.20), residues: 701 sheet: -0.55 (0.20), residues: 584 loop : -1.49 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1019 TYR 0.026 0.002 TYR B 421 PHE 0.034 0.002 PHE B 823 TRP 0.035 0.002 TRP B 633 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (27224) covalent geometry : angle 0.68650 / 0.34 (37027) SS BOND : bond 0.00381 / 0.27 ( 42) SS BOND : angle 1.54246 / 1.04 ( 84) hydrogen bonds : bond 0.03655 / 2.39 ( 1030) hydrogen bonds : angle 6.18765 / 4.20 ( 2928) Misc. bond : bond 0.00218 / 0.11 ( 1) link_ALPHA1-4 : bond 0.00910 / 0.51 ( 6) link_ALPHA1-4 : angle 1.93099 / 1.14 ( 18) link_BETA1-4 : bond 0.00426 / 0.29 ( 25) link_BETA1-4 : angle 1.33881 / 0.86 ( 75) link_BETA1-6 : bond 0.00528 / 0.27 ( 3) link_BETA1-6 : angle 1.11964 / 0.61 ( 9) link_NAG-ASN : bond 0.00600 / 0.35 ( 50) link_NAG-ASN : angle 3.67159 / 2.30 ( 150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 569 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8523 (m-30) cc_final: 0.8025 (p0) REVERT: A 66 HIS cc_start: 0.6467 (m90) cc_final: 0.6267 (t-90) REVERT: A 140 PHE cc_start: 0.6367 (p90) cc_final: 0.5954 (p90) REVERT: A 191 GLU cc_start: 0.6820 (pm20) cc_final: 0.6528 (pm20) REVERT: A 275 PHE cc_start: 0.7110 (m-10) cc_final: 0.6783 (m-80) REVERT: A 313 TYR cc_start: 0.7944 (m-80) cc_final: 0.7286 (m-10) REVERT: A 553 THR cc_start: 0.7266 (m) cc_final: 0.7015 (m) REVERT: A 699 LEU cc_start: 0.8088 (mm) cc_final: 0.7838 (mp) REVERT: A 707 TYR cc_start: 0.6936 (t80) cc_final: 0.6262 (t80) REVERT: A 737 ASP cc_start: 0.6898 (t0) cc_final: 0.6632 (t0) REVERT: A 773 GLU cc_start: 0.7597 (mm-30) cc_final: 0.6915 (tp30) REVERT: A 815 ARG cc_start: 0.5927 (mtm110) cc_final: 0.5374 (mtm-85) REVERT: A 905 ARG cc_start: 0.7487 (mtt-85) cc_final: 0.6986 (mtt-85) REVERT: A 906 PHE cc_start: 0.8711 (m-80) cc_final: 0.8257 (m-80) REVERT: A 916 LEU cc_start: 0.8191 (tp) cc_final: 0.7803 (tp) REVERT: A 920 GLN cc_start: 0.7629 (mp10) cc_final: 0.7371 (mp10) REVERT: A 934 ILE cc_start: 0.7907 (mm) cc_final: 0.7656 (mm) REVERT: A 964 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8184 (mtmt) REVERT: A 1061 VAL cc_start: 0.7394 (t) cc_final: 0.6814 (m) REVERT: B 48 LEU cc_start: 0.8347 (mp) cc_final: 0.7876 (mt) REVERT: B 61 ASN cc_start: 0.3932 (t0) cc_final: 0.3009 (p0) REVERT: B 88 ASP cc_start: 0.6871 (m-30) cc_final: 0.6612 (p0) REVERT: B 92 PHE cc_start: 0.6384 (t80) cc_final: 0.6129 (t80) REVERT: B 115 GLN cc_start: 0.7310 (mp-120) cc_final: 0.6654 (mp10) REVERT: B 158 ARG cc_start: 0.4304 (mmt-90) cc_final: 0.3921 (mmp80) REVERT: B 180 GLU cc_start: 0.4509 (mp0) cc_final: 0.4275 (mm-30) REVERT: B 201 PHE cc_start: 0.7747 (t80) cc_final: 0.7444 (t80) REVERT: B 204 TYR cc_start: 0.6511 (m-80) cc_final: 0.5901 (m-80) REVERT: B 270 LEU cc_start: 0.8142 (tp) cc_final: 0.7136 (tp) REVERT: B 285 ILE cc_start: 0.8489 (mt) cc_final: 0.8188 (pt) REVERT: B 309 GLU cc_start: 0.7617 (mp0) cc_final: 0.7317 (mp0) REVERT: B 495 TYR cc_start: 0.5916 (m-80) cc_final: 0.5447 (m-80) REVERT: B 570 ASP cc_start: 0.7521 (t70) cc_final: 0.7247 (t0) REVERT: B 573 THR cc_start: 0.8175 (p) cc_final: 0.7918 (p) REVERT: B 595 VAL cc_start: 0.7873 (t) cc_final: 0.7399 (t) REVERT: B 613 GLN cc_start: 0.7358 (pm20) cc_final: 0.6770 (pm20) REVERT: B 707 TYR cc_start: 0.7215 (t80) cc_final: 0.6510 (t80) REVERT: B 710 ASN cc_start: 0.8244 (p0) cc_final: 0.7402 (t0) REVERT: B 725 GLU cc_start: 0.8156 (tp30) cc_final: 0.7749 (tp30) REVERT: B 741 TYR cc_start: 0.8487 (t80) cc_final: 0.8214 (t80) REVERT: B 755 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7140 (mm-40) REVERT: B 780 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6808 (mt-10) REVERT: B 867 ASP cc_start: 0.7466 (p0) cc_final: 0.7188 (t0) REVERT: B 882 ILE cc_start: 0.8961 (mm) cc_final: 0.8634 (tt) REVERT: B 900 MET cc_start: 0.8441 (mmp) cc_final: 0.7951 (mmp) REVERT: B 906 PHE cc_start: 0.8639 (m-80) cc_final: 0.8256 (m-80) REVERT: B 957 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.8053 (tp40) REVERT: B 960 ASN cc_start: 0.7739 (t0) cc_final: 0.7522 (t0) REVERT: B 961 THR cc_start: 0.7374 (m) cc_final: 0.7165 (m) REVERT: B 1019 ARG cc_start: 0.7631 (ttt90) cc_final: 0.7337 (tpt90) REVERT: B 1028 LYS cc_start: 0.7869 (ttmm) cc_final: 0.7668 (ttmm) REVERT: B 1031 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6927 (tt0) REVERT: B 1034 LEU cc_start: 0.8460 (mp) cc_final: 0.8195 (mp) REVERT: B 1037 SER cc_start: 0.6928 (p) cc_final: 0.5524 (p) REVERT: C 40 ASP cc_start: 0.8260 (p0) cc_final: 0.7995 (p0) REVERT: C 65 PHE cc_start: 0.7623 (m-80) cc_final: 0.7146 (m-80) REVERT: C 133 PHE cc_start: 0.6517 (m-80) cc_final: 0.6046 (m-80) REVERT: C 153 MET cc_start: 0.4147 (mtm) cc_final: 0.3848 (ttm) REVERT: C 190 ARG cc_start: 0.5762 (tpp-160) cc_final: 0.5534 (tpp80) REVERT: C 568 ASP cc_start: 0.7572 (t70) cc_final: 0.7283 (p0) REVERT: C 742 ILE cc_start: 0.8241 (mm) cc_final: 0.7549 (tt) REVERT: C 773 GLU cc_start: 0.8149 (tt0) cc_final: 0.7090 (tp30) REVERT: C 784 GLN cc_start: 0.7725 (tp40) cc_final: 0.7309 (tp-100) REVERT: C 805 ILE cc_start: 0.8203 (pt) cc_final: 0.7989 (mt) REVERT: C 814 LYS cc_start: 0.7397 (mmtt) cc_final: 0.7051 (mmmt) REVERT: C 820 ASP cc_start: 0.6882 (m-30) cc_final: 0.6289 (m-30) REVERT: C 898 PHE cc_start: 0.7249 (t80) cc_final: 0.6572 (t80) REVERT: C 900 MET cc_start: 0.8368 (mmp) cc_final: 0.7273 (mmp) REVERT: C 902 MET cc_start: 0.8371 (mmm) cc_final: 0.7951 (mmm) REVERT: C 919 ASN cc_start: 0.8443 (t0) cc_final: 0.8177 (t0) REVERT: C 973 ILE cc_start: 0.7715 (pt) cc_final: 0.7445 (pt) REVERT: C 1061 VAL cc_start: 0.8107 (t) cc_final: 0.7724 (m) REVERT: C 1110 TYR cc_start: 0.6791 (t80) cc_final: 0.6560 (t80) REVERT: C 1138 TYR cc_start: 0.7276 (t80) cc_final: 0.6981 (t80) REVERT: C 1148 PHE cc_start: 0.4834 (t80) cc_final: 0.4514 (t80) outliers start: 2 outliers final: 0 residues processed: 569 average time/residue: 0.1641 time to fit residues: 151.5815 Evaluate side-chains 468 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 467 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 311 optimal weight: 3.9990 chunk 279 optimal weight: 9.9990 chunk 137 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 245 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 96 optimal weight: 0.0980 chunk 203 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 137 ASN A 196 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 540 ASN C 895 GLN C 901 GLN C 926 GLN C1054 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.076812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.064416 restraints weight = 143358.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.066277 restraints weight = 87838.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.067601 restraints weight = 59698.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.068550 restraints weight = 44017.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.069142 restraints weight = 34751.919| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27351 Z= 0.185 Angle : 0.791 18.644 37363 Z= 0.386 Chirality : 0.050 0.469 4443 Planarity : 0.005 0.057 4664 Dihedral : 5.862 32.880 3472 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.07 % Allowed : 0.49 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3206 helix: 0.31 (0.19), residues: 704 sheet: -0.65 (0.20), residues: 608 loop : -1.60 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1107 TYR 0.037 0.002 TYR C 505 PHE 0.044 0.002 PHE B 823 TRP 0.034 0.002 TRP B 633 HIS 0.009 0.002 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (27224) covalent geometry : angle 0.74890 / 0.38 (37027) SS BOND : bond 0.00493 / 0.36 ( 42) SS BOND : angle 1.72007 / 1.15 ( 84) hydrogen bonds : bond 0.03995 / 2.63 ( 1030) hydrogen bonds : angle 6.41595 / 4.34 ( 2928) Misc. bond : bond 0.00009 / 0.00 ( 1) link_ALPHA1-4 : bond 0.00914 / 0.49 ( 6) link_ALPHA1-4 : angle 2.17104 / 1.29 ( 18) link_BETA1-4 : bond 0.00402 / 0.26 ( 25) link_BETA1-4 : angle 1.52244 / 0.99 ( 75) link_BETA1-6 : bond 0.00444 / 0.23 ( 3) link_BETA1-6 : angle 1.14306 / 0.62 ( 9) link_NAG-ASN : bond 0.00614 / 0.36 ( 50) link_NAG-ASN : angle 3.71936 / 2.38 ( 150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 548 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7164 (ttm110) cc_final: 0.6927 (ttm110) REVERT: A 40 ASP cc_start: 0.8470 (m-30) cc_final: 0.8022 (p0) REVERT: A 140 PHE cc_start: 0.6333 (p90) cc_final: 0.5896 (p90) REVERT: A 191 GLU cc_start: 0.6747 (pm20) cc_final: 0.6481 (pm20) REVERT: A 275 PHE cc_start: 0.7140 (m-10) cc_final: 0.6890 (m-80) REVERT: A 309 GLU cc_start: 0.6144 (mp0) cc_final: 0.5935 (pm20) REVERT: A 313 TYR cc_start: 0.7937 (m-80) cc_final: 0.7146 (m-10) REVERT: A 410 ILE cc_start: 0.6536 (tp) cc_final: 0.6286 (tp) REVERT: A 553 THR cc_start: 0.7221 (m) cc_final: 0.6973 (m) REVERT: A 643 PHE cc_start: 0.5390 (t80) cc_final: 0.5147 (t80) REVERT: A 699 LEU cc_start: 0.8063 (mm) cc_final: 0.7686 (mp) REVERT: A 707 TYR cc_start: 0.6954 (t80) cc_final: 0.6657 (t80) REVERT: A 737 ASP cc_start: 0.7082 (t0) cc_final: 0.6764 (t0) REVERT: A 773 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7064 (tp30) REVERT: A 806 LEU cc_start: 0.8363 (mt) cc_final: 0.7761 (tt) REVERT: A 815 ARG cc_start: 0.5901 (mtm110) cc_final: 0.5527 (mtm-85) REVERT: A 904 TYR cc_start: 0.7994 (m-10) cc_final: 0.7744 (m-80) REVERT: A 934 ILE cc_start: 0.7935 (mm) cc_final: 0.7683 (mm) REVERT: A 993 ILE cc_start: 0.7577 (mp) cc_final: 0.7373 (tp) REVERT: A 1061 VAL cc_start: 0.7431 (t) cc_final: 0.6861 (m) REVERT: B 48 LEU cc_start: 0.8407 (mp) cc_final: 0.7982 (mt) REVERT: B 88 ASP cc_start: 0.6958 (m-30) cc_final: 0.6608 (p0) REVERT: B 115 GLN cc_start: 0.7317 (mp-120) cc_final: 0.6712 (mp10) REVERT: B 158 ARG cc_start: 0.4330 (mmt-90) cc_final: 0.3899 (mmp80) REVERT: B 180 GLU cc_start: 0.4322 (mp0) cc_final: 0.4018 (mm-30) REVERT: B 201 PHE cc_start: 0.7712 (t80) cc_final: 0.7439 (t80) REVERT: B 204 TYR cc_start: 0.6615 (m-80) cc_final: 0.6044 (m-80) REVERT: B 270 LEU cc_start: 0.8205 (tp) cc_final: 0.7226 (tp) REVERT: B 285 ILE cc_start: 0.8529 (mt) cc_final: 0.8246 (pt) REVERT: B 309 GLU cc_start: 0.7592 (mp0) cc_final: 0.7336 (mp0) REVERT: B 495 TYR cc_start: 0.6085 (m-80) cc_final: 0.5558 (m-80) REVERT: B 568 ASP cc_start: 0.7002 (t0) cc_final: 0.6779 (t0) REVERT: B 570 ASP cc_start: 0.7419 (t70) cc_final: 0.7175 (t0) REVERT: B 573 THR cc_start: 0.8218 (p) cc_final: 0.7944 (p) REVERT: B 595 VAL cc_start: 0.7932 (t) cc_final: 0.7460 (t) REVERT: B 613 GLN cc_start: 0.7403 (pm20) cc_final: 0.6723 (pm20) REVERT: B 707 TYR cc_start: 0.7291 (t80) cc_final: 0.6644 (t80) REVERT: B 710 ASN cc_start: 0.8246 (p0) cc_final: 0.7351 (t0) REVERT: B 741 TYR cc_start: 0.8481 (t80) cc_final: 0.8263 (t80) REVERT: B 755 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7126 (mm-40) REVERT: B 815 ARG cc_start: 0.6919 (ttp-170) cc_final: 0.6546 (ttp-170) REVERT: B 882 ILE cc_start: 0.8945 (mm) cc_final: 0.8644 (tt) REVERT: B 900 MET cc_start: 0.8414 (mmp) cc_final: 0.7821 (mmp) REVERT: B 933 LYS cc_start: 0.7984 (ptpt) cc_final: 0.7569 (mtmt) REVERT: B 960 ASN cc_start: 0.7754 (t0) cc_final: 0.7529 (t0) REVERT: B 1019 ARG cc_start: 0.7636 (ttt90) cc_final: 0.7433 (ttt90) REVERT: B 1031 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7105 (tt0) REVERT: B 1034 LEU cc_start: 0.8439 (mp) cc_final: 0.8144 (mp) REVERT: B 1037 SER cc_start: 0.6871 (p) cc_final: 0.5573 (p) REVERT: B 1105 THR cc_start: 0.6502 (m) cc_final: 0.5794 (t) REVERT: C 40 ASP cc_start: 0.8151 (p0) cc_final: 0.7921 (p0) REVERT: C 41 LYS cc_start: 0.6134 (ttpp) cc_final: 0.5694 (pptt) REVERT: C 65 PHE cc_start: 0.7668 (m-80) cc_final: 0.7140 (m-80) REVERT: C 133 PHE cc_start: 0.6524 (m-80) cc_final: 0.6186 (m-80) REVERT: C 153 MET cc_start: 0.4107 (mtm) cc_final: 0.3823 (ttm) REVERT: C 387 LEU cc_start: 0.8089 (tp) cc_final: 0.7604 (pp) REVERT: C 568 ASP cc_start: 0.7636 (t70) cc_final: 0.7322 (p0) REVERT: C 742 ILE cc_start: 0.8235 (mm) cc_final: 0.7553 (tt) REVERT: C 773 GLU cc_start: 0.8068 (tt0) cc_final: 0.7172 (tp30) REVERT: C 780 GLU cc_start: 0.7751 (pt0) cc_final: 0.7543 (pt0) REVERT: C 814 LYS cc_start: 0.7418 (mmtt) cc_final: 0.7060 (mmmt) REVERT: C 820 ASP cc_start: 0.6923 (m-30) cc_final: 0.6262 (m-30) REVERT: C 898 PHE cc_start: 0.7286 (t80) cc_final: 0.6874 (t80) REVERT: C 919 ASN cc_start: 0.8355 (t0) cc_final: 0.8088 (t0) REVERT: C 973 ILE cc_start: 0.7670 (pt) cc_final: 0.7468 (pt) REVERT: C 1061 VAL cc_start: 0.8265 (t) cc_final: 0.7757 (m) REVERT: C 1110 TYR cc_start: 0.6819 (t80) cc_final: 0.6399 (t80) REVERT: C 1138 TYR cc_start: 0.7263 (t80) cc_final: 0.6983 (t80) outliers start: 2 outliers final: 1 residues processed: 549 average time/residue: 0.1653 time to fit residues: 147.0784 Evaluate side-chains 454 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 194 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 317 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 540 ASN C 784 GLN C 895 GLN C 926 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.077474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.065083 restraints weight = 142261.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.066919 restraints weight = 87549.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.068264 restraints weight = 59757.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.069217 restraints weight = 44161.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.069760 restraints weight = 34912.321| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27351 Z= 0.139 Angle : 0.739 18.478 37363 Z= 0.360 Chirality : 0.049 0.475 4443 Planarity : 0.004 0.056 4664 Dihedral : 5.660 32.873 3472 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.14), residues: 3206 helix: 0.43 (0.20), residues: 708 sheet: -0.58 (0.20), residues: 601 loop : -1.57 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1107 TYR 0.023 0.002 TYR C 741 PHE 0.038 0.002 PHE B 823 TRP 0.027 0.002 TRP B 633 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (27224) covalent geometry : angle 0.69950 / 0.35 (37027) SS BOND : bond 0.00391 / 0.28 ( 42) SS BOND : angle 1.51143 / 1.02 ( 84) hydrogen bonds : bond 0.03706 / 2.43 ( 1030) hydrogen bonds : angle 6.28292 / 4.26 ( 2928) Misc. bond : bond 0.00298 / 0.16 ( 1) link_ALPHA1-4 : bond 0.00899 / 0.50 ( 6) link_ALPHA1-4 : angle 1.96779 / 1.18 ( 18) link_BETA1-4 : bond 0.00424 / 0.28 ( 25) link_BETA1-4 : angle 1.36982 / 0.90 ( 75) link_BETA1-6 : bond 0.00532 / 0.27 ( 3) link_BETA1-6 : angle 1.21160 / 0.66 ( 9) link_NAG-ASN : bond 0.00598 / 0.34 ( 50) link_NAG-ASN : angle 3.52769 / 2.24 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5021.52 seconds wall clock time: 87 minutes 40.94 seconds (5260.94 seconds total)