Starting phenix.real_space_refine on Fri Mar 6 01:30:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n1y_24127/03_2026/7n1y_24127.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n1y_24127/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7n1y_24127/03_2026/7n1y_24127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n1y_24127/03_2026/7n1y_24127.map" model { file = "/net/cci-nas-00/data/ceres_data/7n1y_24127/03_2026/7n1y_24127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n1y_24127/03_2026/7n1y_24127.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 33 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 dihedrals: 30 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.19, per 1000 atoms: 0.23 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 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: 1.16 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: 6.50 Time building geometry restraints manager: 3.31 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 - 24.81: 16334 24.81 - 49.61: 833 49.61 - 74.42: 149 74.42 - 99.23: 51 99.23 - 124.04: 19 Dihedral angle restraints: 17386 sinusoidal: 7946 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 17383 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: 7.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.420 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 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 : 16.157 124.035 11186 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 covalent geometry : bond 0.01610 (27224) covalent geometry : angle 2.10881 (37027) SS BOND : bond 0.01799 ( 42) SS BOND : angle 2.84694 ( 84) hydrogen bonds : bond 0.16785 ( 1030) hydrogen bonds : angle 9.58036 ( 2928) Misc. bond : bond 0.33256 ( 1) link_ALPHA1-4 : bond 0.03580 ( 6) link_ALPHA1-4 : angle 5.16023 ( 18) link_BETA1-4 : bond 0.02522 ( 25) link_BETA1-4 : angle 4.16341 ( 75) link_BETA1-6 : bond 0.03372 ( 3) link_BETA1-6 : angle 3.56731 ( 9) link_NAG-ASN : bond 0.16939 ( 50) link_NAG-ASN : angle 10.71153 ( 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 : 0.962 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: 0.1757 time to fit residues: 212.6939 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 : 0.949 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A 919 ASN A1106 GLN A1113 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.077857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.065356 restraints weight = 137613.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.067251 restraints weight = 83857.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.068590 restraints weight = 57001.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.069530 restraints weight = 41896.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.070188 restraints weight = 33017.174| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.2554 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= 0.186 Angle : 0.951 21.797 37363 Z= 0.459 Chirality : 0.057 0.737 4443 Planarity : 0.005 0.065 4664 Dihedral : 12.193 114.890 5359 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 0.14 % Allowed : 4.69 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.13), residues: 3206 helix: -0.58 (0.18), residues: 698 sheet: -0.51 (0.20), residues: 557 loop : -1.81 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.044 0.003 TYR C 505 PHE 0.041 0.003 PHE A 58 TRP 0.042 0.003 TRP A 64 HIS 0.011 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00393 (27224) covalent geometry : angle 0.85534 (37027) SS BOND : bond 0.00669 ( 42) SS BOND : angle 1.92389 ( 84) hydrogen bonds : bond 0.05083 ( 1030) hydrogen bonds : angle 7.18426 ( 2928) Misc. bond : bond 0.00031 ( 1) link_ALPHA1-4 : bond 0.01638 ( 6) link_ALPHA1-4 : angle 3.52760 ( 18) link_BETA1-4 : bond 0.00556 ( 25) link_BETA1-4 : angle 2.44613 ( 75) link_BETA1-6 : bond 0.01457 ( 3) link_BETA1-6 : angle 2.10497 ( 9) link_NAG-ASN : bond 0.01195 ( 50) link_NAG-ASN : angle 6.16290 ( 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 646 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 642 time to evaluate : 1.030 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: 0.5761 (t80) cc_final: 0.5288 (t80) REVERT: A 106 PHE cc_start: 0.7059 (m-80) cc_final: 0.6774 (m-80) REVERT: A 118 LEU cc_start: 0.7932 (tt) cc_final: 0.7710 (tt) REVERT: A 223 LEU cc_start: 0.7799 (mp) cc_final: 0.7573 (mp) REVERT: A 270 LEU cc_start: 0.8231 (mt) cc_final: 0.8017 (mt) REVERT: A 300 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7813 (mttm) REVERT: A 309 GLU cc_start: 0.7664 (pm20) cc_final: 0.7438 (pm20) REVERT: A 532 ASN cc_start: 0.7577 (m110) cc_final: 0.7108 (p0) REVERT: A 553 THR cc_start: 0.7614 (m) cc_final: 0.7355 (m) REVERT: A 654 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6498 (mm-30) REVERT: A 695 TYR cc_start: 0.7210 (p90) cc_final: 0.6195 (p90) REVERT: A 737 ASP cc_start: 0.7085 (t0) cc_final: 0.6457 (t70) REVERT: A 759 PHE cc_start: 0.7370 (p90) cc_final: 0.7135 (p90) REVERT: A 773 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6725 (tp30) REVERT: A 818 ILE cc_start: 0.8531 (mm) cc_final: 0.8276 (mm) REVERT: A 901 GLN cc_start: 0.7477 (tm-30) cc_final: 0.7140 (tm-30) REVERT: A 906 PHE cc_start: 0.8527 (m-80) cc_final: 0.8103 (m-80) REVERT: A 916 LEU cc_start: 0.8277 (tp) cc_final: 0.7742 (tp) REVERT: A 934 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7827 (mm) REVERT: A 951 VAL cc_start: 0.8118 (t) cc_final: 0.7827 (t) REVERT: A 1034 LEU cc_start: 0.8626 (mp) cc_final: 0.8403 (mp) REVERT: A 1041 ASP cc_start: 0.7981 (t0) cc_final: 0.7737 (t0) REVERT: B 33 THR cc_start: 0.6714 (p) cc_final: 0.5774 (m) REVERT: B 58 PHE cc_start: 0.8062 (m-10) cc_final: 0.7351 (m-80) REVERT: B 64 TRP cc_start: 0.4968 (t60) cc_final: 0.3540 (t60) REVERT: B 80 ASP cc_start: 0.4908 (t0) cc_final: 0.4062 (p0) REVERT: B 81 ASN cc_start: 0.6047 (p0) cc_final: 0.5690 (m-40) REVERT: B 92 PHE cc_start: 0.6703 (t80) cc_final: 0.6330 (t80) REVERT: B 191 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7385 (mt-10) REVERT: B 198 ASP cc_start: 0.5967 (m-30) cc_final: 0.5763 (m-30) REVERT: B 270 LEU cc_start: 0.8087 (tp) cc_final: 0.7827 (tp) REVERT: B 495 TYR cc_start: 0.6062 (m-80) cc_final: 0.5697 (m-80) REVERT: B 693 ILE cc_start: 0.8103 (mt) cc_final: 0.7834 (mp) REVERT: B 710 ASN cc_start: 0.8122 (p0) cc_final: 0.7199 (t0) REVERT: B 731 MET cc_start: 0.7092 (ptt) cc_final: 0.6635 (ptt) REVERT: B 741 TYR cc_start: 0.8371 (t80) cc_final: 0.7910 (t80) REVERT: B 773 GLU cc_start: 0.7219 (pt0) cc_final: 0.6949 (pp20) REVERT: B 815 ARG cc_start: 0.6353 (ttp-170) cc_final: 0.5800 (ttp-170) REVERT: B 819 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7191 (mt-10) REVERT: B 820 ASP cc_start: 0.7307 (m-30) cc_final: 0.6690 (m-30) REVERT: B 900 MET cc_start: 0.8627 (mmp) cc_final: 0.8109 (mmp) REVERT: B 901 GLN cc_start: 0.7538 (tm-30) cc_final: 0.7283 (tm-30) REVERT: B 902 MET cc_start: 0.8289 (tpp) cc_final: 0.7975 (tpt) REVERT: B 905 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7535 (mmt180) REVERT: B 921 LYS cc_start: 0.8026 (mmmm) cc_final: 0.7730 (mmmt) REVERT: B 950 ASP cc_start: 0.7879 (t70) cc_final: 0.7278 (t0) REVERT: B 960 ASN cc_start: 0.7775 (t0) cc_final: 0.7472 (t0) REVERT: B 1028 LYS cc_start: 0.7702 (ttmm) cc_final: 0.7491 (ttmm) REVERT: B 1037 SER cc_start: 0.6741 (p) cc_final: 0.6431 (m) REVERT: B 1088 HIS cc_start: 0.7417 (m-70) cc_final: 0.6933 (m170) REVERT: B 1105 THR cc_start: 0.6561 (m) cc_final: 0.6053 (t) REVERT: B 1111 GLU cc_start: 0.6865 (tm-30) cc_final: 0.6221 (tm-30) REVERT: B 1113 GLN cc_start: 0.6401 (mp10) cc_final: 0.5781 (mp10) REVERT: C 228 ASP cc_start: 0.7025 (t0) cc_final: 0.6762 (t70) REVERT: C 296 LEU cc_start: 0.7639 (tt) cc_final: 0.7353 (tt) REVERT: C 387 LEU cc_start: 0.8091 (tp) cc_final: 0.7771 (pp) REVERT: C 664 ILE cc_start: 0.7433 (mm) cc_final: 0.6642 (mm) REVERT: C 720 ILE cc_start: 0.7923 (mm) cc_final: 0.7408 (tt) REVERT: C 814 LYS cc_start: 0.7327 (mmtt) cc_final: 0.6961 (mmmt) REVERT: C 900 MET cc_start: 0.8541 (mmp) cc_final: 0.7631 (mmp) REVERT: C 904 TYR cc_start: 0.7958 (m-80) cc_final: 0.7466 (m-80) REVERT: C 917 TYR cc_start: 0.8057 (m-80) cc_final: 0.7466 (m-80) REVERT: C 919 ASN cc_start: 0.8454 (t0) cc_final: 0.7776 (t0) REVERT: C 922 LEU cc_start: 0.8198 (tt) cc_final: 0.7874 (tt) REVERT: C 923 ILE cc_start: 0.8474 (mt) cc_final: 0.8177 (mt) REVERT: C 926 GLN cc_start: 0.7812 (pt0) cc_final: 0.7581 (pt0) REVERT: C 973 ILE cc_start: 0.7876 (pt) cc_final: 0.7649 (pt) REVERT: C 1001 LEU cc_start: 0.8076 (tp) cc_final: 0.7797 (tp) REVERT: C 1005 GLN cc_start: 0.7350 (mm-40) cc_final: 0.7128 (mm-40) REVERT: C 1033 VAL cc_start: 0.8861 (t) cc_final: 0.8484 (t) REVERT: C 1039 ARG cc_start: 0.6731 (mtm180) cc_final: 0.6483 (mtm-85) REVERT: C 1061 VAL cc_start: 0.8228 (t) cc_final: 0.7938 (m) REVERT: C 1062 PHE cc_start: 0.7185 (m-80) cc_final: 0.6746 (m-80) REVERT: C 1138 TYR cc_start: 0.7311 (t80) cc_final: 0.7105 (t80) outliers start: 4 outliers final: 0 residues processed: 644 average time/residue: 0.1694 time to fit residues: 174.4680 Evaluate side-chains 498 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 497 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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: 2.9990 chunk 321 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 230 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 254 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 225 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 394 ASN B 66 HIS B 115 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 919 ASN C 196 ASN C 675 GLN C1083 HIS C1125 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.077970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.065198 restraints weight = 139444.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.067123 restraints weight = 83897.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.068474 restraints weight = 56671.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.069426 restraints weight = 41514.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.070123 restraints weight = 32783.356| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.3133 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= 0.149 Angle : 0.821 20.248 37363 Z= 0.394 Chirality : 0.053 0.678 4443 Planarity : 0.005 0.163 4664 Dihedral : 10.929 109.273 5359 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.14 % Allowed : 4.02 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.14), residues: 3206 helix: 0.10 (0.19), residues: 689 sheet: -0.40 (0.21), residues: 519 loop : -1.64 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 214 TYR 0.024 0.002 TYR C 505 PHE 0.042 0.002 PHE C1156 TRP 0.037 0.003 TRP C 64 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00319 (27224) covalent geometry : angle 0.75297 (37027) SS BOND : bond 0.00373 ( 42) SS BOND : angle 1.67997 ( 84) hydrogen bonds : bond 0.04340 ( 1030) hydrogen bonds : angle 6.63261 ( 2928) Misc. bond : bond 0.00084 ( 1) link_ALPHA1-4 : bond 0.01645 ( 6) link_ALPHA1-4 : angle 3.62813 ( 18) link_BETA1-4 : bond 0.00520 ( 25) link_BETA1-4 : angle 2.19857 ( 75) link_BETA1-6 : bond 0.01498 ( 3) link_BETA1-6 : angle 2.21665 ( 9) link_NAG-ASN : bond 0.00759 ( 50) link_NAG-ASN : angle 4.70500 ( 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 607 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 603 time to evaluate : 0.757 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 201 PHE cc_start: 0.7510 (t80) cc_final: 0.7204 (t80) REVERT: A 207 HIS cc_start: 0.6401 (t-90) cc_final: 0.6157 (t-170) REVERT: A 208 THR cc_start: 0.7431 (p) cc_final: 0.7012 (t) REVERT: A 296 LEU cc_start: 0.8854 (tp) cc_final: 0.8620 (tp) REVERT: A 300 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7724 (mttm) REVERT: A 309 GLU cc_start: 0.7677 (pm20) cc_final: 0.7465 (pm20) REVERT: A 313 TYR cc_start: 0.7500 (m-80) cc_final: 0.7175 (m-10) REVERT: A 468 ILE cc_start: 0.7680 (mm) cc_final: 0.7399 (pt) REVERT: A 532 ASN cc_start: 0.7655 (m110) cc_final: 0.7147 (p0) REVERT: A 553 THR cc_start: 0.7574 (m) cc_final: 0.7326 (m) REVERT: A 695 TYR cc_start: 0.7372 (p90) cc_final: 0.6383 (p90) REVERT: A 697 MET cc_start: 0.6908 (ptp) cc_final: 0.6449 (ptm) REVERT: A 699 LEU cc_start: 0.8270 (mm) cc_final: 0.7984 (mp) REVERT: A 707 TYR cc_start: 0.6797 (t80) cc_final: 0.6506 (t80) REVERT: A 737 ASP cc_start: 0.7079 (t0) cc_final: 0.6425 (t0) REVERT: A 759 PHE cc_start: 0.7295 (p90) cc_final: 0.7001 (p90) REVERT: A 773 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6528 (tp30) REVERT: A 815 ARG cc_start: 0.5991 (mtm110) cc_final: 0.5554 (mtm110) REVERT: A 818 ILE cc_start: 0.8486 (mm) cc_final: 0.8214 (mm) REVERT: A 900 MET cc_start: 0.7765 (tpp) cc_final: 0.7468 (mmm) REVERT: A 901 GLN cc_start: 0.7453 (tm-30) cc_final: 0.6528 (tm-30) REVERT: A 905 ARG cc_start: 0.7316 (mtt-85) cc_final: 0.6941 (mtt-85) REVERT: A 906 PHE cc_start: 0.8550 (m-80) cc_final: 0.8156 (m-80) REVERT: A 907 ASN cc_start: 0.8161 (p0) cc_final: 0.7480 (p0) REVERT: A 916 LEU cc_start: 0.8365 (tp) cc_final: 0.7742 (tp) REVERT: A 934 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7709 (mm) REVERT: A 1017 GLU cc_start: 0.7754 (mp0) cc_final: 0.7382 (mp0) REVERT: A 1041 ASP cc_start: 0.7822 (t0) cc_final: 0.7611 (t0) REVERT: A 1047 TYR cc_start: 0.7890 (m-80) cc_final: 0.7402 (m-80) REVERT: B 33 THR cc_start: 0.6780 (p) cc_final: 0.5854 (m) REVERT: B 58 PHE cc_start: 0.8092 (m-10) cc_final: 0.7359 (m-80) REVERT: B 80 ASP cc_start: 0.4930 (t0) cc_final: 0.4299 (p0) REVERT: B 92 PHE cc_start: 0.6641 (t80) cc_final: 0.6146 (t80) REVERT: B 129 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7956 (pttt) REVERT: B 158 ARG cc_start: 0.4785 (mpt180) cc_final: 0.4441 (mmt-90) REVERT: B 200 TYR cc_start: 0.6864 (m-10) cc_final: 0.6560 (m-10) REVERT: B 201 PHE cc_start: 0.7755 (t80) cc_final: 0.7505 (t80) REVERT: B 270 LEU cc_start: 0.8016 (tp) cc_final: 0.7772 (tp) REVERT: B 309 GLU cc_start: 0.7488 (mp0) cc_final: 0.7272 (mp0) REVERT: B 351 TYR cc_start: 0.6119 (p90) cc_final: 0.5778 (p90) REVERT: B 495 TYR cc_start: 0.6099 (m-80) cc_final: 0.5596 (m-80) REVERT: B 557 LYS cc_start: 0.6785 (mtmt) cc_final: 0.6401 (mttp) REVERT: B 573 THR cc_start: 0.8105 (p) cc_final: 0.7824 (p) REVERT: B 613 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.6301 (mp10) REVERT: B 693 ILE cc_start: 0.7892 (mt) cc_final: 0.7612 (mp) REVERT: B 710 ASN cc_start: 0.8103 (p0) cc_final: 0.7224 (t0) REVERT: B 725 GLU cc_start: 0.8015 (tp30) cc_final: 0.7681 (tp30) REVERT: B 731 MET cc_start: 0.6981 (ptt) cc_final: 0.6647 (ptt) REVERT: B 733 LYS cc_start: 0.7525 (mtpt) cc_final: 0.7268 (mtpp) REVERT: B 741 TYR cc_start: 0.8466 (t80) cc_final: 0.7988 (t80) REVERT: B 755 GLN cc_start: 0.7953 (mm110) cc_final: 0.7610 (mm-40) REVERT: B 872 GLN cc_start: 0.8031 (mp10) cc_final: 0.7751 (mm-40) REVERT: B 882 ILE cc_start: 0.8960 (mm) cc_final: 0.8685 (tt) REVERT: B 898 PHE cc_start: 0.7773 (t80) cc_final: 0.7530 (t80) REVERT: B 900 MET cc_start: 0.8369 (mmp) cc_final: 0.8009 (mmp) REVERT: B 902 MET cc_start: 0.8404 (tpp) cc_final: 0.8179 (tpp) REVERT: B 921 LYS cc_start: 0.8085 (mmmm) cc_final: 0.7842 (mmmt) REVERT: B 950 ASP cc_start: 0.7892 (t70) cc_final: 0.7135 (t0) REVERT: B 960 ASN cc_start: 0.7852 (t0) cc_final: 0.7509 (t0) REVERT: B 1017 GLU cc_start: 0.7580 (tt0) cc_final: 0.7361 (tt0) REVERT: B 1028 LYS cc_start: 0.7748 (ttmm) cc_final: 0.7478 (ttmm) REVERT: B 1034 LEU cc_start: 0.8449 (mp) cc_final: 0.8173 (mp) REVERT: B 1088 HIS cc_start: 0.7461 (m-70) cc_final: 0.6989 (m170) REVERT: B 1105 THR cc_start: 0.6401 (m) cc_final: 0.5849 (t) REVERT: C 40 ASP cc_start: 0.8041 (p0) cc_final: 0.7831 (p0) REVERT: C 153 MET cc_start: 0.3783 (mtm) cc_final: 0.3396 (ttm) REVERT: C 189 LEU cc_start: 0.7917 (tp) cc_final: 0.7672 (tp) REVERT: C 190 ARG cc_start: 0.6207 (mmm-85) cc_final: 0.5921 (tpp80) REVERT: C 228 ASP cc_start: 0.6951 (t0) cc_final: 0.6687 (t70) REVERT: C 720 ILE cc_start: 0.7769 (mm) cc_final: 0.7279 (tt) REVERT: C 814 LYS cc_start: 0.7268 (mmtt) cc_final: 0.6872 (mmmt) REVERT: C 886 TRP cc_start: 0.7275 (p90) cc_final: 0.7037 (p90) REVERT: C 900 MET cc_start: 0.8522 (mmp) cc_final: 0.7297 (mmp) REVERT: C 902 MET cc_start: 0.8416 (mmm) cc_final: 0.7966 (mmm) REVERT: C 919 ASN cc_start: 0.8289 (t0) cc_final: 0.7696 (t0) REVERT: C 922 LEU cc_start: 0.8207 (tt) cc_final: 0.7939 (tt) REVERT: C 1013 ILE cc_start: 0.7542 (tp) cc_final: 0.7228 (tt) REVERT: C 1019 ARG cc_start: 0.7165 (ttm170) cc_final: 0.6953 (ttm170) REVERT: C 1061 VAL cc_start: 0.8193 (t) cc_final: 0.7892 (m) REVERT: C 1125 ASN cc_start: 0.7323 (OUTLIER) cc_final: 0.7025 (p0) REVERT: C 1138 TYR cc_start: 0.7388 (t80) cc_final: 0.7120 (t80) outliers start: 4 outliers final: 0 residues processed: 606 average time/residue: 0.1657 time to fit residues: 160.7489 Evaluate side-chains 485 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 482 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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: 5.9990 chunk 25 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 290 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 198 optimal weight: 0.1980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 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 925 ASN C 926 GLN C1083 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.077367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.064846 restraints weight = 140016.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.066654 restraints weight = 86650.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.067954 restraints weight = 59544.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.068886 restraints weight = 44286.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.069506 restraints weight = 35149.288| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.3441 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= 0.161 Angle : 0.805 19.980 37363 Z= 0.383 Chirality : 0.051 0.547 4443 Planarity : 0.004 0.055 4664 Dihedral : 10.521 106.879 5359 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % 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: -1.38 (0.14), residues: 3206 helix: 0.41 (0.20), residues: 682 sheet: -0.46 (0.21), residues: 559 loop : -1.60 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1039 TYR 0.023 0.002 TYR C 365 PHE 0.026 0.002 PHE C 898 TRP 0.040 0.002 TRP A 64 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00346 (27224) covalent geometry : angle 0.74011 (37027) SS BOND : bond 0.00355 ( 42) SS BOND : angle 1.69593 ( 84) hydrogen bonds : bond 0.04135 ( 1030) hydrogen bonds : angle 6.47338 ( 2928) Misc. bond : bond 0.00118 ( 1) link_ALPHA1-4 : bond 0.01783 ( 6) link_ALPHA1-4 : angle 3.49795 ( 18) link_BETA1-4 : bond 0.00463 ( 25) link_BETA1-4 : angle 2.09442 ( 75) link_BETA1-6 : bond 0.01533 ( 3) link_BETA1-6 : angle 2.20707 ( 9) link_NAG-ASN : bond 0.00655 ( 50) link_NAG-ASN : angle 4.53515 ( 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 586 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 585 time to evaluate : 0.968 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 40 ASP cc_start: 0.8404 (m-30) cc_final: 0.8005 (p0) REVERT: A 140 PHE cc_start: 0.6376 (p90) cc_final: 0.6160 (p90) REVERT: A 296 LEU cc_start: 0.8810 (tp) cc_final: 0.8403 (tp) REVERT: A 300 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7689 (mttm) REVERT: A 309 GLU cc_start: 0.7772 (pm20) cc_final: 0.7547 (pm20) REVERT: A 313 TYR cc_start: 0.7558 (m-80) cc_final: 0.7183 (m-10) REVERT: A 468 ILE cc_start: 0.7641 (mm) cc_final: 0.7349 (pt) REVERT: A 532 ASN cc_start: 0.7842 (m110) cc_final: 0.7330 (p0) REVERT: A 553 THR cc_start: 0.7762 (m) cc_final: 0.7398 (m) REVERT: A 695 TYR cc_start: 0.7500 (p90) cc_final: 0.6537 (p90) REVERT: A 697 MET cc_start: 0.6929 (ptp) cc_final: 0.6178 (ptm) REVERT: A 699 LEU cc_start: 0.8268 (mm) cc_final: 0.7863 (mt) REVERT: A 707 TYR cc_start: 0.6904 (t80) cc_final: 0.6633 (t80) REVERT: A 737 ASP cc_start: 0.7121 (t0) cc_final: 0.6415 (t0) REVERT: A 773 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6682 (tp30) REVERT: A 818 ILE cc_start: 0.8519 (mm) cc_final: 0.8179 (mm) REVERT: A 901 GLN cc_start: 0.7472 (tm-30) cc_final: 0.5866 (tm-30) REVERT: A 905 ARG cc_start: 0.7266 (mtt-85) cc_final: 0.6714 (mtt-85) REVERT: A 906 PHE cc_start: 0.8537 (m-80) cc_final: 0.8034 (m-80) REVERT: A 907 ASN cc_start: 0.7787 (p0) cc_final: 0.7494 (m-40) REVERT: A 916 LEU cc_start: 0.8186 (tp) cc_final: 0.7880 (tp) REVERT: A 1017 GLU cc_start: 0.7683 (mp0) cc_final: 0.7135 (mp0) REVERT: B 33 THR cc_start: 0.6865 (p) cc_final: 0.5518 (m) REVERT: B 58 PHE cc_start: 0.8031 (m-10) cc_final: 0.7355 (m-80) REVERT: B 88 ASP cc_start: 0.7002 (m-30) cc_final: 0.6696 (p0) REVERT: B 92 PHE cc_start: 0.6492 (t80) cc_final: 0.6198 (t80) REVERT: B 157 PHE cc_start: 0.4068 (t80) cc_final: 0.3753 (t80) REVERT: B 158 ARG cc_start: 0.4813 (mpt180) cc_final: 0.4412 (mmt-90) REVERT: B 200 TYR cc_start: 0.6764 (m-10) cc_final: 0.6557 (m-10) REVERT: B 201 PHE cc_start: 0.7804 (t80) cc_final: 0.7527 (t80) REVERT: B 204 TYR cc_start: 0.6659 (m-80) cc_final: 0.6110 (m-80) REVERT: B 270 LEU cc_start: 0.8075 (tp) cc_final: 0.7308 (tp) REVERT: B 309 GLU cc_start: 0.7554 (mp0) cc_final: 0.7303 (mp0) REVERT: B 351 TYR cc_start: 0.6168 (p90) cc_final: 0.5887 (p90) REVERT: B 557 LYS cc_start: 0.6779 (mtmt) cc_final: 0.6344 (mttp) REVERT: B 570 ASP cc_start: 0.7247 (t70) cc_final: 0.6965 (t0) REVERT: B 573 THR cc_start: 0.8124 (p) cc_final: 0.7855 (p) REVERT: B 693 ILE cc_start: 0.7885 (mt) cc_final: 0.7639 (mp) REVERT: B 697 MET cc_start: 0.6708 (ttp) cc_final: 0.6318 (ttp) REVERT: B 710 ASN cc_start: 0.8140 (p0) cc_final: 0.7249 (t0) REVERT: B 731 MET cc_start: 0.7016 (ptt) cc_final: 0.6701 (ptt) REVERT: B 741 TYR cc_start: 0.8474 (t80) cc_final: 0.7882 (t80) REVERT: B 755 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7467 (mm-40) REVERT: B 872 GLN cc_start: 0.8050 (mp10) cc_final: 0.7795 (mm-40) REVERT: B 900 MET cc_start: 0.8382 (mmp) cc_final: 0.8108 (mmp) REVERT: B 921 LYS cc_start: 0.8142 (mmmm) cc_final: 0.7851 (mmmt) REVERT: B 960 ASN cc_start: 0.7868 (t0) cc_final: 0.7547 (t0) REVERT: B 1028 LYS cc_start: 0.7781 (ttmm) cc_final: 0.7550 (ttmm) REVERT: B 1034 LEU cc_start: 0.8380 (mp) cc_final: 0.8097 (mp) REVERT: B 1088 HIS cc_start: 0.7508 (m-70) cc_final: 0.7227 (m-70) REVERT: B 1105 THR cc_start: 0.6541 (m) cc_final: 0.6061 (t) REVERT: C 153 MET cc_start: 0.3929 (mtm) cc_final: 0.3477 (ttm) REVERT: C 189 LEU cc_start: 0.7897 (tp) cc_final: 0.7609 (tp) REVERT: C 190 ARG cc_start: 0.6196 (mmm-85) cc_final: 0.5880 (tpp80) REVERT: C 228 ASP cc_start: 0.6981 (t0) cc_final: 0.6736 (t70) REVERT: C 720 ILE cc_start: 0.7724 (mm) cc_final: 0.7246 (tt) REVERT: C 742 ILE cc_start: 0.8246 (mm) cc_final: 0.7573 (tt) REVERT: C 814 LYS cc_start: 0.7394 (mmtt) cc_final: 0.7009 (mmmt) REVERT: C 886 TRP cc_start: 0.7263 (p90) cc_final: 0.7047 (p90) REVERT: C 900 MET cc_start: 0.8438 (mmp) cc_final: 0.7264 (mmp) REVERT: C 919 ASN cc_start: 0.8307 (t0) cc_final: 0.7650 (t0) REVERT: C 922 LEU cc_start: 0.8211 (tt) cc_final: 0.7892 (tt) REVERT: C 973 ILE cc_start: 0.7790 (pt) cc_final: 0.7577 (pt) REVERT: C 1013 ILE cc_start: 0.7508 (tp) cc_final: 0.7289 (tp) REVERT: C 1061 VAL cc_start: 0.8239 (t) cc_final: 0.7842 (m) REVERT: C 1138 TYR cc_start: 0.7355 (t80) cc_final: 0.7070 (t80) outliers start: 1 outliers final: 0 residues processed: 585 average time/residue: 0.1649 time to fit residues: 155.2608 Evaluate side-chains 474 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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: 3.9990 chunk 85 optimal weight: 0.7980 chunk 282 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 804 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.077178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.064618 restraints weight = 139257.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.066418 restraints weight = 86188.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067714 restraints weight = 59339.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.068638 restraints weight = 44192.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.069209 restraints weight = 35138.463| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27351 Z= 0.163 Angle : 0.793 20.018 37363 Z= 0.380 Chirality : 0.051 0.531 4443 Planarity : 0.005 0.054 4664 Dihedral : 10.095 104.373 5359 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.72 % 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: -1.47 (0.14), residues: 3206 helix: 0.34 (0.19), residues: 697 sheet: -0.52 (0.21), residues: 542 loop : -1.67 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 815 TYR 0.030 0.002 TYR B 636 PHE 0.031 0.002 PHE B 490 TRP 0.048 0.002 TRP C 64 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00357 (27224) covalent geometry : angle 0.73315 (37027) SS BOND : bond 0.00346 ( 42) SS BOND : angle 1.75204 ( 84) hydrogen bonds : bond 0.04051 ( 1030) hydrogen bonds : angle 6.45027 ( 2928) Misc. bond : bond 0.00389 ( 1) link_ALPHA1-4 : bond 0.01857 ( 6) link_ALPHA1-4 : angle 3.64540 ( 18) link_BETA1-4 : bond 0.00485 ( 25) link_BETA1-4 : angle 1.99902 ( 75) link_BETA1-6 : bond 0.01666 ( 3) link_BETA1-6 : angle 2.12178 ( 9) link_NAG-ASN : bond 0.00643 ( 50) link_NAG-ASN : angle 4.28496 ( 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 582 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 581 time to evaluate : 0.808 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: 0.8451 (m-30) cc_final: 0.7945 (p0) REVERT: A 140 PHE cc_start: 0.6403 (p90) cc_final: 0.6077 (p90) REVERT: A 296 LEU cc_start: 0.8820 (tp) cc_final: 0.8470 (tp) REVERT: A 300 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7755 (mttm) REVERT: A 313 TYR cc_start: 0.7580 (m-80) cc_final: 0.7332 (m-10) REVERT: A 468 ILE cc_start: 0.7592 (mm) cc_final: 0.7245 (pt) REVERT: A 532 ASN cc_start: 0.7910 (m110) cc_final: 0.7333 (p0) REVERT: A 553 THR cc_start: 0.7686 (m) cc_final: 0.7321 (m) REVERT: A 697 MET cc_start: 0.6847 (ptp) cc_final: 0.6638 (ptm) REVERT: A 699 LEU cc_start: 0.8142 (mm) cc_final: 0.7893 (mt) REVERT: A 707 TYR cc_start: 0.6868 (t80) cc_final: 0.6604 (t80) REVERT: A 737 ASP cc_start: 0.7134 (t0) cc_final: 0.6496 (t0) REVERT: A 773 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6804 (tp30) REVERT: A 815 ARG cc_start: 0.5938 (mtm180) cc_final: 0.5500 (mtm180) REVERT: A 901 GLN cc_start: 0.7733 (tm-30) cc_final: 0.6349 (tm-30) REVERT: A 905 ARG cc_start: 0.7403 (mtt-85) cc_final: 0.7054 (mtt-85) REVERT: A 906 PHE cc_start: 0.8520 (m-80) cc_final: 0.8174 (m-80) REVERT: A 916 LEU cc_start: 0.8150 (tp) cc_final: 0.7881 (tp) REVERT: A 934 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7716 (mm) REVERT: A 1017 GLU cc_start: 0.7695 (mp0) cc_final: 0.7100 (mp0) REVERT: B 33 THR cc_start: 0.6646 (p) cc_final: 0.5250 (m) REVERT: B 48 LEU cc_start: 0.8454 (mp) cc_final: 0.8024 (mt) REVERT: B 58 PHE cc_start: 0.8100 (m-10) cc_final: 0.7340 (m-80) REVERT: B 61 ASN cc_start: 0.3777 (t0) cc_final: 0.3142 (p0) REVERT: B 64 TRP cc_start: 0.4166 (t60) cc_final: 0.3032 (t60) REVERT: B 88 ASP cc_start: 0.6908 (m-30) cc_final: 0.6615 (p0) REVERT: B 92 PHE cc_start: 0.6468 (t80) cc_final: 0.6196 (t80) REVERT: B 129 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7819 (tttt) REVERT: B 201 PHE cc_start: 0.7802 (t80) cc_final: 0.7502 (t80) REVERT: B 204 TYR cc_start: 0.6654 (m-80) cc_final: 0.6069 (m-80) REVERT: B 270 LEU cc_start: 0.8157 (tp) cc_final: 0.7305 (tp) REVERT: B 309 GLU cc_start: 0.7583 (mp0) cc_final: 0.7345 (mp0) REVERT: B 351 TYR cc_start: 0.6149 (p90) cc_final: 0.5900 (p90) REVERT: B 495 TYR cc_start: 0.5845 (m-80) cc_final: 0.5469 (m-80) REVERT: B 570 ASP cc_start: 0.7305 (t70) cc_final: 0.7000 (t0) REVERT: B 573 THR cc_start: 0.8154 (p) cc_final: 0.7881 (p) REVERT: B 693 ILE cc_start: 0.7866 (mt) cc_final: 0.7621 (mp) REVERT: B 697 MET cc_start: 0.6594 (ttp) cc_final: 0.6339 (ttp) REVERT: B 707 TYR cc_start: 0.7071 (t80) cc_final: 0.6433 (t80) REVERT: B 710 ASN cc_start: 0.8131 (p0) cc_final: 0.7246 (t0) REVERT: B 725 GLU cc_start: 0.8107 (tp30) cc_final: 0.7791 (tp30) REVERT: B 731 MET cc_start: 0.7039 (ptt) cc_final: 0.6723 (ptt) REVERT: B 741 TYR cc_start: 0.8469 (t80) cc_final: 0.7808 (t80) REVERT: B 752 LEU cc_start: 0.7694 (tp) cc_final: 0.7446 (tp) REVERT: B 755 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7315 (mm-40) REVERT: B 815 ARG cc_start: 0.6527 (ttp-170) cc_final: 0.6221 (ttp-170) REVERT: B 872 GLN cc_start: 0.8185 (mp10) cc_final: 0.7849 (mm-40) REVERT: B 900 MET cc_start: 0.8358 (mmp) cc_final: 0.7898 (mmp) REVERT: B 960 ASN cc_start: 0.7848 (t0) cc_final: 0.7596 (t0) REVERT: B 1028 LYS cc_start: 0.7795 (ttmm) cc_final: 0.7557 (ttmm) REVERT: B 1037 SER cc_start: 0.6676 (p) cc_final: 0.6328 (m) REVERT: B 1088 HIS cc_start: 0.7521 (m-70) cc_final: 0.7268 (m-70) REVERT: B 1105 THR cc_start: 0.6453 (m) cc_final: 0.6003 (t) REVERT: C 40 ASP cc_start: 0.8061 (p0) cc_final: 0.7768 (p0) REVERT: C 133 PHE cc_start: 0.5974 (m-80) cc_final: 0.5750 (m-10) REVERT: C 153 MET cc_start: 0.4048 (mtm) cc_final: 0.3657 (ttm) REVERT: C 177 MET cc_start: 0.4215 (mpp) cc_final: 0.3893 (mmt) REVERT: C 189 LEU cc_start: 0.7930 (tp) cc_final: 0.7697 (tp) REVERT: C 190 ARG cc_start: 0.6336 (mmm-85) cc_final: 0.6060 (tpp80) REVERT: C 228 ASP cc_start: 0.6987 (t0) cc_final: 0.6783 (t70) REVERT: C 720 ILE cc_start: 0.7661 (mm) cc_final: 0.7080 (tt) REVERT: C 742 ILE cc_start: 0.8212 (mm) cc_final: 0.7545 (tt) REVERT: C 814 LYS cc_start: 0.7523 (mmtt) cc_final: 0.7117 (mmmt) REVERT: C 886 TRP cc_start: 0.7257 (p90) cc_final: 0.7020 (p90) REVERT: C 898 PHE cc_start: 0.7417 (t80) cc_final: 0.6961 (t80) REVERT: C 900 MET cc_start: 0.8428 (mmp) cc_final: 0.7241 (mmp) REVERT: C 902 MET cc_start: 0.8368 (mmm) cc_final: 0.7933 (mmm) REVERT: C 919 ASN cc_start: 0.8338 (t0) cc_final: 0.7677 (t0) REVERT: C 922 LEU cc_start: 0.8150 (tt) cc_final: 0.7675 (tt) REVERT: C 1013 ILE cc_start: 0.7549 (tp) cc_final: 0.7303 (tp) REVERT: C 1138 TYR cc_start: 0.7350 (t80) cc_final: 0.7113 (t80) outliers start: 1 outliers final: 0 residues processed: 581 average time/residue: 0.1652 time to fit residues: 153.8611 Evaluate side-chains 482 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 481 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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: 0.3980 chunk 240 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 299 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 196 ASN A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 895 GLN B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.077507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.064761 restraints weight = 137905.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066661 restraints weight = 84307.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.068019 restraints weight = 57329.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.068997 restraints weight = 42270.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.069661 restraints weight = 33315.517| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.3929 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= 0.150 Angle : 0.768 19.727 37363 Z= 0.367 Chirality : 0.050 0.530 4443 Planarity : 0.004 0.054 4664 Dihedral : 9.568 100.339 5359 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.07 % Allowed : 2.47 % 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: -1.38 (0.14), residues: 3206 helix: 0.57 (0.20), residues: 683 sheet: -0.57 (0.20), residues: 583 loop : -1.64 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 214 TYR 0.033 0.002 TYR B 421 PHE 0.047 0.002 PHE B 157 TRP 0.046 0.003 TRP C 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00331 (27224) covalent geometry : angle 0.71219 (37027) SS BOND : bond 0.00435 ( 42) SS BOND : angle 2.01447 ( 84) hydrogen bonds : bond 0.03902 ( 1030) hydrogen bonds : angle 6.34438 ( 2928) Misc. bond : bond 0.00070 ( 1) link_ALPHA1-4 : bond 0.01916 ( 6) link_ALPHA1-4 : angle 3.76428 ( 18) link_BETA1-4 : bond 0.00465 ( 25) link_BETA1-4 : angle 1.87956 ( 75) link_BETA1-6 : bond 0.01698 ( 3) link_BETA1-6 : angle 2.17311 ( 9) link_NAG-ASN : bond 0.00636 ( 50) link_NAG-ASN : angle 3.96495 ( 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 595 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 593 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8477 (m-30) cc_final: 0.7993 (p0) REVERT: A 140 PHE cc_start: 0.6344 (p90) cc_final: 0.6014 (p90) REVERT: A 296 LEU cc_start: 0.8807 (tp) cc_final: 0.8500 (tp) REVERT: A 300 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7718 (mttm) REVERT: A 309 GLU cc_start: 0.7881 (pm20) cc_final: 0.7678 (pm20) REVERT: A 313 TYR cc_start: 0.7595 (m-80) cc_final: 0.7289 (m-10) REVERT: A 468 ILE cc_start: 0.7655 (mm) cc_final: 0.7118 (tt) REVERT: A 532 ASN cc_start: 0.8017 (m110) cc_final: 0.7406 (p0) REVERT: A 553 THR cc_start: 0.7698 (m) cc_final: 0.7290 (m) REVERT: A 702 GLU cc_start: 0.7512 (tt0) cc_final: 0.7294 (mp0) REVERT: A 707 TYR cc_start: 0.6833 (t80) cc_final: 0.6626 (t80) REVERT: A 737 ASP cc_start: 0.7153 (t0) cc_final: 0.6734 (t0) REVERT: A 773 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6768 (tp30) REVERT: A 815 ARG cc_start: 0.5891 (mtm180) cc_final: 0.5393 (mtm110) REVERT: A 901 GLN cc_start: 0.7563 (tm-30) cc_final: 0.6960 (tm-30) REVERT: A 906 PHE cc_start: 0.8631 (m-80) cc_final: 0.8186 (m-80) REVERT: A 1017 GLU cc_start: 0.7649 (mp0) cc_final: 0.7162 (mp0) REVERT: B 48 LEU cc_start: 0.8421 (mp) cc_final: 0.7951 (mt) REVERT: B 88 ASP cc_start: 0.6963 (m-30) cc_final: 0.6654 (p0) REVERT: B 92 PHE cc_start: 0.6449 (t80) cc_final: 0.6008 (t80) REVERT: B 115 GLN cc_start: 0.7352 (mp-120) cc_final: 0.6666 (mp10) REVERT: B 129 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7947 (tttt) REVERT: B 201 PHE cc_start: 0.7844 (t80) cc_final: 0.7607 (t80) REVERT: B 204 TYR cc_start: 0.6507 (m-80) cc_final: 0.5992 (m-80) REVERT: B 270 LEU cc_start: 0.8045 (tp) cc_final: 0.7000 (tp) REVERT: B 309 GLU cc_start: 0.7595 (mp0) cc_final: 0.7310 (mp0) REVERT: B 351 TYR cc_start: 0.6244 (p90) cc_final: 0.6040 (p90) REVERT: B 495 TYR cc_start: 0.5918 (m-80) cc_final: 0.5484 (m-80) REVERT: B 570 ASP cc_start: 0.7464 (t70) cc_final: 0.7227 (t0) REVERT: B 573 THR cc_start: 0.8175 (p) cc_final: 0.7937 (p) REVERT: B 693 ILE cc_start: 0.7851 (mt) cc_final: 0.7632 (mp) REVERT: B 697 MET cc_start: 0.6504 (ttp) cc_final: 0.6219 (ttp) REVERT: B 707 TYR cc_start: 0.7093 (t80) cc_final: 0.6404 (t80) REVERT: B 710 ASN cc_start: 0.8182 (p0) cc_final: 0.7299 (t0) REVERT: B 725 GLU cc_start: 0.8170 (tp30) cc_final: 0.7763 (tp30) REVERT: B 731 MET cc_start: 0.7023 (ptt) cc_final: 0.6752 (ptt) REVERT: B 741 TYR cc_start: 0.8482 (t80) cc_final: 0.7817 (t80) REVERT: B 752 LEU cc_start: 0.7659 (tp) cc_final: 0.7398 (tp) REVERT: B 755 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7294 (mm-40) REVERT: B 872 GLN cc_start: 0.8174 (mp10) cc_final: 0.7835 (mm110) REVERT: B 882 ILE cc_start: 0.8933 (mm) cc_final: 0.8664 (tt) REVERT: B 900 MET cc_start: 0.8407 (mmp) cc_final: 0.7939 (mmp) REVERT: B 960 ASN cc_start: 0.7844 (t0) cc_final: 0.7552 (t0) REVERT: B 961 THR cc_start: 0.7376 (m) cc_final: 0.7127 (m) REVERT: B 1028 LYS cc_start: 0.7791 (ttmm) cc_final: 0.7552 (ttmm) REVERT: B 1034 LEU cc_start: 0.8375 (mp) cc_final: 0.8164 (mp) REVERT: B 1037 SER cc_start: 0.6531 (p) cc_final: 0.6150 (m) REVERT: B 1040 VAL cc_start: 0.8227 (p) cc_final: 0.8004 (m) REVERT: B 1088 HIS cc_start: 0.7519 (m-70) cc_final: 0.7296 (m-70) REVERT: B 1105 THR cc_start: 0.6408 (m) cc_final: 0.6012 (t) REVERT: B 1121 PHE cc_start: 0.6686 (p90) cc_final: 0.6395 (p90) REVERT: C 40 ASP cc_start: 0.8094 (p0) cc_final: 0.7808 (p0) REVERT: C 153 MET cc_start: 0.4107 (mtm) cc_final: 0.3759 (ttm) REVERT: C 189 LEU cc_start: 0.7914 (tp) cc_final: 0.7694 (tp) REVERT: C 190 ARG cc_start: 0.6313 (mmm-85) cc_final: 0.6104 (tpp80) REVERT: C 646 ARG cc_start: 0.8345 (mmt90) cc_final: 0.8076 (mmm-85) REVERT: C 720 ILE cc_start: 0.7617 (mm) cc_final: 0.7000 (tt) REVERT: C 742 ILE cc_start: 0.8275 (mm) cc_final: 0.7631 (tt) REVERT: C 814 LYS cc_start: 0.7447 (mmtt) cc_final: 0.7054 (mmmt) REVERT: C 886 TRP cc_start: 0.7319 (p90) cc_final: 0.7052 (p90) REVERT: C 898 PHE cc_start: 0.7323 (t80) cc_final: 0.6910 (t80) REVERT: C 900 MET cc_start: 0.8399 (mmp) cc_final: 0.6972 (mmp) REVERT: C 919 ASN cc_start: 0.8376 (t0) cc_final: 0.7750 (t0) REVERT: C 922 LEU cc_start: 0.8168 (tt) cc_final: 0.7764 (tt) REVERT: C 973 ILE cc_start: 0.7728 (pt) cc_final: 0.7474 (pt) REVERT: C 1013 ILE cc_start: 0.7479 (tp) cc_final: 0.7217 (tp) REVERT: C 1030 SER cc_start: 0.7574 (m) cc_final: 0.7208 (m) REVERT: C 1138 TYR cc_start: 0.7372 (t80) cc_final: 0.7110 (t80) outliers start: 2 outliers final: 0 residues processed: 593 average time/residue: 0.1685 time to fit residues: 160.4561 Evaluate side-chains 488 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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: 0.9990 chunk 320 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 183 optimal weight: 0.0000 chunk 88 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN C 115 GLN C 564 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 = 0.3678 r_free = 0.3678 target = 0.077965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.065157 restraints weight = 139545.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.067056 restraints weight = 84476.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.068444 restraints weight = 57348.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.069386 restraints weight = 42086.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.070126 restraints weight = 33155.724| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27351 Z= 0.140 Angle : 0.755 19.505 37363 Z= 0.362 Chirality : 0.049 0.532 4443 Planarity : 0.004 0.056 4664 Dihedral : 9.098 102.970 5359 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.07 % Allowed : 1.52 % Favored : 98.41 % 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: -1.39 (0.14), residues: 3206 helix: 0.42 (0.19), residues: 705 sheet: -0.56 (0.20), residues: 611 loop : -1.63 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1019 TYR 0.026 0.002 TYR C 265 PHE 0.067 0.002 PHE B 823 TRP 0.051 0.003 TRP B 633 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00306 (27224) covalent geometry : angle 0.70291 (37027) SS BOND : bond 0.00504 ( 42) SS BOND : angle 1.82221 ( 84) hydrogen bonds : bond 0.03816 ( 1030) hydrogen bonds : angle 6.25306 ( 2928) Misc. bond : bond 0.00697 ( 1) link_ALPHA1-4 : bond 0.01880 ( 6) link_ALPHA1-4 : angle 3.86680 ( 18) link_BETA1-4 : bond 0.00461 ( 25) link_BETA1-4 : angle 1.78797 ( 75) link_BETA1-6 : bond 0.01766 ( 3) link_BETA1-6 : angle 2.14157 ( 9) link_NAG-ASN : bond 0.00618 ( 50) link_NAG-ASN : angle 3.80633 ( 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 589 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 587 time to evaluate : 0.938 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: 0.8497 (m-30) cc_final: 0.7999 (p0) REVERT: A 66 HIS cc_start: 0.6430 (m90) cc_final: 0.5955 (t-90) REVERT: A 81 ASN cc_start: 0.6482 (t0) cc_final: 0.6110 (t0) REVERT: A 140 PHE cc_start: 0.6390 (p90) cc_final: 0.6014 (p90) REVERT: A 240 THR cc_start: 0.6976 (t) cc_final: 0.6758 (t) REVERT: A 275 PHE cc_start: 0.7190 (m-10) cc_final: 0.6937 (m-80) REVERT: A 296 LEU cc_start: 0.8824 (tp) cc_final: 0.8418 (tp) REVERT: A 300 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7631 (mttm) REVERT: A 392 PHE cc_start: 0.5824 (m-80) cc_final: 0.5508 (m-80) REVERT: A 532 ASN cc_start: 0.8086 (m110) cc_final: 0.7467 (p0) REVERT: A 553 THR cc_start: 0.7586 (m) cc_final: 0.7199 (m) REVERT: A 613 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7569 (mt0) REVERT: A 699 LEU cc_start: 0.8103 (mp) cc_final: 0.7694 (mp) REVERT: A 702 GLU cc_start: 0.7663 (tt0) cc_final: 0.7346 (mp0) REVERT: A 707 TYR cc_start: 0.6863 (t80) cc_final: 0.6218 (t80) REVERT: A 718 PHE cc_start: 0.7519 (p90) cc_final: 0.7248 (p90) REVERT: A 737 ASP cc_start: 0.7285 (t0) cc_final: 0.6772 (t0) REVERT: A 773 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6779 (tp30) REVERT: A 815 ARG cc_start: 0.5938 (mtm180) cc_final: 0.5419 (mtm110) REVERT: A 886 TRP cc_start: 0.7969 (p90) cc_final: 0.7698 (p90) REVERT: A 906 PHE cc_start: 0.8597 (m-80) cc_final: 0.8195 (m-80) REVERT: A 916 LEU cc_start: 0.8195 (tp) cc_final: 0.7776 (tp) REVERT: A 920 GLN cc_start: 0.7656 (mp10) cc_final: 0.7418 (mp10) REVERT: A 934 ILE cc_start: 0.7918 (mm) cc_final: 0.7683 (mm) REVERT: B 48 LEU cc_start: 0.8298 (mp) cc_final: 0.7749 (mt) REVERT: B 88 ASP cc_start: 0.6896 (m-30) cc_final: 0.6663 (p0) REVERT: B 115 GLN cc_start: 0.7406 (mp-120) cc_final: 0.6685 (mp10) REVERT: B 201 PHE cc_start: 0.7803 (t80) cc_final: 0.7540 (t80) REVERT: B 204 TYR cc_start: 0.6476 (m-80) cc_final: 0.5922 (m-80) REVERT: B 270 LEU cc_start: 0.8052 (tp) cc_final: 0.7069 (tp) REVERT: B 309 GLU cc_start: 0.7609 (mp0) cc_final: 0.7328 (mp0) REVERT: B 495 TYR cc_start: 0.5862 (m-80) cc_final: 0.5429 (m-80) REVERT: B 570 ASP cc_start: 0.7453 (t70) cc_final: 0.7219 (t0) REVERT: B 595 VAL cc_start: 0.7767 (t) cc_final: 0.7330 (t) REVERT: B 613 GLN cc_start: 0.7319 (pm20) cc_final: 0.6644 (pm20) REVERT: B 693 ILE cc_start: 0.7816 (mt) cc_final: 0.7589 (mp) REVERT: B 707 TYR cc_start: 0.7234 (t80) cc_final: 0.6558 (t80) REVERT: B 710 ASN cc_start: 0.8170 (p0) cc_final: 0.7355 (t0) REVERT: B 731 MET cc_start: 0.7009 (ptt) cc_final: 0.6675 (ptt) REVERT: B 741 TYR cc_start: 0.8477 (t80) cc_final: 0.7795 (t80) REVERT: B 752 LEU cc_start: 0.7586 (tp) cc_final: 0.7311 (tp) REVERT: B 755 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7275 (mm-40) REVERT: B 872 GLN cc_start: 0.8252 (mp10) cc_final: 0.7893 (mm110) REVERT: B 882 ILE cc_start: 0.8922 (mm) cc_final: 0.8659 (tt) REVERT: B 900 MET cc_start: 0.8401 (mmp) cc_final: 0.7918 (mmp) REVERT: B 933 LYS cc_start: 0.7993 (ptpt) cc_final: 0.7757 (mtmt) REVERT: B 954 GLN cc_start: 0.7719 (mt0) cc_final: 0.7513 (tt0) REVERT: B 957 GLN cc_start: 0.8220 (tp40) cc_final: 0.7859 (tp40) REVERT: B 961 THR cc_start: 0.7423 (m) cc_final: 0.7125 (m) REVERT: B 1014 ARG cc_start: 0.6116 (ttm170) cc_final: 0.5514 (ttm170) REVERT: B 1028 LYS cc_start: 0.7774 (ttmm) cc_final: 0.7550 (ttmm) REVERT: B 1034 LEU cc_start: 0.8387 (mp) cc_final: 0.8158 (mp) REVERT: B 1037 SER cc_start: 0.6477 (p) cc_final: 0.6088 (m) REVERT: B 1088 HIS cc_start: 0.7549 (m-70) cc_final: 0.7339 (m-70) REVERT: B 1105 THR cc_start: 0.6442 (m) cc_final: 0.6242 (m) REVERT: C 40 ASP cc_start: 0.8107 (p0) cc_final: 0.7829 (p0) REVERT: C 99 ASN cc_start: 0.6948 (m110) cc_final: 0.6711 (m110) REVERT: C 133 PHE cc_start: 0.5838 (m-10) cc_final: 0.5626 (m-10) REVERT: C 153 MET cc_start: 0.4020 (mtm) cc_final: 0.3699 (ttm) REVERT: C 189 LEU cc_start: 0.7900 (tp) cc_final: 0.7688 (tp) REVERT: C 190 ARG cc_start: 0.6347 (mmm-85) cc_final: 0.6083 (tpp80) REVERT: C 568 ASP cc_start: 0.7667 (t70) cc_final: 0.7136 (t70) REVERT: C 646 ARG cc_start: 0.8333 (mmt90) cc_final: 0.8067 (mmm-85) REVERT: C 742 ILE cc_start: 0.8341 (mm) cc_final: 0.7677 (tt) REVERT: C 814 LYS cc_start: 0.7469 (mmtt) cc_final: 0.7112 (mmmt) REVERT: C 886 TRP cc_start: 0.7294 (p90) cc_final: 0.6974 (p90) REVERT: C 898 PHE cc_start: 0.7313 (t80) cc_final: 0.6637 (t80) REVERT: C 900 MET cc_start: 0.8398 (mmp) cc_final: 0.6970 (mmp) REVERT: C 902 MET cc_start: 0.8362 (mmm) cc_final: 0.7924 (mmm) REVERT: C 919 ASN cc_start: 0.8368 (t0) cc_final: 0.7640 (t0) REVERT: C 922 LEU cc_start: 0.8135 (tt) cc_final: 0.7714 (tt) REVERT: C 973 ILE cc_start: 0.7710 (pt) cc_final: 0.7480 (pt) REVERT: C 1013 ILE cc_start: 0.7418 (tp) cc_final: 0.7196 (tp) REVERT: C 1029 MET cc_start: 0.8400 (tpp) cc_final: 0.7338 (tpp) REVERT: C 1061 VAL cc_start: 0.8109 (t) cc_final: 0.7615 (m) REVERT: C 1062 PHE cc_start: 0.6793 (m-80) cc_final: 0.6571 (m-80) REVERT: C 1138 TYR cc_start: 0.7399 (t80) cc_final: 0.7167 (t80) REVERT: C 1148 PHE cc_start: 0.4827 (t80) cc_final: 0.4552 (t80) outliers start: 2 outliers final: 0 residues processed: 587 average time/residue: 0.1625 time to fit residues: 153.2147 Evaluate side-chains 480 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 479 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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: 1.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 85 optimal weight: 0.0040 chunk 108 optimal weight: 0.9980 chunk 237 optimal weight: 0.0070 chunk 4 optimal weight: 6.9990 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN C 564 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.077984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065215 restraints weight = 140011.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.067158 restraints weight = 85028.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.068534 restraints weight = 57472.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.069511 restraints weight = 42185.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.070204 restraints weight = 33196.364| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27351 Z= 0.134 Angle : 0.747 19.313 37363 Z= 0.358 Chirality : 0.049 0.529 4443 Planarity : 0.004 0.054 4664 Dihedral : 8.661 104.763 5359 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.04 % Allowed : 1.06 % Favored : 98.91 % 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: -1.31 (0.14), residues: 3206 helix: 0.50 (0.20), residues: 705 sheet: -0.55 (0.20), residues: 623 loop : -1.57 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1019 TYR 0.025 0.002 TYR C 265 PHE 0.053 0.002 PHE B 823 TRP 0.042 0.002 TRP B 633 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00296 (27224) covalent geometry : angle 0.69842 (37027) SS BOND : bond 0.00398 ( 42) SS BOND : angle 1.59740 ( 84) hydrogen bonds : bond 0.03677 ( 1030) hydrogen bonds : angle 6.14183 ( 2928) Misc. bond : bond 0.00296 ( 1) link_ALPHA1-4 : bond 0.01925 ( 6) link_ALPHA1-4 : angle 3.71543 ( 18) link_BETA1-4 : bond 0.00447 ( 25) link_BETA1-4 : angle 1.73198 ( 75) link_BETA1-6 : bond 0.01741 ( 3) link_BETA1-6 : angle 2.14704 ( 9) link_NAG-ASN : bond 0.00612 ( 50) link_NAG-ASN : angle 3.70845 ( 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 581 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 580 time to evaluate : 0.939 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: 0.8494 (m-30) cc_final: 0.7974 (p0) REVERT: A 66 HIS cc_start: 0.6398 (m90) cc_final: 0.6149 (t-90) REVERT: A 140 PHE cc_start: 0.6342 (p90) cc_final: 0.6006 (p90) REVERT: A 201 PHE cc_start: 0.7686 (t80) cc_final: 0.7435 (t80) REVERT: A 275 PHE cc_start: 0.7091 (m-10) cc_final: 0.6887 (m-80) REVERT: A 296 LEU cc_start: 0.8829 (tp) cc_final: 0.8399 (tp) REVERT: A 300 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7673 (mttm) REVERT: A 313 TYR cc_start: 0.7600 (m-80) cc_final: 0.7242 (m-10) REVERT: A 392 PHE cc_start: 0.5882 (m-80) cc_final: 0.5542 (m-10) REVERT: A 553 THR cc_start: 0.7596 (m) cc_final: 0.7221 (m) REVERT: A 702 GLU cc_start: 0.7716 (tt0) cc_final: 0.7405 (mp0) REVERT: A 707 TYR cc_start: 0.6880 (t80) cc_final: 0.6239 (t80) REVERT: A 718 PHE cc_start: 0.7469 (p90) cc_final: 0.7210 (p90) REVERT: A 737 ASP cc_start: 0.7189 (t0) cc_final: 0.6658 (t0) REVERT: A 759 PHE cc_start: 0.7284 (p90) cc_final: 0.7044 (p90) REVERT: A 773 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6841 (tp30) REVERT: A 792 PRO cc_start: 0.7217 (Cg_exo) cc_final: 0.7005 (Cg_endo) REVERT: A 815 ARG cc_start: 0.6035 (mtm180) cc_final: 0.5549 (mtm110) REVERT: A 906 PHE cc_start: 0.8543 (m-80) cc_final: 0.8186 (m-80) REVERT: A 916 LEU cc_start: 0.8164 (tp) cc_final: 0.7877 (tp) REVERT: A 934 ILE cc_start: 0.7890 (mm) cc_final: 0.7656 (mm) REVERT: A 964 LYS cc_start: 0.8523 (mmmm) cc_final: 0.8230 (mtmt) REVERT: B 48 LEU cc_start: 0.8286 (mp) cc_final: 0.7830 (mt) REVERT: B 88 ASP cc_start: 0.6897 (m-30) cc_final: 0.6544 (p0) REVERT: B 115 GLN cc_start: 0.7393 (mp-120) cc_final: 0.6678 (mp10) REVERT: B 158 ARG cc_start: 0.4963 (mmt-90) cc_final: 0.4337 (mmp80) REVERT: B 201 PHE cc_start: 0.7737 (t80) cc_final: 0.7476 (t80) REVERT: B 204 TYR cc_start: 0.6543 (m-80) cc_final: 0.5963 (m-80) REVERT: B 270 LEU cc_start: 0.8117 (tp) cc_final: 0.7107 (tp) REVERT: B 285 ILE cc_start: 0.8515 (mt) cc_final: 0.8220 (pt) REVERT: B 309 GLU cc_start: 0.7612 (mp0) cc_final: 0.7326 (mp0) REVERT: B 351 TYR cc_start: 0.6144 (p90) cc_final: 0.5851 (p90) REVERT: B 495 TYR cc_start: 0.5848 (m-80) cc_final: 0.5383 (m-80) REVERT: B 570 ASP cc_start: 0.7509 (t70) cc_final: 0.7238 (t0) REVERT: B 573 THR cc_start: 0.8235 (p) cc_final: 0.8033 (p) REVERT: B 595 VAL cc_start: 0.7821 (t) cc_final: 0.7578 (t) REVERT: B 613 GLN cc_start: 0.7233 (pm20) cc_final: 0.6423 (pm20) REVERT: B 693 ILE cc_start: 0.7769 (mt) cc_final: 0.7536 (mp) REVERT: B 707 TYR cc_start: 0.7224 (t80) cc_final: 0.6509 (t80) REVERT: B 710 ASN cc_start: 0.8179 (p0) cc_final: 0.7372 (t0) REVERT: B 731 MET cc_start: 0.6963 (ptt) cc_final: 0.6752 (ptt) REVERT: B 741 TYR cc_start: 0.8482 (t80) cc_final: 0.8081 (t80) REVERT: B 752 LEU cc_start: 0.7538 (tp) cc_final: 0.7258 (tp) REVERT: B 755 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7301 (mm-40) REVERT: B 815 ARG cc_start: 0.5771 (ttp-170) cc_final: 0.5334 (ttp-170) REVERT: B 882 ILE cc_start: 0.8933 (mm) cc_final: 0.8697 (tt) REVERT: B 960 ASN cc_start: 0.7776 (t0) cc_final: 0.7524 (t0) REVERT: B 1031 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6898 (tt0) REVERT: B 1034 LEU cc_start: 0.8373 (mp) cc_final: 0.8118 (mp) REVERT: B 1037 SER cc_start: 0.6484 (p) cc_final: 0.4871 (p) REVERT: B 1105 THR cc_start: 0.6355 (m) cc_final: 0.6140 (m) REVERT: C 40 ASP cc_start: 0.8230 (p0) cc_final: 0.7998 (p0) REVERT: C 133 PHE cc_start: 0.5681 (m-80) cc_final: 0.5363 (m-10) REVERT: C 153 MET cc_start: 0.4141 (mtm) cc_final: 0.3821 (ttm) REVERT: C 189 LEU cc_start: 0.7894 (tp) cc_final: 0.7664 (tp) REVERT: C 568 ASP cc_start: 0.7552 (t70) cc_final: 0.7252 (p0) REVERT: C 742 ILE cc_start: 0.8342 (mm) cc_final: 0.7683 (tt) REVERT: C 773 GLU cc_start: 0.8052 (tt0) cc_final: 0.7118 (tp30) REVERT: C 814 LYS cc_start: 0.7427 (mmtt) cc_final: 0.7069 (mmmt) REVERT: C 886 TRP cc_start: 0.7293 (p90) cc_final: 0.6960 (p90) REVERT: C 898 PHE cc_start: 0.7240 (t80) cc_final: 0.6693 (t80) REVERT: C 900 MET cc_start: 0.8365 (mmp) cc_final: 0.6861 (mmp) REVERT: C 902 MET cc_start: 0.8362 (mmm) cc_final: 0.7900 (mmm) REVERT: C 919 ASN cc_start: 0.8508 (t0) cc_final: 0.8241 (t0) REVERT: C 973 ILE cc_start: 0.7731 (pt) cc_final: 0.7492 (pt) REVERT: C 1061 VAL cc_start: 0.8075 (t) cc_final: 0.7554 (m) REVERT: C 1110 TYR cc_start: 0.6807 (t80) cc_final: 0.6517 (t80) REVERT: C 1148 PHE cc_start: 0.4842 (t80) cc_final: 0.4571 (t80) outliers start: 1 outliers final: 0 residues processed: 580 average time/residue: 0.1660 time to fit residues: 154.7489 Evaluate side-chains 466 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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: 1.9990 chunk 200 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 311 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1108 ASN C 564 GLN C 895 GLN C 901 GLN C 926 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.077773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.065010 restraints weight = 139660.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.066939 restraints weight = 84898.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.068314 restraints weight = 57705.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.069305 restraints weight = 42329.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.069905 restraints weight = 33255.242| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.4411 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= 0.142 Angle : 0.755 19.126 37363 Z= 0.363 Chirality : 0.049 0.520 4443 Planarity : 0.004 0.056 4664 Dihedral : 8.388 106.041 5359 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.07 % Allowed : 0.85 % Favored : 99.08 % 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: 0.56 (0.20), residues: 699 sheet: -0.54 (0.20), residues: 626 loop : -1.58 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 905 TYR 0.043 0.002 TYR B 421 PHE 0.046 0.002 PHE B 823 TRP 0.035 0.002 TRP B 633 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00314 (27224) covalent geometry : angle 0.70676 (37027) SS BOND : bond 0.00323 ( 42) SS BOND : angle 1.55454 ( 84) hydrogen bonds : bond 0.03707 ( 1030) hydrogen bonds : angle 6.15800 ( 2928) Misc. bond : bond 0.00195 ( 1) link_ALPHA1-4 : bond 0.01947 ( 6) link_ALPHA1-4 : angle 3.79449 ( 18) link_BETA1-4 : bond 0.00433 ( 25) link_BETA1-4 : angle 1.72884 ( 75) link_BETA1-6 : bond 0.01664 ( 3) link_BETA1-6 : angle 2.09079 ( 9) link_NAG-ASN : bond 0.00607 ( 50) link_NAG-ASN : angle 3.73697 ( 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 573 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 571 time to evaluate : 0.917 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: 0.8542 (m-30) cc_final: 0.8003 (p0) REVERT: A 59 PHE cc_start: 0.8244 (m-10) cc_final: 0.8031 (m-80) REVERT: A 66 HIS cc_start: 0.6515 (m90) cc_final: 0.6070 (t-90) REVERT: A 140 PHE cc_start: 0.6339 (p90) cc_final: 0.5955 (p90) REVERT: A 275 PHE cc_start: 0.7140 (m-10) cc_final: 0.6875 (m-80) REVERT: A 296 LEU cc_start: 0.8836 (tp) cc_final: 0.8408 (tp) REVERT: A 300 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7648 (mttm) REVERT: A 309 GLU cc_start: 0.7817 (pm20) cc_final: 0.7492 (pm20) REVERT: A 392 PHE cc_start: 0.6000 (m-80) cc_final: 0.5617 (m-80) REVERT: A 410 ILE cc_start: 0.6699 (tp) cc_final: 0.6450 (tp) REVERT: A 466 ARG cc_start: 0.5706 (mmt90) cc_final: 0.4679 (mmm160) REVERT: A 553 THR cc_start: 0.7254 (m) cc_final: 0.7007 (m) REVERT: A 643 PHE cc_start: 0.5383 (t80) cc_final: 0.5122 (t80) REVERT: A 697 MET cc_start: 0.7330 (ptm) cc_final: 0.7123 (ptm) REVERT: A 707 TYR cc_start: 0.6893 (t80) cc_final: 0.6242 (t80) REVERT: A 737 ASP cc_start: 0.7261 (t0) cc_final: 0.6684 (t70) REVERT: A 759 PHE cc_start: 0.7364 (p90) cc_final: 0.7140 (p90) REVERT: A 773 GLU cc_start: 0.7441 (mm-30) cc_final: 0.6828 (tp30) REVERT: A 815 ARG cc_start: 0.6040 (mtm180) cc_final: 0.5553 (mtm110) REVERT: A 906 PHE cc_start: 0.8677 (m-80) cc_final: 0.8215 (m-80) REVERT: A 916 LEU cc_start: 0.8193 (tp) cc_final: 0.7770 (tp) REVERT: A 920 GLN cc_start: 0.7655 (mp10) cc_final: 0.7395 (mp10) REVERT: A 934 ILE cc_start: 0.7924 (mm) cc_final: 0.7664 (mm) REVERT: A 1061 VAL cc_start: 0.7416 (t) cc_final: 0.6840 (m) REVERT: B 48 LEU cc_start: 0.8356 (mp) cc_final: 0.7894 (mt) REVERT: B 88 ASP cc_start: 0.6910 (m-30) cc_final: 0.6647 (p0) REVERT: B 115 GLN cc_start: 0.7359 (mp-120) cc_final: 0.6671 (mp10) REVERT: B 158 ARG cc_start: 0.4945 (mmt-90) cc_final: 0.4319 (mmp80) REVERT: B 201 PHE cc_start: 0.7725 (t80) cc_final: 0.7446 (t80) REVERT: B 204 TYR cc_start: 0.6508 (m-80) cc_final: 0.5974 (m-80) REVERT: B 270 LEU cc_start: 0.8161 (tp) cc_final: 0.7179 (tp) REVERT: B 285 ILE cc_start: 0.8485 (mt) cc_final: 0.8205 (pt) REVERT: B 309 GLU cc_start: 0.7619 (mp0) cc_final: 0.7322 (mp0) REVERT: B 351 TYR cc_start: 0.6094 (p90) cc_final: 0.5856 (p90) REVERT: B 495 TYR cc_start: 0.5800 (m-80) cc_final: 0.5346 (m-80) REVERT: B 570 ASP cc_start: 0.7524 (t70) cc_final: 0.7239 (t0) REVERT: B 573 THR cc_start: 0.8238 (p) cc_final: 0.8025 (p) REVERT: B 595 VAL cc_start: 0.7888 (t) cc_final: 0.7602 (t) REVERT: B 613 GLN cc_start: 0.7230 (pm20) cc_final: 0.6439 (pm20) REVERT: B 693 ILE cc_start: 0.7744 (mt) cc_final: 0.7535 (mp) REVERT: B 707 TYR cc_start: 0.7268 (t80) cc_final: 0.6596 (t80) REVERT: B 710 ASN cc_start: 0.8227 (p0) cc_final: 0.7401 (t0) REVERT: B 725 GLU cc_start: 0.8062 (tp30) cc_final: 0.7685 (tp30) REVERT: B 731 MET cc_start: 0.7042 (ptt) cc_final: 0.6792 (ptt) REVERT: B 741 TYR cc_start: 0.8441 (t80) cc_final: 0.8169 (t80) REVERT: B 752 LEU cc_start: 0.7573 (tp) cc_final: 0.7286 (tp) REVERT: B 755 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7255 (mm-40) REVERT: B 780 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6717 (mt-10) REVERT: B 815 ARG cc_start: 0.5862 (ttp-170) cc_final: 0.5449 (ttp-170) REVERT: B 900 MET cc_start: 0.8520 (mmp) cc_final: 0.7945 (mmp) REVERT: B 957 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7949 (tp40) REVERT: B 960 ASN cc_start: 0.7766 (t0) cc_final: 0.7509 (t0) REVERT: B 1019 ARG cc_start: 0.7644 (ttt90) cc_final: 0.7357 (tpt90) REVERT: B 1028 LYS cc_start: 0.8071 (ttmm) cc_final: 0.7863 (mttt) REVERT: B 1031 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7032 (tt0) REVERT: B 1034 LEU cc_start: 0.8334 (mp) cc_final: 0.8105 (mp) REVERT: B 1037 SER cc_start: 0.6479 (p) cc_final: 0.4951 (p) REVERT: C 40 ASP cc_start: 0.8165 (p0) cc_final: 0.7935 (p0) REVERT: C 41 LYS cc_start: 0.6998 (ttpt) cc_final: 0.6750 (ttpp) REVERT: C 133 PHE cc_start: 0.6097 (m-80) cc_final: 0.5781 (m-10) REVERT: C 153 MET cc_start: 0.4212 (mtm) cc_final: 0.3895 (ttm) REVERT: C 568 ASP cc_start: 0.7583 (t70) cc_final: 0.7364 (p0) REVERT: C 773 GLU cc_start: 0.8124 (tt0) cc_final: 0.7205 (tp30) REVERT: C 780 GLU cc_start: 0.7720 (pt0) cc_final: 0.7517 (pt0) REVERT: C 814 LYS cc_start: 0.7431 (mmtt) cc_final: 0.7066 (mmmt) REVERT: C 886 TRP cc_start: 0.7288 (p90) cc_final: 0.6893 (p90) REVERT: C 898 PHE cc_start: 0.7228 (t80) cc_final: 0.6665 (t80) REVERT: C 900 MET cc_start: 0.8366 (mmp) cc_final: 0.6855 (mmp) REVERT: C 902 MET cc_start: 0.8358 (mmm) cc_final: 0.7930 (mmm) REVERT: C 914 ASN cc_start: 0.8134 (p0) cc_final: 0.7931 (p0) REVERT: C 919 ASN cc_start: 0.8406 (t0) cc_final: 0.8159 (t0) REVERT: C 973 ILE cc_start: 0.7701 (pt) cc_final: 0.7471 (pt) REVERT: C 1061 VAL cc_start: 0.8038 (t) cc_final: 0.7684 (m) REVERT: C 1110 TYR cc_start: 0.6769 (t80) cc_final: 0.6498 (t80) REVERT: C 1138 TYR cc_start: 0.7296 (t80) cc_final: 0.6997 (t80) outliers start: 2 outliers final: 0 residues processed: 571 average time/residue: 0.1597 time to fit residues: 147.0028 Evaluate side-chains 474 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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: 1.9990 chunk 279 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 245 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 282 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1002 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN C 207 HIS C 234 ASN C 564 GLN C 895 GLN C 926 GLN C 957 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.076821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064372 restraints weight = 139229.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.066240 restraints weight = 85389.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.067569 restraints weight = 58502.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.068515 restraints weight = 43377.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.069217 restraints weight = 34097.895| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.4465 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= 0.186 Angle : 0.814 18.786 37363 Z= 0.394 Chirality : 0.051 0.499 4443 Planarity : 0.005 0.071 4664 Dihedral : 8.673 106.934 5359 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.07 % Allowed : 0.46 % Favored : 99.47 % 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: -1.50 (0.14), residues: 3206 helix: 0.30 (0.19), residues: 708 sheet: -0.68 (0.20), residues: 620 loop : -1.68 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 905 TYR 0.029 0.002 TYR B 421 PHE 0.046 0.002 PHE B 823 TRP 0.062 0.003 TRP B1102 HIS 0.008 0.002 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00414 (27224) covalent geometry : angle 0.76477 (37027) SS BOND : bond 0.00488 ( 42) SS BOND : angle 1.69730 ( 84) hydrogen bonds : bond 0.04024 ( 1030) hydrogen bonds : angle 6.35666 ( 2928) Misc. bond : bond 0.00191 ( 1) link_ALPHA1-4 : bond 0.02051 ( 6) link_ALPHA1-4 : angle 3.95373 ( 18) link_BETA1-4 : bond 0.00420 ( 25) link_BETA1-4 : angle 1.83836 ( 75) link_BETA1-6 : bond 0.01672 ( 3) link_BETA1-6 : angle 2.03069 ( 9) link_NAG-ASN : bond 0.00645 ( 50) link_NAG-ASN : angle 3.90612 ( 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 559 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 557 time to evaluate : 0.944 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: 0.8458 (m-30) cc_final: 0.7955 (p0) REVERT: A 66 HIS cc_start: 0.6576 (m90) cc_final: 0.6139 (t-90) REVERT: A 140 PHE cc_start: 0.6291 (p90) cc_final: 0.5913 (p90) REVERT: A 177 MET cc_start: 0.3051 (mtt) cc_final: 0.1997 (mpp) REVERT: A 313 TYR cc_start: 0.7631 (m-80) cc_final: 0.7320 (m-10) REVERT: A 410 ILE cc_start: 0.6585 (tp) cc_final: 0.6340 (tp) REVERT: A 553 THR cc_start: 0.7205 (m) cc_final: 0.6962 (m) REVERT: A 697 MET cc_start: 0.7408 (ptm) cc_final: 0.7141 (ptm) REVERT: A 702 GLU cc_start: 0.7699 (tt0) cc_final: 0.7271 (mp0) REVERT: A 707 TYR cc_start: 0.6911 (t80) cc_final: 0.6660 (t80) REVERT: A 737 ASP cc_start: 0.7379 (t0) cc_final: 0.6791 (t70) REVERT: A 773 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7077 (tp30) REVERT: A 797 PHE cc_start: 0.6295 (m-80) cc_final: 0.6083 (m-80) REVERT: A 815 ARG cc_start: 0.6081 (mtm180) cc_final: 0.5631 (mtm-85) REVERT: A 904 TYR cc_start: 0.8264 (m-10) cc_final: 0.7829 (m-10) REVERT: A 906 PHE cc_start: 0.8601 (m-80) cc_final: 0.8237 (m-80) REVERT: A 916 LEU cc_start: 0.8258 (tp) cc_final: 0.8026 (tp) REVERT: A 934 ILE cc_start: 0.7984 (mm) cc_final: 0.7718 (mm) REVERT: A 993 ILE cc_start: 0.7572 (mp) cc_final: 0.7368 (tp) REVERT: A 1050 MET cc_start: 0.7398 (ptm) cc_final: 0.7189 (ptm) REVERT: A 1061 VAL cc_start: 0.7371 (t) cc_final: 0.6833 (m) REVERT: B 48 LEU cc_start: 0.8389 (mp) cc_final: 0.7945 (mt) REVERT: B 88 ASP cc_start: 0.6971 (m-30) cc_final: 0.6553 (p0) REVERT: B 115 GLN cc_start: 0.7409 (mp-120) cc_final: 0.6721 (mp10) REVERT: B 158 ARG cc_start: 0.4919 (mmt-90) cc_final: 0.4339 (mmp80) REVERT: B 201 PHE cc_start: 0.7750 (t80) cc_final: 0.7471 (t80) REVERT: B 204 TYR cc_start: 0.6524 (m-80) cc_final: 0.6005 (m-80) REVERT: B 270 LEU cc_start: 0.8205 (tp) cc_final: 0.7194 (tp) REVERT: B 285 ILE cc_start: 0.8540 (mt) cc_final: 0.8247 (pt) REVERT: B 309 GLU cc_start: 0.7621 (mp0) cc_final: 0.7335 (mp0) REVERT: B 495 TYR cc_start: 0.5966 (m-80) cc_final: 0.5474 (m-80) REVERT: B 557 LYS cc_start: 0.6708 (pttm) cc_final: 0.6291 (ttpt) REVERT: B 570 ASP cc_start: 0.7443 (t70) cc_final: 0.7180 (t0) REVERT: B 573 THR cc_start: 0.8250 (p) cc_final: 0.8015 (p) REVERT: B 707 TYR cc_start: 0.7211 (t80) cc_final: 0.6606 (t80) REVERT: B 710 ASN cc_start: 0.8233 (p0) cc_final: 0.7347 (t0) REVERT: B 731 MET cc_start: 0.7050 (ptt) cc_final: 0.6696 (ptt) REVERT: B 741 TYR cc_start: 0.8452 (t80) cc_final: 0.8228 (t80) REVERT: B 755 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7211 (mm-40) REVERT: B 815 ARG cc_start: 0.5998 (ttp-170) cc_final: 0.5536 (ttp-170) REVERT: B 933 LYS cc_start: 0.8000 (ptpt) cc_final: 0.7629 (mtmt) REVERT: B 960 ASN cc_start: 0.7771 (t0) cc_final: 0.7488 (t0) REVERT: B 1019 ARG cc_start: 0.7708 (ttt90) cc_final: 0.7408 (ttt90) REVERT: B 1031 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6840 (tt0) REVERT: B 1034 LEU cc_start: 0.8381 (mp) cc_final: 0.8090 (mp) REVERT: B 1037 SER cc_start: 0.6529 (p) cc_final: 0.5094 (p) REVERT: B 1105 THR cc_start: 0.6503 (m) cc_final: 0.5895 (t) REVERT: C 40 ASP cc_start: 0.8176 (p0) cc_final: 0.7956 (p0) REVERT: C 41 LYS cc_start: 0.6984 (ttpt) cc_final: 0.6528 (ttmt) REVERT: C 133 PHE cc_start: 0.6138 (m-80) cc_final: 0.5865 (m-10) REVERT: C 153 MET cc_start: 0.4084 (mtm) cc_final: 0.3795 (ttm) REVERT: C 387 LEU cc_start: 0.8097 (tp) cc_final: 0.7608 (pp) REVERT: C 541 PHE cc_start: 0.6875 (p90) cc_final: 0.6635 (p90) REVERT: C 612 TYR cc_start: 0.7084 (m-80) cc_final: 0.6814 (m-80) REVERT: C 742 ILE cc_start: 0.8078 (mm) cc_final: 0.7418 (tt) REVERT: C 773 GLU cc_start: 0.8105 (tt0) cc_final: 0.7210 (tp30) REVERT: C 780 GLU cc_start: 0.7757 (pt0) cc_final: 0.7452 (pt0) REVERT: C 814 LYS cc_start: 0.7470 (mmtt) cc_final: 0.7112 (mmmt) REVERT: C 820 ASP cc_start: 0.6770 (m-30) cc_final: 0.6195 (m-30) REVERT: C 886 TRP cc_start: 0.7257 (p90) cc_final: 0.6786 (p90) REVERT: C 898 PHE cc_start: 0.7142 (t80) cc_final: 0.6669 (t80) REVERT: C 900 MET cc_start: 0.8352 (mmp) cc_final: 0.6697 (mmp) REVERT: C 919 ASN cc_start: 0.8345 (t0) cc_final: 0.8112 (t0) REVERT: C 973 ILE cc_start: 0.7686 (pt) cc_final: 0.7459 (pt) REVERT: C 1061 VAL cc_start: 0.8073 (t) cc_final: 0.7687 (m) REVERT: C 1110 TYR cc_start: 0.6845 (t80) cc_final: 0.6450 (t80) REVERT: C 1138 TYR cc_start: 0.7256 (t80) cc_final: 0.6966 (t80) outliers start: 2 outliers final: 0 residues processed: 558 average time/residue: 0.1599 time to fit residues: 144.7526 Evaluate side-chains 455 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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: 0.9990 chunk 40 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 317 optimal weight: 0.8980 chunk 112 optimal weight: 0.0670 chunk 70 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1108 ASN C 564 GLN C 895 GLN C 926 GLN C1083 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.077510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065192 restraints weight = 142128.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.067030 restraints weight = 87252.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.068351 restraints weight = 59788.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.069293 restraints weight = 44145.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.069963 restraints weight = 34804.032| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.4586 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= 0.147 Angle : 0.768 18.645 37363 Z= 0.372 Chirality : 0.049 0.519 4443 Planarity : 0.005 0.110 4664 Dihedral : 8.308 108.236 5359 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.51 % 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: -1.43 (0.14), residues: 3206 helix: 0.36 (0.19), residues: 708 sheet: -0.62 (0.20), residues: 618 loop : -1.64 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1014 TYR 0.028 0.002 TYR B 421 PHE 0.043 0.002 PHE B 823 TRP 0.046 0.003 TRP B1102 HIS 0.009 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00329 (27224) covalent geometry : angle 0.71971 (37027) SS BOND : bond 0.00398 ( 42) SS BOND : angle 1.62695 ( 84) hydrogen bonds : bond 0.03767 ( 1030) hydrogen bonds : angle 6.29050 ( 2928) Misc. bond : bond 0.00180 ( 1) link_ALPHA1-4 : bond 0.01959 ( 6) link_ALPHA1-4 : angle 3.90781 ( 18) link_BETA1-4 : bond 0.00453 ( 25) link_BETA1-4 : angle 1.74492 ( 75) link_BETA1-6 : bond 0.01715 ( 3) link_BETA1-6 : angle 1.99405 ( 9) link_NAG-ASN : bond 0.00614 ( 50) link_NAG-ASN : angle 3.74638 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4770.91 seconds wall clock time: 83 minutes 14.45 seconds (4994.45 seconds total)