Starting phenix.real_space_refine on Mon May 26 03:12:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxj_35078/05_2025/8hxj_35078.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxj_35078/05_2025/8hxj_35078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hxj_35078/05_2025/8hxj_35078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxj_35078/05_2025/8hxj_35078.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxj_35078/05_2025/8hxj_35078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxj_35078/05_2025/8hxj_35078.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17523 2.51 5 N 4521 2.21 5 O 5475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27639 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8835 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 55, 'TRANS': 1077} Chain: "B" Number of atoms: 8835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8835 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 55, 'TRANS': 1077} Chain: "C" Number of atoms: 8835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8835 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 55, 'TRANS': 1077} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: 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: "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: 15.39, per 1000 atoms: 0.56 Number of scatterers: 27639 At special positions: 0 Unit cell: (151.84, 139.36, 182, 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 120 16.00 O 5475 8.00 N 4521 7.00 C 17523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.01 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=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B 836 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.47 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C 836 " - pdb=" SG CYS C 847 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 370 " " NAG A1307 " - " ASN A 30 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 705 " " NAG A1311 " - " ASN A1094 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 30 " " NAG B1305 " - " ASN B 705 " " NAG B1306 " - " ASN B 61 " " NAG B1307 " - " ASN B1094 " " NAG B1308 " - " ASN B 343 " " NAG B1309 " - " ASN B 17 " " NAG B1310 " - " ASN B 370 " " NAG B1311 " - " ASN B 282 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 705 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C1094 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 30 " " NAG C1311 " - " ASN C 370 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 713 " " NAG I 1 " - " ASN A 797 " " NAG J 1 " - " ASN A1070 " " NAG K 1 " - " ASN A1130 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 165 " " NAG N 1 " - " ASN B 797 " " NAG O 1 " - " ASN B1130 " " NAG P 1 " - " ASN B1070 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN B 713 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 797 " " NAG V 1 " - " ASN C1070 " " NAG W 1 " - " ASN C 331 " " NAG X 1 " - " ASN C 713 " " NAG Y 1 " - " ASN C 165 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C1130 " Time building additional restraints: 8.05 Conformation dependent library (CDL) restraints added in 3.6 seconds 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6354 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 50 sheets defined 25.4% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.619A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.882A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.554A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.991A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 626 through 629 Processing helix chain 'A' and resid 630 through 636 removed outlier: 3.545A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 removed outlier: 3.829A pdb=" N ASN A 679 " --> pdb=" O THR A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 removed outlier: 4.192A pdb=" N ILE A 738 " --> pdb=" O CYS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 753 Processing helix chain 'A' and resid 755 through 778 removed outlier: 3.572A pdb=" N LEU A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG A 761 " --> pdb=" O THR A 757 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 778 " --> pdb=" O THR A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 832 through 838 removed outlier: 3.513A pdb=" N CYS A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 852 Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 893 through 906 Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.713A pdb=" N ALA A 938 " --> pdb=" O LEU A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 961 removed outlier: 4.255A pdb=" N VAL A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 981 through 1029 removed outlier: 4.939A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1145 removed outlier: 4.190A pdb=" N ASP A1142 " --> pdb=" O GLN A1138 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.615A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.866A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.280A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.075A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 626 through 629 Processing helix chain 'B' and resid 630 through 636 removed outlier: 3.662A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 removed outlier: 4.175A pdb=" N SER B 680 " --> pdb=" O THR B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 740 removed outlier: 4.188A pdb=" N TYR B 737 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 738 " --> pdb=" O CYS B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 753 Processing helix chain 'B' and resid 755 through 778 removed outlier: 3.527A pdb=" N LEU B 759 " --> pdb=" O PHE B 755 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG B 761 " --> pdb=" O THR B 757 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 778 " --> pdb=" O THR B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 822 Processing helix chain 'B' and resid 832 through 838 removed outlier: 3.605A pdb=" N CYS B 836 " --> pdb=" O GLN B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 852 Processing helix chain 'B' and resid 862 through 880 Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 893 through 906 Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.732A pdb=" N ALA B 938 " --> pdb=" O LEU B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 961 removed outlier: 3.919A pdb=" N VAL B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.868A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1138 through 1145 removed outlier: 4.201A pdb=" N ASP B1142 " --> pdb=" O GLN B1138 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.608A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.794A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.250A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.223A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 626 through 629 Processing helix chain 'C' and resid 630 through 636 Processing helix chain 'C' and resid 734 through 739 removed outlier: 4.018A pdb=" N ILE C 738 " --> pdb=" O CYS C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 753 Processing helix chain 'C' and resid 755 through 778 removed outlier: 3.598A pdb=" N LEU C 759 " --> pdb=" O PHE C 755 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG C 761 " --> pdb=" O THR C 757 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE C 778 " --> pdb=" O THR C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 822 removed outlier: 4.212A pdb=" N GLU C 815 " --> pdb=" O ARG C 811 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP C 816 " --> pdb=" O SER C 812 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU C 817 " --> pdb=" O PHE C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 838 removed outlier: 3.618A pdb=" N CYS C 836 " --> pdb=" O GLN C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 852 Processing helix chain 'C' and resid 862 through 880 Processing helix chain 'C' and resid 882 through 886 Processing helix chain 'C' and resid 893 through 905 Processing helix chain 'C' and resid 916 through 938 removed outlier: 3.735A pdb=" N ALA C 938 " --> pdb=" O LEU C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 961 removed outlier: 4.229A pdb=" N VAL C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 Processing helix chain 'C' and resid 981 through 1029 removed outlier: 4.911A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C1029 " --> pdb=" O MET C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 4.145A pdb=" N ASP C1142 " --> pdb=" O GLN C1138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.666A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.978A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 278 through 279 removed outlier: 3.957A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 310 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 327 removed outlier: 6.905A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.024A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 567 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.710A pdb=" N GLU A 654 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N THR A 692 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 697 through 699 removed outlier: 6.340A pdb=" N ALA A 697 " --> pdb=" O ILE B 784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 708 through 714 removed outlier: 7.214A pdb=" N GLN A1067 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE A 714 " --> pdb=" O PRO A1065 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A1072 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A1074 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE A1091 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 724 removed outlier: 3.646A pdb=" N MET A1046 " --> pdb=" O VAL A1061 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 730 through 731 Processing sheet with id=AB7, first strand: chain 'A' and resid 783 through 785 Processing sheet with id=AB8, first strand: chain 'A' and resid 1085 through 1086 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 7.337A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.658A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 278 through 279 removed outlier: 4.006A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 310 through 314 Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.888A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.893A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 565 through 567 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.373A pdb=" N GLU B 654 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR B 692 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 697 through 699 removed outlier: 6.286A pdb=" N ALA B 697 " --> pdb=" O ILE C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 708 through 714 removed outlier: 7.249A pdb=" N GLN B1067 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 714 " --> pdb=" O PRO B1065 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 717 through 724 removed outlier: 3.664A pdb=" N MET B1046 " --> pdb=" O VAL B1061 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 730 through 731 Processing sheet with id=AD6, first strand: chain 'B' and resid 1085 through 1086 Processing sheet with id=AD7, first strand: chain 'B' and resid 1090 through 1093 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.712A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.433A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.060A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 278 through 279 removed outlier: 3.924A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 310 through 314 Processing sheet with id=AE4, first strand: chain 'C' and resid 324 through 327 removed outlier: 6.905A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.915A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 565 through 567 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.604A pdb=" N GLU C 654 " --> pdb=" O ALA C 690 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 708 through 714 removed outlier: 7.211A pdb=" N GLN C1067 " --> pdb=" O THR C 712 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE C 714 " --> pdb=" O PRO C1065 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 717 through 724 removed outlier: 3.660A pdb=" N MET C1046 " --> pdb=" O VAL C1061 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 730 through 731 Processing sheet with id=AF4, first strand: chain 'C' and resid 1085 through 1086 Processing sheet with id=AF5, first strand: chain 'C' and resid 1090 through 1092 893 hydrogen bonds defined for protein. 2400 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: 12.93 Time building geometry restraints manager: 8.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8767 1.34 - 1.46: 6276 1.46 - 1.58: 13067 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 28260 Sorted by residual: bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" N VAL B1124 " pdb=" CA VAL B1124 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" CA SER B1119 " pdb=" CB SER B1119 " ideal model delta sigma weight residual 1.536 1.490 0.046 1.46e-02 4.69e+03 9.98e+00 bond pdb=" N GLY B1120 " pdb=" CA GLY B1120 " ideal model delta sigma weight residual 1.446 1.477 -0.031 1.08e-02 8.57e+03 8.04e+00 bond pdb=" N VAL A1125 " pdb=" CA VAL A1125 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.25e-02 6.40e+03 8.01e+00 ... (remaining 28255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 38386 3.72 - 7.45: 89 7.45 - 11.17: 7 11.17 - 14.90: 1 14.90 - 18.62: 1 Bond angle restraints: 38484 Sorted by residual: angle pdb=" N GLY C1120 " pdb=" CA GLY C1120 " pdb=" C GLY C1120 " ideal model delta sigma weight residual 111.64 130.26 -18.62 1.57e+00 4.06e-01 1.41e+02 angle pdb=" C ARG B 246 " pdb=" N SER B 247 " pdb=" CA SER B 247 " ideal model delta sigma weight residual 121.54 131.37 -9.83 1.91e+00 2.74e-01 2.65e+01 angle pdb=" N ASP C1123 " pdb=" CA ASP C1123 " pdb=" C ASP C1123 " ideal model delta sigma weight residual 113.38 108.01 5.37 1.17e+00 7.31e-01 2.10e+01 angle pdb=" CA GLY B1120 " pdb=" C GLY B1120 " pdb=" O GLY B1120 " ideal model delta sigma weight residual 122.57 118.45 4.12 9.20e-01 1.18e+00 2.01e+01 angle pdb=" N ASN C1121 " pdb=" CA ASN C1121 " pdb=" C ASN C1121 " ideal model delta sigma weight residual 113.19 107.92 5.27 1.19e+00 7.06e-01 1.96e+01 ... (remaining 38479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 16130 17.50 - 35.00: 1431 35.00 - 52.51: 257 52.51 - 70.01: 51 70.01 - 87.51: 23 Dihedral angle restraints: 17892 sinusoidal: 7995 harmonic: 9897 Sorted by residual: dihedral pdb=" CB CYS B1078 " pdb=" SG CYS B1078 " pdb=" SG CYS B1122 " pdb=" CB CYS B1122 " ideal model delta sinusoidal sigma weight residual -86.00 -27.49 -58.51 1 1.00e+01 1.00e-02 4.58e+01 dihedral pdb=" CA SER A 247 " pdb=" C SER A 247 " pdb=" N TYR A 248 " pdb=" CA TYR A 248 " ideal model delta harmonic sigma weight residual 180.00 156.22 23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -46.98 -39.02 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 17889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 4534 0.140 - 0.281: 45 0.281 - 0.421: 6 0.421 - 0.562: 3 0.562 - 0.702: 2 Chirality restraints: 4590 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.46e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.21e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.96e+01 ... (remaining 4587 not shown) Planarity restraints: 4950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1311 " -0.347 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG A1311 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A1311 " -0.063 2.00e-02 2.50e+03 pdb=" N2 NAG A1311 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A1311 " -0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " -0.337 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG C1304 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " -0.074 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " 0.518 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " -0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " -0.333 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG N 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " -0.032 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.211 2.00e-02 2.50e+03 ... (remaining 4947 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 7 1.97 - 2.71: 904 2.71 - 3.44: 39730 3.44 - 4.17: 64293 4.17 - 4.90: 116205 Nonbonded interactions: 221139 Sorted by model distance: nonbonded pdb=" OD2 ASP A 568 " pdb=" NH1 ARG B 843 " model vdw 1.242 3.120 nonbonded pdb=" O ALA A1076 " pdb=" CD1 ILE A1128 " model vdw 1.439 3.460 nonbonded pdb=" O ALA B1076 " pdb=" CD1 ILE B1128 " model vdw 1.449 3.460 nonbonded pdb=" O ALA C1076 " pdb=" CD1 ILE C1128 " model vdw 1.486 3.460 nonbonded pdb=" C ALA A1076 " pdb=" CD1 ILE A1128 " model vdw 1.614 3.690 ... (remaining 221134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.400 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: 0.000 Extract box with map and model: 3.280 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 61.650 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.005 0.439 28386 Z= 0.243 Angle : 0.749 31.966 38817 Z= 0.370 Chirality : 0.054 0.702 4590 Planarity : 0.020 0.299 4893 Dihedral : 13.253 87.512 11403 Min Nonbonded Distance : 1.242 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.14), residues: 3393 helix: 0.44 (0.20), residues: 753 sheet: -0.68 (0.22), residues: 591 loop : -2.21 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1098 HIS 0.007 0.001 HIS B 245 PHE 0.035 0.001 PHE B 429 TYR 0.017 0.001 TYR C 248 ARG 0.007 0.000 ARG A 811 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 57) link_NAG-ASN : angle 3.67554 ( 171) link_BETA1-4 : bond 0.01069 ( 24) link_BETA1-4 : angle 3.56546 ( 72) hydrogen bonds : bond 0.12408 ( 893) hydrogen bonds : angle 6.68084 ( 2400) SS BOND : bond 0.06561 ( 45) SS BOND : angle 3.98271 ( 90) covalent geometry : bond 0.00393 (28260) covalent geometry : angle 0.66748 (38484) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 PHE cc_start: 0.7332 (m-10) cc_final: 0.7047 (m-10) REVERT: B 1025 MET cc_start: 0.9324 (tpp) cc_final: 0.8752 (tpt) REVERT: C 747 ASN cc_start: 0.8406 (m-40) cc_final: 0.8111 (m-40) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.3278 time to fit residues: 127.5648 Evaluate side-chains 164 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 3.9990 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 265 optimal weight: 0.0670 chunk 102 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 GLN A 961 GLN A1121 ASN B 99 ASN B 422 ASN C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.075626 restraints weight = 61376.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.078258 restraints weight = 32849.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.079999 restraints weight = 22537.937| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 28386 Z= 0.215 Angle : 0.682 16.445 38817 Z= 0.329 Chirality : 0.050 0.456 4590 Planarity : 0.004 0.034 4893 Dihedral : 7.228 59.322 5361 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 1.08 % Allowed : 7.10 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3393 helix: 0.91 (0.20), residues: 762 sheet: -0.84 (0.21), residues: 621 loop : -2.25 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1098 HIS 0.005 0.001 HIS B 245 PHE 0.024 0.001 PHE C1144 TYR 0.016 0.001 TYR C 144 ARG 0.006 0.000 ARG A 811 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 57) link_NAG-ASN : angle 3.14217 ( 171) link_BETA1-4 : bond 0.01051 ( 24) link_BETA1-4 : angle 3.10472 ( 72) hydrogen bonds : bond 0.04370 ( 893) hydrogen bonds : angle 5.38466 ( 2400) SS BOND : bond 0.00563 ( 45) SS BOND : angle 1.25858 ( 90) covalent geometry : bond 0.00498 (28260) covalent geometry : angle 0.63503 (38484) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.8857 (t80) cc_final: 0.8474 (t80) REVERT: A 981 ASP cc_start: 0.8276 (p0) cc_final: 0.7965 (p0) REVERT: B 175 PHE cc_start: 0.7381 (m-10) cc_final: 0.7092 (m-10) REVERT: B 378 LYS cc_start: 0.8978 (tppp) cc_final: 0.8775 (ttmm) REVERT: B 1025 MET cc_start: 0.8960 (tpp) cc_final: 0.8376 (tpp) REVERT: C 981 ASP cc_start: 0.8196 (p0) cc_final: 0.7971 (p0) outliers start: 32 outliers final: 25 residues processed: 188 average time/residue: 0.3151 time to fit residues: 103.3299 Evaluate side-chains 180 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1119 SER Chi-restraints excluded: chain B residue 1137 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1036 VAL Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 248 optimal weight: 0.6980 chunk 234 optimal weight: 0.1980 chunk 197 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 311 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 99 ASN C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.099282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.077403 restraints weight = 60940.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080083 restraints weight = 32460.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.081859 restraints weight = 22194.304| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28386 Z= 0.121 Angle : 0.616 16.770 38817 Z= 0.298 Chirality : 0.047 0.409 4590 Planarity : 0.003 0.034 4893 Dihedral : 6.592 59.695 5361 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 1.22 % Allowed : 9.84 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.14), residues: 3393 helix: 1.42 (0.21), residues: 723 sheet: -0.80 (0.22), residues: 588 loop : -2.17 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1098 HIS 0.004 0.001 HIS B 245 PHE 0.028 0.001 PHE C 157 TYR 0.016 0.001 TYR A 145 ARG 0.002 0.000 ARG A1015 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 57) link_NAG-ASN : angle 2.81372 ( 171) link_BETA1-4 : bond 0.01074 ( 24) link_BETA1-4 : angle 3.08790 ( 72) hydrogen bonds : bond 0.03645 ( 893) hydrogen bonds : angle 5.05065 ( 2400) SS BOND : bond 0.00269 ( 45) SS BOND : angle 0.86283 ( 90) covalent geometry : bond 0.00262 (28260) covalent geometry : angle 0.57299 (38484) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 ASP cc_start: 0.8285 (p0) cc_final: 0.7947 (p0) REVERT: B 175 PHE cc_start: 0.7306 (m-10) cc_final: 0.7035 (m-10) REVERT: B 378 LYS cc_start: 0.8982 (tppp) cc_final: 0.8673 (tppt) REVERT: B 1025 MET cc_start: 0.8844 (tpp) cc_final: 0.8303 (tpp) REVERT: C 981 ASP cc_start: 0.8119 (p0) cc_final: 0.7831 (p0) outliers start: 36 outliers final: 27 residues processed: 204 average time/residue: 0.3177 time to fit residues: 113.6835 Evaluate side-chains 185 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1119 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1036 VAL Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 37 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 253 optimal weight: 8.9990 chunk 263 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 234 optimal weight: 0.4980 chunk 259 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 HIS ** 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 = 0.3390 r_free = 0.3390 target = 0.097131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.075346 restraints weight = 61437.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.077988 restraints weight = 33115.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.079701 restraints weight = 22747.904| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 28386 Z= 0.203 Angle : 0.654 16.520 38817 Z= 0.316 Chirality : 0.048 0.412 4590 Planarity : 0.004 0.034 4893 Dihedral : 6.574 57.676 5361 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.46 % Favored : 89.51 % Rotamer: Outliers : 2.06 % Allowed : 11.83 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3393 helix: 1.36 (0.20), residues: 723 sheet: -0.84 (0.22), residues: 603 loop : -2.22 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1098 HIS 0.004 0.001 HIS B1054 PHE 0.030 0.001 PHE C 157 TYR 0.020 0.001 TYR C 752 ARG 0.005 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 57) link_NAG-ASN : angle 2.84979 ( 171) link_BETA1-4 : bond 0.00962 ( 24) link_BETA1-4 : angle 3.01116 ( 72) hydrogen bonds : bond 0.03964 ( 893) hydrogen bonds : angle 5.08678 ( 2400) SS BOND : bond 0.00367 ( 45) SS BOND : angle 1.03587 ( 90) covalent geometry : bond 0.00470 (28260) covalent geometry : angle 0.61280 (38484) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 ASP cc_start: 0.8325 (p0) cc_final: 0.7908 (p0) REVERT: B 175 PHE cc_start: 0.7427 (m-10) cc_final: 0.7208 (m-10) REVERT: B 418 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9095 (mp) REVERT: B 1025 MET cc_start: 0.8743 (tpp) cc_final: 0.8222 (tpp) REVERT: C 981 ASP cc_start: 0.8191 (p0) cc_final: 0.7837 (p0) outliers start: 61 outliers final: 36 residues processed: 212 average time/residue: 0.3356 time to fit residues: 121.5002 Evaluate side-chains 186 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1054 HIS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 735 THR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1036 VAL Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 81 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 271 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 234 optimal weight: 0.0670 chunk 113 optimal weight: 10.0000 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 931 GLN B 49 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 HIS ** 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 = 0.3393 r_free = 0.3393 target = 0.097300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.075587 restraints weight = 60836.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.078217 restraints weight = 32833.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079949 restraints weight = 22575.913| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28386 Z= 0.176 Angle : 0.640 16.786 38817 Z= 0.311 Chirality : 0.048 0.405 4590 Planarity : 0.004 0.035 4893 Dihedral : 6.470 57.271 5361 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.61 % Favored : 90.36 % Rotamer: Outliers : 2.06 % Allowed : 13.62 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3393 helix: 1.41 (0.20), residues: 723 sheet: -0.79 (0.21), residues: 609 loop : -2.21 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 258 HIS 0.003 0.001 HIS C 146 PHE 0.040 0.001 PHE A 157 TYR 0.020 0.001 TYR C1134 ARG 0.004 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 57) link_NAG-ASN : angle 2.75391 ( 171) link_BETA1-4 : bond 0.01068 ( 24) link_BETA1-4 : angle 3.04422 ( 72) hydrogen bonds : bond 0.03808 ( 893) hydrogen bonds : angle 5.02121 ( 2400) SS BOND : bond 0.00394 ( 45) SS BOND : angle 1.13853 ( 90) covalent geometry : bond 0.00403 (28260) covalent geometry : angle 0.59932 (38484) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 165 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 ASP cc_start: 0.8359 (p0) cc_final: 0.7992 (p0) REVERT: B 153 MET cc_start: 0.5215 (ttm) cc_final: 0.5002 (ttm) REVERT: B 418 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9097 (mp) REVERT: B 1025 MET cc_start: 0.8680 (tpp) cc_final: 0.8243 (tpp) REVERT: B 1103 ARG cc_start: 0.7725 (mpt180) cc_final: 0.7390 (mpt180) REVERT: C 981 ASP cc_start: 0.8197 (p0) cc_final: 0.7842 (p0) outliers start: 61 outliers final: 40 residues processed: 211 average time/residue: 0.3217 time to fit residues: 116.7239 Evaluate side-chains 194 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1054 HIS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1036 VAL Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 122 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 288 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 325 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN C 49 HIS ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.075169 restraints weight = 61020.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.077794 restraints weight = 32711.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.079493 restraints weight = 22406.257| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28386 Z= 0.187 Angle : 0.649 16.648 38817 Z= 0.315 Chirality : 0.048 0.408 4590 Planarity : 0.004 0.035 4893 Dihedral : 6.478 57.164 5361 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.49 % Favored : 89.45 % Rotamer: Outliers : 2.03 % Allowed : 14.98 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3393 helix: 1.43 (0.20), residues: 726 sheet: -0.82 (0.21), residues: 609 loop : -2.23 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS B1054 PHE 0.032 0.001 PHE A 157 TYR 0.021 0.001 TYR A1134 ARG 0.004 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 57) link_NAG-ASN : angle 2.73712 ( 171) link_BETA1-4 : bond 0.00988 ( 24) link_BETA1-4 : angle 3.01422 ( 72) hydrogen bonds : bond 0.03855 ( 893) hydrogen bonds : angle 5.02057 ( 2400) SS BOND : bond 0.00355 ( 45) SS BOND : angle 1.21018 ( 90) covalent geometry : bond 0.00430 (28260) covalent geometry : angle 0.60936 (38484) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 158 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.7378 (m-10) cc_final: 0.7113 (m-10) REVERT: A 981 ASP cc_start: 0.8374 (p0) cc_final: 0.8006 (p0) REVERT: B 153 MET cc_start: 0.5290 (ttm) cc_final: 0.5048 (ttm) REVERT: B 418 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9070 (mp) REVERT: B 1025 MET cc_start: 0.8616 (tpp) cc_final: 0.8242 (tpp) outliers start: 60 outliers final: 48 residues processed: 205 average time/residue: 0.3276 time to fit residues: 115.5459 Evaluate side-chains 202 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1054 HIS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 869 TYR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1026 SER Chi-restraints excluded: chain C residue 1036 VAL Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 120 optimal weight: 0.5980 chunk 234 optimal weight: 0.1980 chunk 98 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 285 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 334 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 ASN B 961 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 146 HIS ** 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 = 0.3402 r_free = 0.3402 target = 0.097793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.076143 restraints weight = 60717.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.078797 restraints weight = 32678.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.080516 restraints weight = 22417.168| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 28386 Z= 0.146 Angle : 0.631 16.762 38817 Z= 0.307 Chirality : 0.047 0.397 4590 Planarity : 0.004 0.035 4893 Dihedral : 6.341 57.286 5361 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.49 % Favored : 90.45 % Rotamer: Outliers : 2.06 % Allowed : 15.48 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3393 helix: 1.53 (0.20), residues: 720 sheet: -0.78 (0.21), residues: 609 loop : -2.18 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 152 HIS 0.003 0.001 HIS A 245 PHE 0.027 0.001 PHE A 157 TYR 0.021 0.001 TYR C1134 ARG 0.004 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 57) link_NAG-ASN : angle 2.60737 ( 171) link_BETA1-4 : bond 0.01026 ( 24) link_BETA1-4 : angle 3.01924 ( 72) hydrogen bonds : bond 0.03621 ( 893) hydrogen bonds : angle 4.94760 ( 2400) SS BOND : bond 0.00332 ( 45) SS BOND : angle 1.40158 ( 90) covalent geometry : bond 0.00330 (28260) covalent geometry : angle 0.59152 (38484) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 3.511 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 981 ASP cc_start: 0.8356 (p0) cc_final: 0.7985 (p0) REVERT: B 153 MET cc_start: 0.5280 (ttm) cc_final: 0.5035 (ttm) REVERT: B 418 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9064 (mp) REVERT: B 975 ASP cc_start: 0.8061 (t0) cc_final: 0.7700 (t0) REVERT: B 1025 MET cc_start: 0.8702 (tpp) cc_final: 0.8351 (tpp) outliers start: 61 outliers final: 48 residues processed: 224 average time/residue: 0.3410 time to fit residues: 132.3914 Evaluate side-chains 209 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1054 HIS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 756 CYS Chi-restraints excluded: chain C residue 869 TYR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1036 VAL Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 17 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 335 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 277 optimal weight: 0.3980 chunk 274 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.075999 restraints weight = 60899.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.078636 restraints weight = 32789.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.080365 restraints weight = 22524.224| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 28386 Z= 0.154 Angle : 0.632 16.704 38817 Z= 0.308 Chirality : 0.047 0.395 4590 Planarity : 0.004 0.035 4893 Dihedral : 6.295 57.307 5361 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.70 % Favored : 90.24 % Rotamer: Outliers : 2.27 % Allowed : 15.75 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3393 helix: 1.52 (0.20), residues: 723 sheet: -0.76 (0.21), residues: 642 loop : -2.18 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 152 HIS 0.003 0.001 HIS B 245 PHE 0.026 0.001 PHE A 157 TYR 0.020 0.001 TYR C1134 ARG 0.004 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 57) link_NAG-ASN : angle 2.59928 ( 171) link_BETA1-4 : bond 0.01016 ( 24) link_BETA1-4 : angle 2.99936 ( 72) hydrogen bonds : bond 0.03604 ( 893) hydrogen bonds : angle 4.91397 ( 2400) SS BOND : bond 0.00478 ( 45) SS BOND : angle 1.28308 ( 90) covalent geometry : bond 0.00352 (28260) covalent geometry : angle 0.59352 (38484) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 165 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 ASP cc_start: 0.8340 (p0) cc_final: 0.7906 (p0) REVERT: B 153 MET cc_start: 0.5344 (ttm) cc_final: 0.5099 (ttm) REVERT: B 418 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9057 (mp) REVERT: B 975 ASP cc_start: 0.8072 (t0) cc_final: 0.7710 (t0) REVERT: B 1025 MET cc_start: 0.8693 (tpp) cc_final: 0.8380 (tpp) REVERT: C 568 ASP cc_start: 0.7359 (t70) cc_final: 0.7139 (t70) outliers start: 67 outliers final: 55 residues processed: 221 average time/residue: 0.3218 time to fit residues: 123.0724 Evaluate side-chains 214 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1054 HIS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 756 CYS Chi-restraints excluded: chain C residue 869 TYR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1026 SER Chi-restraints excluded: chain C residue 1036 VAL Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 230 optimal weight: 3.9990 chunk 321 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 329 optimal weight: 0.0970 chunk 176 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 319 optimal weight: 2.9990 chunk 286 optimal weight: 0.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.076301 restraints weight = 60641.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.078958 restraints weight = 32575.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080691 restraints weight = 22309.576| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28386 Z= 0.148 Angle : 0.633 16.770 38817 Z= 0.308 Chirality : 0.047 0.393 4590 Planarity : 0.004 0.035 4893 Dihedral : 6.259 57.342 5361 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.70 % Favored : 90.22 % Rotamer: Outliers : 1.99 % Allowed : 16.43 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3393 helix: 1.57 (0.20), residues: 720 sheet: -0.75 (0.21), residues: 642 loop : -2.19 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 152 HIS 0.003 0.001 HIS A 245 PHE 0.026 0.001 PHE C 486 TYR 0.021 0.001 TYR C1134 ARG 0.004 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 57) link_NAG-ASN : angle 2.56070 ( 171) link_BETA1-4 : bond 0.01022 ( 24) link_BETA1-4 : angle 2.99728 ( 72) hydrogen bonds : bond 0.03572 ( 893) hydrogen bonds : angle 4.89085 ( 2400) SS BOND : bond 0.00418 ( 45) SS BOND : angle 1.14790 ( 90) covalent geometry : bond 0.00337 (28260) covalent geometry : angle 0.59615 (38484) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 166 time to evaluate : 3.353 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 981 ASP cc_start: 0.8344 (p0) cc_final: 0.7909 (p0) REVERT: B 153 MET cc_start: 0.5353 (ttm) cc_final: 0.5107 (ttm) REVERT: B 418 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9051 (mp) REVERT: B 975 ASP cc_start: 0.8068 (t0) cc_final: 0.7710 (t0) REVERT: B 1025 MET cc_start: 0.8684 (tpp) cc_final: 0.8362 (tpp) REVERT: C 568 ASP cc_start: 0.7343 (t70) cc_final: 0.7120 (t70) outliers start: 59 outliers final: 52 residues processed: 215 average time/residue: 0.3420 time to fit residues: 127.0259 Evaluate side-chains 214 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 756 CYS Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 869 TYR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1026 SER Chi-restraints excluded: chain C residue 1036 VAL Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 187 optimal weight: 0.9990 chunk 224 optimal weight: 0.0970 chunk 265 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 328 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 316 optimal weight: 0.0770 chunk 14 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.098691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.077299 restraints weight = 60437.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.079940 restraints weight = 32222.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.081683 restraints weight = 22013.306| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28386 Z= 0.127 Angle : 0.617 16.783 38817 Z= 0.301 Chirality : 0.046 0.381 4590 Planarity : 0.004 0.035 4893 Dihedral : 6.111 57.730 5361 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.14 % Favored : 90.75 % Rotamer: Outliers : 1.86 % Allowed : 16.70 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3393 helix: 1.65 (0.20), residues: 720 sheet: -0.71 (0.21), residues: 642 loop : -2.15 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 152 HIS 0.003 0.001 HIS A 245 PHE 0.027 0.001 PHE C 486 TYR 0.021 0.001 TYR C1134 ARG 0.003 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 57) link_NAG-ASN : angle 2.49501 ( 171) link_BETA1-4 : bond 0.01026 ( 24) link_BETA1-4 : angle 2.98060 ( 72) hydrogen bonds : bond 0.03409 ( 893) hydrogen bonds : angle 4.79209 ( 2400) SS BOND : bond 0.00353 ( 45) SS BOND : angle 0.99166 ( 90) covalent geometry : bond 0.00282 (28260) covalent geometry : angle 0.58034 (38484) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 3.346 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 981 ASP cc_start: 0.8329 (p0) cc_final: 0.7888 (p0) REVERT: B 153 MET cc_start: 0.5359 (ttm) cc_final: 0.5124 (ttm) REVERT: B 418 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9017 (mp) REVERT: B 975 ASP cc_start: 0.8033 (t0) cc_final: 0.7683 (t0) REVERT: B 1025 MET cc_start: 0.8706 (tpp) cc_final: 0.8380 (tpp) REVERT: C 69 HIS cc_start: 0.7130 (m90) cc_final: 0.6801 (m-70) REVERT: C 568 ASP cc_start: 0.7303 (t70) cc_final: 0.7100 (t70) outliers start: 55 outliers final: 47 residues processed: 225 average time/residue: 0.3238 time to fit residues: 125.9434 Evaluate side-chains 215 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 756 CYS Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1026 SER Chi-restraints excluded: chain C residue 1036 VAL Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 230 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 218 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 273 optimal weight: 0.9990 chunk 301 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 953 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.098903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.077374 restraints weight = 60764.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.080044 restraints weight = 32523.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081776 restraints weight = 22244.184| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28386 Z= 0.127 Angle : 0.619 16.766 38817 Z= 0.302 Chirality : 0.047 0.381 4590 Planarity : 0.004 0.035 4893 Dihedral : 6.031 57.651 5361 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.34 % Favored : 90.54 % Rotamer: Outliers : 1.72 % Allowed : 17.04 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3393 helix: 1.66 (0.20), residues: 720 sheet: -0.68 (0.21), residues: 642 loop : -2.13 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1098 HIS 0.003 0.001 HIS A 245 PHE 0.027 0.001 PHE C 486 TYR 0.020 0.001 TYR C1134 ARG 0.003 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 57) link_NAG-ASN : angle 2.47168 ( 171) link_BETA1-4 : bond 0.01009 ( 24) link_BETA1-4 : angle 2.95087 ( 72) hydrogen bonds : bond 0.03406 ( 893) hydrogen bonds : angle 4.77347 ( 2400) SS BOND : bond 0.00345 ( 45) SS BOND : angle 0.98179 ( 90) covalent geometry : bond 0.00284 (28260) covalent geometry : angle 0.58349 (38484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7161.42 seconds wall clock time: 128 minutes 4.58 seconds (7684.58 seconds total)