Starting phenix.real_space_refine on Mon Aug 25 11:48:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxj_35078/08_2025/8hxj_35078.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxj_35078/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hxj_35078/08_2025/8hxj_35078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxj_35078/08_2025/8hxj_35078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hxj_35078/08_2025/8hxj_35078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxj_35078/08_2025/8hxj_35078.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.19, per 1000 atoms: 0.26 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: 2.81 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.33 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: 6.74 Time building geometry restraints manager: 3.64 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: 0.04 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: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.890 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- 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 : 11.97 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG A 811 TYR 0.017 0.001 TYR C 248 PHE 0.035 0.001 PHE B 429 TRP 0.008 0.001 TRP C1098 HIS 0.007 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00393 (28260) covalent geometry : angle 0.66748 (38484) SS BOND : bond 0.06561 ( 45) SS BOND : angle 3.98271 ( 90) hydrogen bonds : bond 0.12408 ( 893) hydrogen bonds : angle 6.68084 ( 2400) link_BETA1-4 : bond 0.01069 ( 24) link_BETA1-4 : angle 3.56546 ( 72) link_NAG-ASN : bond 0.00571 ( 57) link_NAG-ASN : angle 3.67554 ( 171) *********************** 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 : 1.181 Fit side-chains 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: 0.8751 (tpt) REVERT: C 747 ASN cc_start: 0.8406 (m-40) cc_final: 0.8109 (m-40) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1629 time to fit residues: 62.8189 Evaluate side-chains 165 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 B 52 GLN B 99 ASN B 422 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.077018 restraints weight = 61427.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.079687 restraints weight = 32702.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.081462 restraints weight = 22375.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.082595 restraints weight = 17627.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.083320 restraints weight = 15153.841| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28386 Z= 0.164 Angle : 0.657 16.531 38817 Z= 0.317 Chirality : 0.048 0.442 4590 Planarity : 0.004 0.035 4893 Dihedral : 7.137 58.913 5361 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 0.85 % Allowed : 6.63 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.14), residues: 3393 helix: 1.06 (0.20), residues: 744 sheet: -0.78 (0.22), residues: 588 loop : -2.18 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 811 TYR 0.015 0.001 TYR C 144 PHE 0.024 0.001 PHE C1144 TRP 0.010 0.001 TRP C1098 HIS 0.005 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00371 (28260) covalent geometry : angle 0.61035 (38484) SS BOND : bond 0.00602 ( 45) SS BOND : angle 1.09688 ( 90) hydrogen bonds : bond 0.04114 ( 893) hydrogen bonds : angle 5.30469 ( 2400) link_BETA1-4 : bond 0.01034 ( 24) link_BETA1-4 : angle 3.13375 ( 72) link_NAG-ASN : bond 0.00531 ( 57) link_NAG-ASN : angle 3.06733 ( 171) *********************** 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 202 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 ASP cc_start: 0.8223 (p0) cc_final: 0.7918 (p0) REVERT: B 175 PHE cc_start: 0.7356 (m-10) cc_final: 0.7077 (m-10) REVERT: B 1025 MET cc_start: 0.8968 (tpp) cc_final: 0.8352 (tpp) REVERT: C 981 ASP cc_start: 0.8133 (p0) cc_final: 0.7916 (p0) outliers start: 25 outliers final: 20 residues processed: 189 average time/residue: 0.1589 time to fit residues: 52.5931 Evaluate side-chains 180 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 1121 ASN 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 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 1054 HIS Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1119 SER Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 398 ASP 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 174 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 305 optimal weight: 0.0040 chunk 80 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 658 ASN B 99 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 GLN ** C1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.096469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.074697 restraints weight = 61420.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.077313 restraints weight = 33189.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.079014 restraints weight = 22871.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.080122 restraints weight = 18146.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.080782 restraints weight = 15657.163| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28386 Z= 0.230 Angle : 0.684 16.395 38817 Z= 0.332 Chirality : 0.049 0.428 4590 Planarity : 0.004 0.035 4893 Dihedral : 6.862 58.126 5361 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 1.49 % Allowed : 10.65 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.14), residues: 3393 helix: 1.18 (0.20), residues: 723 sheet: -0.84 (0.21), residues: 609 loop : -2.26 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 811 TYR 0.012 0.001 TYR C 144 PHE 0.029 0.002 PHE C 157 TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS C1054 Details of bonding type rmsd covalent geometry : bond 0.00536 (28260) covalent geometry : angle 0.64081 (38484) SS BOND : bond 0.00472 ( 45) SS BOND : angle 1.23163 ( 90) hydrogen bonds : bond 0.04210 ( 893) hydrogen bonds : angle 5.24286 ( 2400) link_BETA1-4 : bond 0.00965 ( 24) link_BETA1-4 : angle 3.03034 ( 72) link_NAG-ASN : bond 0.00489 ( 57) link_NAG-ASN : angle 3.00307 ( 171) *********************** 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 216 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 ASP cc_start: 0.8353 (p0) cc_final: 0.7941 (p0) REVERT: B 175 PHE cc_start: 0.7437 (m-10) cc_final: 0.7212 (m-10) REVERT: B 418 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9080 (mp) REVERT: C 981 ASP cc_start: 0.8203 (p0) cc_final: 0.7867 (p0) outliers start: 44 outliers final: 30 residues processed: 200 average time/residue: 0.1446 time to fit residues: 50.4210 Evaluate side-chains 186 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 903 ASN Chi-restraints excluded: chain A residue 1026 SER 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 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 B residue 1119 SER Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 248 TYR 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 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 1133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 196 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 226 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 294 optimal weight: 0.8980 chunk 313 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 292 optimal weight: 0.0370 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 B 49 HIS B 99 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3422 r_free = 0.3422 target = 0.099033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.077400 restraints weight = 60287.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.080074 restraints weight = 32333.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081830 restraints weight = 22165.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082961 restraints weight = 17470.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.083665 restraints weight = 15052.010| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28386 Z= 0.119 Angle : 0.613 16.854 38817 Z= 0.297 Chirality : 0.047 0.401 4590 Planarity : 0.003 0.034 4893 Dihedral : 6.419 57.318 5361 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.43 % Favored : 90.54 % Rotamer: Outliers : 1.56 % Allowed : 12.71 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.14), residues: 3393 helix: 1.47 (0.21), residues: 723 sheet: -0.71 (0.21), residues: 642 loop : -2.22 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1103 TYR 0.021 0.001 TYR C 752 PHE 0.028 0.001 PHE C 157 TRP 0.008 0.001 TRP C 152 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00254 (28260) covalent geometry : angle 0.57282 (38484) SS BOND : bond 0.00583 ( 45) SS BOND : angle 0.81818 ( 90) hydrogen bonds : bond 0.03547 ( 893) hydrogen bonds : angle 4.95073 ( 2400) link_BETA1-4 : bond 0.01069 ( 24) link_BETA1-4 : angle 3.06538 ( 72) link_NAG-ASN : bond 0.00467 ( 57) link_NAG-ASN : angle 2.69239 ( 171) *********************** 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 231 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6334 (ttm) cc_final: 0.6053 (ttm) REVERT: A 981 ASP cc_start: 0.8319 (p0) cc_final: 0.7928 (p0) REVERT: B 175 PHE cc_start: 0.7353 (m-10) cc_final: 0.7142 (m-10) REVERT: B 1025 MET cc_start: 0.8757 (tpp) cc_final: 0.8340 (tpp) REVERT: C 53 ASP cc_start: 0.7738 (t70) cc_final: 0.7492 (t70) REVERT: C 865 MET cc_start: 0.8398 (mmm) cc_final: 0.8141 (mtt) REVERT: C 981 ASP cc_start: 0.8167 (p0) cc_final: 0.7818 (p0) outliers start: 46 outliers final: 22 residues processed: 222 average time/residue: 0.1340 time to fit residues: 51.8228 Evaluate side-chains 188 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 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 B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1054 HIS Chi-restraints excluded: chain B residue 1071 PHE 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 693 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 176 optimal weight: 2.9990 chunk 173 optimal weight: 0.0870 chunk 335 optimal weight: 5.9990 chunk 324 optimal weight: 4.9990 chunk 163 optimal weight: 0.0070 chunk 244 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN C 49 HIS C 52 GLN ** 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 = 0.3433 r_free = 0.3433 target = 0.099655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.078061 restraints weight = 60654.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.080754 restraints weight = 32446.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.082510 restraints weight = 22175.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.083637 restraints weight = 17480.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.084357 restraints weight = 15053.570| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28386 Z= 0.112 Angle : 0.609 16.696 38817 Z= 0.293 Chirality : 0.046 0.384 4590 Planarity : 0.003 0.034 4893 Dihedral : 6.155 57.068 5361 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.08 % Favored : 90.89 % Rotamer: Outliers : 1.45 % Allowed : 14.30 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.14), residues: 3393 helix: 1.57 (0.21), residues: 720 sheet: -0.72 (0.21), residues: 636 loop : -2.18 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1103 TYR 0.019 0.001 TYR A1134 PHE 0.029 0.001 PHE C 157 TRP 0.009 0.001 TRP C 152 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00241 (28260) covalent geometry : angle 0.56885 (38484) SS BOND : bond 0.00204 ( 45) SS BOND : angle 1.00568 ( 90) hydrogen bonds : bond 0.03391 ( 893) hydrogen bonds : angle 4.84008 ( 2400) link_BETA1-4 : bond 0.01045 ( 24) link_BETA1-4 : angle 3.02978 ( 72) link_NAG-ASN : bond 0.00441 ( 57) link_NAG-ASN : angle 2.61333 ( 171) *********************** 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 220 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 ASP cc_start: 0.8317 (p0) cc_final: 0.7914 (p0) REVERT: B 175 PHE cc_start: 0.7319 (m-10) cc_final: 0.7026 (m-10) REVERT: B 874 LEU cc_start: 0.9107 (mt) cc_final: 0.8824 (mt) REVERT: B 975 ASP cc_start: 0.7990 (t0) cc_final: 0.7637 (t0) REVERT: B 1025 MET cc_start: 0.8685 (tpp) cc_final: 0.8302 (tpp) REVERT: B 1103 ARG cc_start: 0.7630 (mpt180) cc_final: 0.7367 (mpt180) REVERT: C 69 HIS cc_start: 0.7043 (m90) cc_final: 0.6647 (m-70) REVERT: C 865 MET cc_start: 0.8380 (mmm) cc_final: 0.8133 (mtt) REVERT: C 981 ASP cc_start: 0.8144 (p0) cc_final: 0.7774 (p0) outliers start: 43 outliers final: 31 residues processed: 212 average time/residue: 0.1458 time to fit residues: 54.1685 Evaluate side-chains 194 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 749 LEU 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 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 642 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER 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 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 903 ASN Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 222 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 79 optimal weight: 0.0370 chunk 36 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- 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** A 317 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 949 ASN ** 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 = 0.3383 r_free = 0.3383 target = 0.096704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.074947 restraints weight = 61168.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.077532 restraints weight = 33035.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.079243 restraints weight = 22840.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.080328 restraints weight = 18103.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.081042 restraints weight = 15632.297| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 28386 Z= 0.210 Angle : 0.661 16.532 38817 Z= 0.321 Chirality : 0.048 0.405 4590 Planarity : 0.004 0.034 4893 Dihedral : 6.418 57.244 5361 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.67 % Favored : 89.24 % Rotamer: Outliers : 1.83 % Allowed : 15.11 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.14), residues: 3393 helix: 1.40 (0.20), residues: 729 sheet: -0.77 (0.21), residues: 642 loop : -2.22 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1103 TYR 0.017 0.001 TYR B1134 PHE 0.027 0.001 PHE C 157 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS B1054 Details of bonding type rmsd covalent geometry : bond 0.00488 (28260) covalent geometry : angle 0.62184 (38484) SS BOND : bond 0.00387 ( 45) SS BOND : angle 1.20415 ( 90) hydrogen bonds : bond 0.03918 ( 893) hydrogen bonds : angle 5.01959 ( 2400) link_BETA1-4 : bond 0.00985 ( 24) link_BETA1-4 : angle 2.99296 ( 72) link_NAG-ASN : bond 0.00450 ( 57) link_NAG-ASN : angle 2.75536 ( 171) *********************** 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 215 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.7291 (m-10) cc_final: 0.6992 (m-10) REVERT: A 420 ASP cc_start: 0.8344 (m-30) cc_final: 0.8040 (m-30) REVERT: A 981 ASP cc_start: 0.8363 (p0) cc_final: 0.7922 (p0) REVERT: B 418 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9057 (mt) REVERT: B 953 GLN cc_start: 0.8121 (tt0) cc_final: 0.7815 (tt0) REVERT: B 975 ASP cc_start: 0.8042 (t0) cc_final: 0.7685 (t0) REVERT: B 1025 MET cc_start: 0.8682 (tpp) cc_final: 0.8253 (tpp) outliers start: 54 outliers final: 36 residues processed: 205 average time/residue: 0.1489 time to fit residues: 53.3228 Evaluate side-chains 191 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL 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 701 VAL Chi-restraints excluded: chain A residue 749 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 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 903 ASN Chi-restraints excluded: chain B residue 1026 SER 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 701 VAL 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 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 169 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 327 optimal weight: 2.9990 chunk 312 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 178 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.097661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.076092 restraints weight = 60716.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.078731 restraints weight = 32622.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.080447 restraints weight = 22372.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.081559 restraints weight = 17705.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.082211 restraints weight = 15258.397| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 28386 Z= 0.156 Angle : 0.637 16.825 38817 Z= 0.310 Chirality : 0.047 0.400 4590 Planarity : 0.004 0.034 4893 Dihedral : 6.328 57.298 5361 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.73 % Favored : 90.19 % Rotamer: Outliers : 1.99 % Allowed : 15.52 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.14), residues: 3393 helix: 1.46 (0.20), residues: 729 sheet: -0.75 (0.21), residues: 642 loop : -2.20 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1103 TYR 0.021 0.001 TYR C1134 PHE 0.024 0.001 PHE B 429 TRP 0.008 0.001 TRP C 152 HIS 0.003 0.001 HIS B1054 Details of bonding type rmsd covalent geometry : bond 0.00359 (28260) covalent geometry : angle 0.59749 (38484) SS BOND : bond 0.00345 ( 45) SS BOND : angle 1.39834 ( 90) hydrogen bonds : bond 0.03654 ( 893) hydrogen bonds : angle 4.95455 ( 2400) link_BETA1-4 : bond 0.01028 ( 24) link_BETA1-4 : angle 3.01840 ( 72) link_NAG-ASN : bond 0.00428 ( 57) link_NAG-ASN : angle 2.60709 ( 171) *********************** 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 231 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 172 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 ASP cc_start: 0.8359 (p0) cc_final: 0.7983 (p0) REVERT: B 418 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9066 (mt) REVERT: B 953 GLN cc_start: 0.8088 (tt0) cc_final: 0.7767 (tt0) REVERT: B 975 ASP cc_start: 0.8037 (t0) cc_final: 0.7676 (t0) REVERT: B 1025 MET cc_start: 0.8623 (tpp) cc_final: 0.8243 (tpp) outliers start: 59 outliers final: 41 residues processed: 220 average time/residue: 0.1530 time to fit residues: 58.7726 Evaluate side-chains 206 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 213 VAL 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 749 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 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 418 ILE Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 708 ILE 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 398 ASP 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 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 1133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 118 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 280 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 148 optimal weight: 0.0170 chunk 6 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.096919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.075273 restraints weight = 61257.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.077897 restraints weight = 32958.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.079610 restraints weight = 22631.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.080716 restraints weight = 17914.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.081331 restraints weight = 15447.727| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 28386 Z= 0.182 Angle : 0.651 16.689 38817 Z= 0.317 Chirality : 0.048 0.403 4590 Planarity : 0.004 0.034 4893 Dihedral : 6.393 57.315 5361 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.37 % Favored : 89.54 % Rotamer: Outliers : 1.79 % Allowed : 16.06 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.14), residues: 3393 helix: 1.26 (0.20), residues: 747 sheet: -0.78 (0.21), residues: 642 loop : -2.23 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1103 TYR 0.020 0.001 TYR C1134 PHE 0.024 0.001 PHE C 486 TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS B1054 Details of bonding type rmsd covalent geometry : bond 0.00421 (28260) covalent geometry : angle 0.61250 (38484) SS BOND : bond 0.00499 ( 45) SS BOND : angle 1.35680 ( 90) hydrogen bonds : bond 0.03758 ( 893) hydrogen bonds : angle 4.97663 ( 2400) link_BETA1-4 : bond 0.00987 ( 24) link_BETA1-4 : angle 2.99092 ( 72) link_NAG-ASN : bond 0.00430 ( 57) link_NAG-ASN : angle 2.64721 ( 171) *********************** 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 223 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 ASP cc_start: 0.8368 (p0) cc_final: 0.7923 (p0) REVERT: B 418 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.9057 (mt) REVERT: B 874 LEU cc_start: 0.9210 (mt) cc_final: 0.8939 (mt) REVERT: B 953 GLN cc_start: 0.8128 (tt0) cc_final: 0.7808 (tt0) REVERT: B 975 ASP cc_start: 0.8051 (t0) cc_final: 0.7689 (t0) REVERT: B 1025 MET cc_start: 0.8618 (tpp) cc_final: 0.8192 (tpp) outliers start: 53 outliers final: 44 residues processed: 213 average time/residue: 0.1342 time to fit residues: 50.1416 Evaluate side-chains 206 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL 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 701 VAL Chi-restraints excluded: chain A residue 749 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 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 418 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 735 THR 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 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 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 1133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 139 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 292 optimal weight: 0.0870 chunk 204 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 265 optimal weight: 0.0870 chunk 159 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** 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 = 0.3426 r_free = 0.3426 target = 0.099207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.077838 restraints weight = 60403.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.080521 restraints weight = 32113.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.082264 restraints weight = 21842.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.083393 restraints weight = 17209.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.084077 restraints weight = 14766.683| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 0.051 28386 Z= 0.116 Angle : 0.621 16.811 38817 Z= 0.304 Chirality : 0.046 0.379 4590 Planarity : 0.004 0.036 4893 Dihedral : 6.116 57.812 5361 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.11 % Favored : 90.80 % Rotamer: Outliers : 1.39 % Allowed : 16.77 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.14), residues: 3393 helix: 1.60 (0.20), residues: 729 sheet: -0.68 (0.21), residues: 642 loop : -2.15 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1103 TYR 0.020 0.001 TYR C1134 PHE 0.026 0.001 PHE C 486 TRP 0.008 0.001 TRP C 152 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00250 (28260) covalent geometry : angle 0.58536 (38484) SS BOND : bond 0.00322 ( 45) SS BOND : angle 1.11821 ( 90) hydrogen bonds : bond 0.03347 ( 893) hydrogen bonds : angle 4.77640 ( 2400) link_BETA1-4 : bond 0.01044 ( 24) link_BETA1-4 : angle 3.00088 ( 72) link_NAG-ASN : bond 0.00444 ( 57) link_NAG-ASN : angle 2.46533 ( 171) *********************** 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: 41 poor density : 184 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 ASP cc_start: 0.8339 (p0) cc_final: 0.7952 (p0) REVERT: B 418 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9030 (mt) REVERT: B 874 LEU cc_start: 0.9105 (mt) cc_final: 0.8813 (mt) REVERT: B 975 ASP cc_start: 0.7991 (t0) cc_final: 0.7652 (t0) REVERT: B 1025 MET cc_start: 0.8695 (tpp) cc_final: 0.8367 (tpp) REVERT: C 69 HIS cc_start: 0.7119 (m90) cc_final: 0.6669 (m90) REVERT: C 981 ASP cc_start: 0.8184 (p0) cc_final: 0.7889 (p0) REVERT: C 1088 GLU cc_start: 0.6707 (tp30) cc_final: 0.6463 (tp30) outliers start: 41 outliers final: 33 residues processed: 216 average time/residue: 0.1498 time to fit residues: 56.3104 Evaluate side-chains 197 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL 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 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 1132 THR Chi-restraints excluded: chain B residue 51 THR 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 689 ILE Chi-restraints excluded: chain B residue 735 THR 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 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 701 VAL Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1036 VAL Chi-restraints excluded: chain C residue 1046 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 137 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 309 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 270 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 65 optimal weight: 0.0470 chunk 111 optimal weight: 0.6980 overall best weight: 0.5656 ------------------------------------------------------------------------------- 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 GLN C 52 GLN ** 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 = 0.3430 r_free = 0.3430 target = 0.099448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.078083 restraints weight = 60551.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.080769 restraints weight = 32224.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082525 restraints weight = 21936.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.083666 restraints weight = 17207.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.084304 restraints weight = 14766.669| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28386 Z= 0.117 Angle : 0.621 16.912 38817 Z= 0.304 Chirality : 0.046 0.373 4590 Planarity : 0.003 0.037 4893 Dihedral : 5.999 57.277 5361 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.96 % Favored : 90.92 % Rotamer: Outliers : 1.25 % Allowed : 16.94 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.14), residues: 3393 helix: 1.65 (0.20), residues: 726 sheet: -0.65 (0.21), residues: 645 loop : -2.14 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1103 TYR 0.020 0.001 TYR C1134 PHE 0.027 0.001 PHE C 486 TRP 0.006 0.001 TRP C 152 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00255 (28260) covalent geometry : angle 0.58515 (38484) SS BOND : bond 0.00324 ( 45) SS BOND : angle 1.10698 ( 90) hydrogen bonds : bond 0.03313 ( 893) hydrogen bonds : angle 4.74174 ( 2400) link_BETA1-4 : bond 0.01064 ( 24) link_BETA1-4 : angle 2.97338 ( 72) link_NAG-ASN : bond 0.00427 ( 57) link_NAG-ASN : angle 2.44881 ( 171) ********************** 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 208 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 ASP cc_start: 0.8314 (p0) cc_final: 0.7852 (p0) REVERT: B 418 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.9003 (mt) REVERT: B 874 LEU cc_start: 0.9141 (mt) cc_final: 0.8855 (mt) REVERT: B 975 ASP cc_start: 0.7996 (t0) cc_final: 0.7650 (t0) REVERT: B 1025 MET cc_start: 0.8689 (tpp) cc_final: 0.8343 (tpp) REVERT: C 69 HIS cc_start: 0.7121 (m90) cc_final: 0.6709 (m90) REVERT: C 981 ASP cc_start: 0.8153 (p0) cc_final: 0.7762 (p0) REVERT: C 1088 GLU cc_start: 0.6883 (tp30) cc_final: 0.6636 (tp30) outliers start: 37 outliers final: 31 residues processed: 201 average time/residue: 0.1483 time to fit residues: 51.8101 Evaluate side-chains 195 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 642 VAL 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 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 689 ILE 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 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 701 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 312 optimal weight: 0.0570 chunk 245 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 221 optimal weight: 0.8980 overall best weight: 1.3502 ------------------------------------------------------------------------------- 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 C 52 GLN ** 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 = 0.3407 r_free = 0.3407 target = 0.098050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.076432 restraints weight = 60799.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.079079 restraints weight = 32809.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.080800 restraints weight = 22565.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.081901 restraints weight = 17849.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082613 restraints weight = 15400.563| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28386 Z= 0.164 Angle : 0.642 16.814 38817 Z= 0.315 Chirality : 0.047 0.386 4590 Planarity : 0.004 0.037 4893 Dihedral : 6.098 57.445 5361 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.67 % Favored : 90.22 % Rotamer: Outliers : 1.62 % Allowed : 16.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.14), residues: 3393 helix: 1.41 (0.20), residues: 747 sheet: -0.66 (0.21), residues: 642 loop : -2.16 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1103 TYR 0.021 0.001 TYR C1134 PHE 0.029 0.001 PHE C 486 TRP 0.007 0.001 TRP A 436 HIS 0.004 0.001 HIS B1054 Details of bonding type rmsd covalent geometry : bond 0.00377 (28260) covalent geometry : angle 0.60661 (38484) SS BOND : bond 0.00431 ( 45) SS BOND : angle 1.23866 ( 90) hydrogen bonds : bond 0.03569 ( 893) hydrogen bonds : angle 4.82619 ( 2400) link_BETA1-4 : bond 0.01003 ( 24) link_BETA1-4 : angle 2.95001 ( 72) link_NAG-ASN : bond 0.00419 ( 57) link_NAG-ASN : angle 2.51344 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3839.73 seconds wall clock time: 67 minutes 51.95 seconds (4071.95 seconds total)