Starting phenix.real_space_refine on Mon Jun 23 22:51:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxj_35078/06_2025/8hxj_35078.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxj_35078/06_2025/8hxj_35078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hxj_35078/06_2025/8hxj_35078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxj_35078/06_2025/8hxj_35078.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxj_35078/06_2025/8hxj_35078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxj_35078/06_2025/8hxj_35078.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17523 2.51 5 N 4521 2.21 5 O 5475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27639 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8835 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 55, 'TRANS': 1077} Chain: "B" Number of atoms: 8835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8835 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 55, 'TRANS': 1077} Chain: "C" Number of atoms: 8835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8835 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 55, 'TRANS': 1077} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 23.49, per 1000 atoms: 0.85 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: 16.68 Conformation dependent library (CDL) restraints added in 6.2 seconds 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6354 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 50 sheets defined 25.4% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.67 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: 18.79 Time building geometry restraints manager: 18.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8767 1.34 - 1.46: 6276 1.46 - 1.58: 13067 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 28260 Sorted by residual: bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" N VAL B1124 " pdb=" CA VAL B1124 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" CA SER B1119 " pdb=" CB SER B1119 " ideal model delta sigma weight residual 1.536 1.490 0.046 1.46e-02 4.69e+03 9.98e+00 bond pdb=" N GLY B1120 " pdb=" CA GLY B1120 " ideal model delta sigma weight residual 1.446 1.477 -0.031 1.08e-02 8.57e+03 8.04e+00 bond pdb=" N VAL A1125 " pdb=" CA VAL A1125 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.25e-02 6.40e+03 8.01e+00 ... (remaining 28255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 38386 3.72 - 7.45: 89 7.45 - 11.17: 7 11.17 - 14.90: 1 14.90 - 18.62: 1 Bond angle restraints: 38484 Sorted by residual: angle pdb=" N GLY C1120 " pdb=" CA GLY C1120 " pdb=" C GLY C1120 " ideal model delta sigma weight residual 111.64 130.26 -18.62 1.57e+00 4.06e-01 1.41e+02 angle pdb=" C ARG B 246 " pdb=" N SER B 247 " pdb=" CA SER B 247 " ideal model delta sigma weight residual 121.54 131.37 -9.83 1.91e+00 2.74e-01 2.65e+01 angle pdb=" N ASP C1123 " pdb=" CA ASP C1123 " pdb=" C ASP C1123 " ideal model delta sigma weight residual 113.38 108.01 5.37 1.17e+00 7.31e-01 2.10e+01 angle pdb=" CA GLY B1120 " pdb=" C GLY B1120 " pdb=" O GLY B1120 " ideal model delta sigma weight residual 122.57 118.45 4.12 9.20e-01 1.18e+00 2.01e+01 angle pdb=" N ASN C1121 " pdb=" CA ASN C1121 " pdb=" C ASN C1121 " ideal model delta sigma weight residual 113.19 107.92 5.27 1.19e+00 7.06e-01 1.96e+01 ... (remaining 38479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 16130 17.50 - 35.00: 1431 35.00 - 52.51: 257 52.51 - 70.01: 51 70.01 - 87.51: 23 Dihedral angle restraints: 17892 sinusoidal: 7995 harmonic: 9897 Sorted by residual: dihedral pdb=" CB CYS B1078 " pdb=" SG CYS B1078 " pdb=" SG CYS B1122 " pdb=" CB CYS B1122 " ideal model delta sinusoidal sigma weight residual -86.00 -27.49 -58.51 1 1.00e+01 1.00e-02 4.58e+01 dihedral pdb=" CA SER A 247 " pdb=" C SER A 247 " pdb=" N TYR A 248 " pdb=" CA TYR A 248 " ideal model delta harmonic sigma weight residual 180.00 156.22 23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -46.98 -39.02 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 17889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 4534 0.140 - 0.281: 45 0.281 - 0.421: 6 0.421 - 0.562: 3 0.562 - 0.702: 2 Chirality restraints: 4590 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.46e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.21e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.96e+01 ... (remaining 4587 not shown) Planarity restraints: 4950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1311 " -0.347 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG A1311 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A1311 " -0.063 2.00e-02 2.50e+03 pdb=" N2 NAG A1311 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A1311 " -0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " -0.337 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG C1304 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " -0.074 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " 0.518 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " -0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " -0.333 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG N 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " -0.032 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.211 2.00e-02 2.50e+03 ... (remaining 4947 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 7 1.97 - 2.71: 904 2.71 - 3.44: 39730 3.44 - 4.17: 64293 4.17 - 4.90: 116205 Nonbonded interactions: 221139 Sorted by model distance: nonbonded pdb=" OD2 ASP A 568 " pdb=" NH1 ARG B 843 " model vdw 1.242 3.120 nonbonded pdb=" O ALA A1076 " pdb=" CD1 ILE A1128 " model vdw 1.439 3.460 nonbonded pdb=" O ALA B1076 " pdb=" CD1 ILE B1128 " model vdw 1.449 3.460 nonbonded pdb=" O ALA C1076 " pdb=" CD1 ILE C1128 " model vdw 1.486 3.460 nonbonded pdb=" C ALA A1076 " pdb=" CD1 ILE A1128 " model vdw 1.614 3.690 ... (remaining 221134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 70.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 6.940 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 101.020 Find NCS groups from input model: 2.470 Set up NCS constraints: 1.310 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: 0.040 Load rotamer database and sin/cos tables:5.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.439 28386 Z= 0.243 Angle : 0.749 31.966 38817 Z= 0.370 Chirality : 0.054 0.702 4590 Planarity : 0.020 0.299 4893 Dihedral : 13.253 87.512 11403 Min Nonbonded Distance : 1.242 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.14), residues: 3393 helix: 0.44 (0.20), residues: 753 sheet: -0.68 (0.22), residues: 591 loop : -2.21 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1098 HIS 0.007 0.001 HIS B 245 PHE 0.035 0.001 PHE B 429 TYR 0.017 0.001 TYR C 248 ARG 0.007 0.000 ARG A 811 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 57) link_NAG-ASN : angle 3.67554 ( 171) link_BETA1-4 : bond 0.01069 ( 24) link_BETA1-4 : angle 3.56546 ( 72) hydrogen bonds : bond 0.12408 ( 893) hydrogen bonds : angle 6.68084 ( 2400) SS BOND : bond 0.06561 ( 45) SS BOND : angle 3.98271 ( 90) covalent geometry : bond 0.00393 (28260) covalent geometry : angle 0.66748 (38484) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 PHE cc_start: 0.7332 (m-10) cc_final: 0.7047 (m-10) REVERT: B 1025 MET cc_start: 0.9324 (tpp) cc_final: 0.8752 (tpt) REVERT: C 747 ASN cc_start: 0.8406 (m-40) cc_final: 0.8111 (m-40) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.3904 time to fit residues: 156.1012 Evaluate side-chains 164 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 3.9990 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 265 optimal weight: 0.0670 chunk 102 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 GLN A 961 GLN A1121 ASN B 99 ASN B 422 ASN C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.075620 restraints weight = 61376.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.078249 restraints weight = 32869.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.079984 restraints weight = 22558.090| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 28386 Z= 0.215 Angle : 0.682 16.445 38817 Z= 0.329 Chirality : 0.050 0.456 4590 Planarity : 0.004 0.034 4893 Dihedral : 7.228 59.322 5361 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 1.08 % Allowed : 7.10 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3393 helix: 0.91 (0.20), residues: 762 sheet: -0.84 (0.21), residues: 621 loop : -2.25 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1098 HIS 0.005 0.001 HIS B 245 PHE 0.024 0.001 PHE C1144 TYR 0.016 0.001 TYR C 144 ARG 0.006 0.000 ARG A 811 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 57) link_NAG-ASN : angle 3.14217 ( 171) link_BETA1-4 : bond 0.01051 ( 24) link_BETA1-4 : angle 3.10472 ( 72) hydrogen bonds : bond 0.04370 ( 893) hydrogen bonds : angle 5.38465 ( 2400) SS BOND : bond 0.00563 ( 45) SS BOND : angle 1.25858 ( 90) covalent geometry : bond 0.00498 (28260) covalent geometry : angle 0.63503 (38484) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.8862 (t80) cc_final: 0.8481 (t80) REVERT: A 981 ASP cc_start: 0.8276 (p0) cc_final: 0.7969 (p0) REVERT: B 175 PHE cc_start: 0.7384 (m-10) cc_final: 0.7097 (m-10) REVERT: B 378 LYS cc_start: 0.8984 (tppp) cc_final: 0.8781 (ttmm) REVERT: B 1025 MET cc_start: 0.8960 (tpp) cc_final: 0.8376 (tpp) REVERT: C 981 ASP cc_start: 0.8195 (p0) cc_final: 0.7972 (p0) outliers start: 32 outliers final: 25 residues processed: 188 average time/residue: 0.3388 time to fit residues: 112.3129 Evaluate side-chains 180 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1119 SER Chi-restraints excluded: chain B residue 1137 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1036 VAL Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 248 optimal weight: 0.6980 chunk 234 optimal weight: 0.5980 chunk 197 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 99 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.077198 restraints weight = 60945.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.079892 restraints weight = 32519.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.081660 restraints weight = 22206.817| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1075 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= 0.124 Angle : 0.618 16.927 38817 Z= 0.299 Chirality : 0.047 0.409 4590 Planarity : 0.004 0.034 4893 Dihedral : 6.608 59.188 5361 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 1.25 % Allowed : 9.97 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.14), residues: 3393 helix: 1.41 (0.21), residues: 723 sheet: -0.80 (0.22), residues: 588 loop : -2.17 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1098 HIS 0.004 0.001 HIS B 245 PHE 0.029 0.001 PHE C 157 TYR 0.016 0.001 TYR A 145 ARG 0.002 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 57) link_NAG-ASN : angle 2.81957 ( 171) link_BETA1-4 : bond 0.01076 ( 24) link_BETA1-4 : angle 3.09291 ( 72) hydrogen bonds : bond 0.03668 ( 893) hydrogen bonds : angle 5.05688 ( 2400) SS BOND : bond 0.00237 ( 45) SS BOND : angle 0.86783 ( 90) covalent geometry : bond 0.00270 (28260) covalent geometry : angle 0.57469 (38484) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 ASP cc_start: 0.8290 (p0) cc_final: 0.7951 (p0) REVERT: B 175 PHE cc_start: 0.7314 (m-10) cc_final: 0.7044 (m-10) REVERT: B 378 LYS cc_start: 0.8982 (tppp) cc_final: 0.8671 (tppt) REVERT: B 1025 MET cc_start: 0.8847 (tpp) cc_final: 0.8313 (tpp) REVERT: C 981 ASP cc_start: 0.8125 (p0) cc_final: 0.7835 (p0) outliers start: 37 outliers final: 27 residues processed: 202 average time/residue: 0.3243 time to fit residues: 115.4412 Evaluate side-chains 182 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1119 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1137 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 37 optimal weight: 0.9980 chunk 230 optimal weight: 0.8980 chunk 253 optimal weight: 5.9990 chunk 263 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 chunk 259 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 326 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.077223 restraints weight = 61654.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.079929 restraints weight = 32757.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.081706 restraints weight = 22311.249| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28386 Z= 0.123 Angle : 0.604 16.706 38817 Z= 0.291 Chirality : 0.046 0.392 4590 Planarity : 0.003 0.034 4893 Dihedral : 6.337 57.426 5361 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.43 % Favored : 90.54 % Rotamer: Outliers : 1.56 % Allowed : 11.60 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3393 helix: 1.51 (0.21), residues: 723 sheet: -0.79 (0.22), residues: 588 loop : -2.15 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1098 HIS 0.004 0.001 HIS B 245 PHE 0.029 0.001 PHE C 157 TYR 0.021 0.001 TYR C 752 ARG 0.004 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 57) link_NAG-ASN : angle 2.70066 ( 171) link_BETA1-4 : bond 0.01038 ( 24) link_BETA1-4 : angle 3.03651 ( 72) hydrogen bonds : bond 0.03496 ( 893) hydrogen bonds : angle 4.90941 ( 2400) SS BOND : bond 0.00224 ( 45) SS BOND : angle 0.77415 ( 90) covalent geometry : bond 0.00271 (28260) covalent geometry : angle 0.56260 (38484) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 ASP cc_start: 0.8291 (p0) cc_final: 0.7940 (p0) REVERT: B 175 PHE cc_start: 0.7297 (m-10) cc_final: 0.7057 (m-10) REVERT: B 378 LYS cc_start: 0.8985 (tppp) cc_final: 0.8674 (tppt) REVERT: B 418 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9071 (mp) REVERT: B 1025 MET cc_start: 0.8776 (tpp) cc_final: 0.8316 (tpp) REVERT: B 1103 ARG cc_start: 0.7661 (mpt180) cc_final: 0.7320 (mpt180) REVERT: C 69 HIS cc_start: 0.7065 (m90) cc_final: 0.6510 (m90) REVERT: C 981 ASP cc_start: 0.8130 (p0) cc_final: 0.7801 (p0) outliers start: 46 outliers final: 32 residues processed: 209 average time/residue: 0.3266 time to fit residues: 118.5086 Evaluate side-chains 188 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 2.839 ------------------------------------------------------------------------------- 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 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 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 418 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1137 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 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 Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 81 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 247 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 234 optimal weight: 0.0060 chunk 113 optimal weight: 10.0000 overall best weight: 2.3202 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 GLN B 949 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.095921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.074175 restraints weight = 61131.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.076752 restraints weight = 33120.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.078452 restraints weight = 22864.033| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 28386 Z= 0.243 Angle : 0.686 16.646 38817 Z= 0.334 Chirality : 0.049 0.415 4590 Planarity : 0.004 0.035 4893 Dihedral : 6.653 57.381 5361 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.96 % Favored : 89.01 % Rotamer: Outliers : 2.20 % Allowed : 13.02 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.14), residues: 3393 helix: 1.32 (0.20), residues: 723 sheet: -0.81 (0.21), residues: 642 loop : -2.25 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS B1054 PHE 0.029 0.002 PHE C 157 TYR 0.017 0.001 TYR A 145 ARG 0.006 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 57) link_NAG-ASN : angle 2.87179 ( 171) link_BETA1-4 : bond 0.00971 ( 24) link_BETA1-4 : angle 3.01481 ( 72) hydrogen bonds : bond 0.04200 ( 893) hydrogen bonds : angle 5.16251 ( 2400) SS BOND : bond 0.00440 ( 45) SS BOND : angle 1.37299 ( 90) covalent geometry : bond 0.00563 (28260) covalent geometry : angle 0.64589 (38484) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 158 time to evaluate : 3.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8328 (m-30) cc_final: 0.8041 (m-30) REVERT: A 429 PHE cc_start: 0.8911 (t80) cc_final: 0.8625 (t80) REVERT: A 981 ASP cc_start: 0.8379 (p0) cc_final: 0.7959 (p0) REVERT: A 1103 ARG cc_start: 0.7884 (mpt180) cc_final: 0.7080 (mpt-90) REVERT: B 153 MET cc_start: 0.5247 (ttm) cc_final: 0.5043 (ttm) REVERT: B 418 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9061 (mp) REVERT: B 1103 ARG cc_start: 0.7690 (mpt180) cc_final: 0.7294 (mpt180) outliers start: 65 outliers final: 41 residues processed: 205 average time/residue: 0.3338 time to fit residues: 118.1487 Evaluate side-chains 191 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 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 689 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1054 HIS Chi-restraints excluded: chain B residue 1137 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1026 SER Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 122 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 288 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 325 optimal weight: 0.6980 chunk 294 optimal weight: 0.0030 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.077052 restraints weight = 60704.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.079730 restraints weight = 32497.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.081465 restraints weight = 22235.057| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1547 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= 0.121 Angle : 0.617 16.939 38817 Z= 0.300 Chirality : 0.047 0.391 4590 Planarity : 0.003 0.034 4893 Dihedral : 6.282 57.011 5361 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.55 % Favored : 90.39 % Rotamer: Outliers : 1.62 % Allowed : 14.54 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3393 helix: 1.54 (0.20), residues: 729 sheet: -0.75 (0.21), residues: 609 loop : -2.16 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 152 HIS 0.003 0.001 HIS C 146 PHE 0.025 0.001 PHE C 157 TYR 0.020 0.001 TYR C1134 ARG 0.005 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 57) link_NAG-ASN : angle 2.60603 ( 171) link_BETA1-4 : bond 0.01070 ( 24) link_BETA1-4 : angle 3.05278 ( 72) hydrogen bonds : bond 0.03530 ( 893) hydrogen bonds : angle 4.89928 ( 2400) SS BOND : bond 0.00330 ( 45) SS BOND : angle 0.99992 ( 90) covalent geometry : bond 0.00262 (28260) covalent geometry : angle 0.57823 (38484) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.8808 (t80) cc_final: 0.8582 (t80) REVERT: A 981 ASP cc_start: 0.8342 (p0) cc_final: 0.7943 (p0) REVERT: B 153 MET cc_start: 0.5182 (ttm) cc_final: 0.4969 (ttm) REVERT: B 418 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9048 (mp) REVERT: B 1025 MET cc_start: 0.8716 (tpp) cc_final: 0.8472 (tpp) REVERT: B 1103 ARG cc_start: 0.7706 (mpt180) cc_final: 0.7438 (mpt180) REVERT: C 69 HIS cc_start: 0.7058 (m90) cc_final: 0.6555 (m-70) REVERT: C 420 ASP cc_start: 0.8057 (m-30) cc_final: 0.7846 (m-30) REVERT: C 981 ASP cc_start: 0.8190 (p0) cc_final: 0.7913 (p0) outliers start: 48 outliers final: 33 residues processed: 211 average time/residue: 0.3339 time to fit residues: 122.5262 Evaluate side-chains 200 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 2.724 ------------------------------------------------------------------------------- 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 695 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 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 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 1026 SER Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1054 HIS Chi-restraints excluded: chain B residue 1137 LEU 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 642 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 120 optimal weight: 1.9990 chunk 234 optimal weight: 0.0270 chunk 98 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 334 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 99 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.097649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.076118 restraints weight = 60748.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.078763 restraints weight = 32555.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.080469 restraints weight = 22266.631| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28386 Z= 0.159 Angle : 0.633 16.679 38817 Z= 0.307 Chirality : 0.047 0.395 4590 Planarity : 0.004 0.035 4893 Dihedral : 6.258 57.297 5361 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.87 % Favored : 90.07 % Rotamer: Outliers : 1.99 % Allowed : 15.18 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3393 helix: 1.55 (0.20), residues: 723 sheet: -0.74 (0.21), residues: 642 loop : -2.18 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 258 HIS 0.003 0.001 HIS B1054 PHE 0.026 0.001 PHE C 157 TYR 0.020 0.001 TYR C1134 ARG 0.005 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 57) link_NAG-ASN : angle 2.62268 ( 171) link_BETA1-4 : bond 0.01005 ( 24) link_BETA1-4 : angle 2.99580 ( 72) hydrogen bonds : bond 0.03632 ( 893) hydrogen bonds : angle 4.89521 ( 2400) SS BOND : bond 0.00303 ( 45) SS BOND : angle 1.05303 ( 90) covalent geometry : bond 0.00364 (28260) covalent geometry : angle 0.59484 (38484) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 166 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.8848 (t80) cc_final: 0.8578 (t80) REVERT: A 981 ASP cc_start: 0.8337 (p0) cc_final: 0.7958 (p0) REVERT: B 153 MET cc_start: 0.5223 (ttm) cc_final: 0.4982 (ttm) REVERT: B 418 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9062 (mp) REVERT: B 874 LEU cc_start: 0.9191 (mt) cc_final: 0.8909 (mt) REVERT: B 953 GLN cc_start: 0.8110 (tt0) cc_final: 0.7800 (tt0) REVERT: B 975 ASP cc_start: 0.8058 (t0) cc_final: 0.7708 (t0) REVERT: B 1025 MET cc_start: 0.8710 (tpp) cc_final: 0.8463 (tpp) REVERT: C 69 HIS cc_start: 0.7064 (m90) cc_final: 0.6689 (m-70) REVERT: C 420 ASP cc_start: 0.8094 (m-30) cc_final: 0.7879 (m-30) outliers start: 59 outliers final: 43 residues processed: 210 average time/residue: 0.3570 time to fit residues: 131.0066 Evaluate side-chains 205 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 3.079 ------------------------------------------------------------------------------- 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 398 ASP Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1132 THR 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 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 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 1137 LEU 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 642 VAL Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 869 TYR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1026 SER Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 17 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 335 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 760 ASN B 961 GLN C 49 HIS ** 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 = 0.3385 r_free = 0.3385 target = 0.096821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.075141 restraints weight = 61176.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.077757 restraints weight = 33031.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.079447 restraints weight = 22756.986| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28386 Z= 0.193 Angle : 0.653 16.740 38817 Z= 0.319 Chirality : 0.048 0.404 4590 Planarity : 0.004 0.035 4893 Dihedral : 6.407 57.347 5361 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.14 % Favored : 89.80 % Rotamer: Outliers : 1.96 % Allowed : 15.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3393 helix: 1.31 (0.20), residues: 741 sheet: -0.80 (0.21), residues: 642 loop : -2.21 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS B1054 PHE 0.027 0.001 PHE B 429 TYR 0.021 0.001 TYR C1134 ARG 0.005 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 57) link_NAG-ASN : angle 2.67043 ( 171) link_BETA1-4 : bond 0.00986 ( 24) link_BETA1-4 : angle 2.99339 ( 72) hydrogen bonds : bond 0.03808 ( 893) hydrogen bonds : angle 5.00991 ( 2400) SS BOND : bond 0.00404 ( 45) SS BOND : angle 1.39437 ( 90) covalent geometry : bond 0.00446 (28260) covalent geometry : angle 0.61386 (38484) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 163 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.8857 (t80) cc_final: 0.8596 (t80) REVERT: A 981 ASP cc_start: 0.8376 (p0) cc_final: 0.7931 (p0) REVERT: B 153 MET cc_start: 0.5410 (ttm) cc_final: 0.5170 (ttm) REVERT: B 418 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9064 (mp) REVERT: B 953 GLN cc_start: 0.8125 (tt0) cc_final: 0.7803 (tt0) REVERT: B 975 ASP cc_start: 0.8082 (t0) cc_final: 0.7723 (t0) REVERT: B 1025 MET cc_start: 0.8656 (tpp) cc_final: 0.8451 (tpp) REVERT: C 420 ASP cc_start: 0.8100 (m-30) cc_final: 0.7887 (m-30) outliers start: 58 outliers final: 47 residues processed: 206 average time/residue: 0.3305 time to fit residues: 117.8776 Evaluate side-chains 202 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 2.820 ------------------------------------------------------------------------------- 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 544 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1132 THR 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 213 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 336 CYS 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 1046 MET Chi-restraints excluded: chain B residue 1054 HIS Chi-restraints excluded: chain B residue 1137 LEU 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 547 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 869 TYR Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1026 SER Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 230 optimal weight: 4.9990 chunk 321 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 329 optimal weight: 2.9990 chunk 176 optimal weight: 0.1980 chunk 151 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 319 optimal weight: 0.8980 chunk 286 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.098515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.076955 restraints weight = 60583.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.079617 restraints weight = 32472.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.081346 restraints weight = 22242.671| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 28386 Z= 0.129 Angle : 0.626 16.814 38817 Z= 0.305 Chirality : 0.047 0.387 4590 Planarity : 0.003 0.035 4893 Dihedral : 6.198 57.651 5361 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.20 % Favored : 90.72 % Rotamer: Outliers : 1.72 % Allowed : 16.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3393 helix: 1.60 (0.20), residues: 723 sheet: -0.73 (0.21), residues: 642 loop : -2.15 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 152 HIS 0.003 0.001 HIS A 245 PHE 0.025 0.001 PHE C 486 TYR 0.021 0.001 TYR C1134 ARG 0.005 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 57) link_NAG-ASN : angle 2.51603 ( 171) link_BETA1-4 : bond 0.01035 ( 24) link_BETA1-4 : angle 3.00465 ( 72) hydrogen bonds : bond 0.03477 ( 893) hydrogen bonds : angle 4.85138 ( 2400) SS BOND : bond 0.00380 ( 45) SS BOND : angle 1.17522 ( 90) covalent geometry : bond 0.00289 (28260) covalent geometry : angle 0.58891 (38484) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 2.805 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 429 PHE cc_start: 0.8802 (t80) cc_final: 0.8547 (t80) REVERT: A 981 ASP cc_start: 0.8338 (p0) cc_final: 0.7961 (p0) REVERT: B 153 MET cc_start: 0.5342 (ttm) cc_final: 0.5105 (ttm) REVERT: B 418 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9035 (mp) REVERT: B 874 LEU cc_start: 0.9152 (mt) cc_final: 0.8869 (mt) REVERT: B 953 GLN cc_start: 0.8118 (tt0) cc_final: 0.7813 (tt0) REVERT: B 975 ASP cc_start: 0.8059 (t0) cc_final: 0.7708 (t0) REVERT: C 69 HIS cc_start: 0.7131 (m90) cc_final: 0.6773 (m-70) REVERT: C 981 ASP cc_start: 0.8192 (p0) cc_final: 0.7900 (p0) outliers start: 51 outliers final: 41 residues processed: 212 average time/residue: 0.3204 time to fit residues: 117.6270 Evaluate side-chains 205 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1132 THR 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 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 678 THR 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 B residue 1137 LEU Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 756 CYS Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1026 SER Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 187 optimal weight: 0.8980 chunk 224 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 208 optimal weight: 0.4980 chunk 328 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 316 optimal weight: 2.9990 chunk 14 optimal weight: 0.0070 chunk 298 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 52 GLN C 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.077567 restraints weight = 60485.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.080237 restraints weight = 32412.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.081969 restraints weight = 22195.248| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28386 Z= 0.119 Angle : 0.615 16.783 38817 Z= 0.300 Chirality : 0.046 0.378 4590 Planarity : 0.003 0.035 4893 Dihedral : 6.062 57.518 5361 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.11 % Favored : 90.78 % Rotamer: Outliers : 1.56 % Allowed : 16.33 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3393 helix: 1.68 (0.21), residues: 720 sheet: -0.68 (0.21), residues: 642 loop : -2.13 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 152 HIS 0.003 0.001 HIS A 245 PHE 0.028 0.001 PHE C 486 TYR 0.021 0.001 TYR C1134 ARG 0.005 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 57) link_NAG-ASN : angle 2.47257 ( 171) link_BETA1-4 : bond 0.01023 ( 24) link_BETA1-4 : angle 2.97249 ( 72) hydrogen bonds : bond 0.03381 ( 893) hydrogen bonds : angle 4.77741 ( 2400) SS BOND : bond 0.00319 ( 45) SS BOND : angle 0.98551 ( 90) covalent geometry : bond 0.00262 (28260) covalent geometry : angle 0.57881 (38484) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6786 Ramachandran restraints generated. 3393 Oldfield, 0 Emsley, 3393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.8773 (t80) cc_final: 0.8483 (t80) REVERT: A 981 ASP cc_start: 0.8309 (p0) cc_final: 0.7862 (p0) REVERT: B 153 MET cc_start: 0.5337 (ttm) cc_final: 0.5103 (ttm) REVERT: B 418 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.9019 (mp) REVERT: B 874 LEU cc_start: 0.9142 (mt) cc_final: 0.8860 (mt) REVERT: B 953 GLN cc_start: 0.8129 (tt0) cc_final: 0.7814 (tt0) REVERT: B 975 ASP cc_start: 0.8024 (t0) cc_final: 0.7676 (t0) REVERT: C 69 HIS cc_start: 0.7146 (m90) cc_final: 0.6655 (m90) outliers start: 46 outliers final: 38 residues processed: 208 average time/residue: 0.3399 time to fit residues: 123.4576 Evaluate side-chains 197 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 3.443 ------------------------------------------------------------------------------- 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 695 LEU Chi-restraints excluded: chain A residue 701 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 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 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 678 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1137 LEU 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 525 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 756 CYS Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 1026 SER Chi-restraints excluded: chain C residue 1046 MET Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 230 optimal weight: 0.6980 chunk 127 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 218 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 273 optimal weight: 0.6980 chunk 301 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.099589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.078107 restraints weight = 60781.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.080785 restraints weight = 32502.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082528 restraints weight = 22205.308| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1838 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 : 0.615 16.839 38817 Z= 0.301 Chirality : 0.046 0.372 4590 Planarity : 0.003 0.036 4893 Dihedral : 5.971 57.467 5361 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.11 % Favored : 90.78 % Rotamer: Outliers : 1.49 % Allowed : 16.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.14), residues: 3393 helix: 1.71 (0.21), residues: 720 sheet: -0.64 (0.21), residues: 642 loop : -2.10 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 152 HIS 0.003 0.001 HIS A 245 PHE 0.028 0.001 PHE C 486 TYR 0.020 0.001 TYR A1134 ARG 0.005 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 57) link_NAG-ASN : angle 2.42132 ( 171) link_BETA1-4 : bond 0.01039 ( 24) link_BETA1-4 : angle 2.95848 ( 72) hydrogen bonds : bond 0.03327 ( 893) hydrogen bonds : angle 4.73093 ( 2400) SS BOND : bond 0.00315 ( 45) SS BOND : angle 0.94718 ( 90) covalent geometry : bond 0.00255 (28260) covalent geometry : angle 0.58036 (38484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7834.93 seconds wall clock time: 138 minutes 27.73 seconds (8307.73 seconds total)