Starting phenix.real_space_refine on Sat Feb 7 14:48:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4q_48902/02_2026/9n4q_48902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4q_48902/02_2026/9n4q_48902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n4q_48902/02_2026/9n4q_48902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4q_48902/02_2026/9n4q_48902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n4q_48902/02_2026/9n4q_48902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4q_48902/02_2026/9n4q_48902.map" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.029 sd= 1.097 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 198 5.16 5 C 21423 2.51 5 N 5357 2.21 5 O 6340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33333 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6655 Classifications: {'peptide': 840} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 806} Chain: "B" Number of atoms: 6477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6477 Classifications: {'peptide': 818} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 784} Chain: "C" Number of atoms: 6666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6666 Classifications: {'peptide': 841} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 807} Chain: "D" Number of atoms: 6477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6477 Classifications: {'peptide': 818} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 784} Chain: "E" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2700 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 19, 'TRANS': 320} Chain: "F" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2705 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 19, 'TRANS': 321} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "A" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 278 Unusual residues: {'NAG': 5, 'POV': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 132 Unusual residues: {'NAG': 2, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 264 Unusual residues: {'NAG': 4, 'POV': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 236 Unusual residues: {'NAG': 2, 'POV': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.12, per 1000 atoms: 0.21 Number of scatterers: 33333 At special positions: 0 Unit cell: (124.5, 156.87, 219.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 198 16.00 P 15 15.00 O 6340 8.00 N 5357 7.00 C 21423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.04 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.04 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS E 177 " - pdb=" SG CYS E 207 " distance=2.04 Simple disulfide: pdb=" SG CYS E 234 " - pdb=" SG CYS E 256 " distance=2.03 Simple disulfide: pdb=" SG CYS E 297 " - pdb=" SG CYS E 309 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 322 " distance=2.03 Simple disulfide: pdb=" SG CYS E 316 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS F 45 " - pdb=" SG CYS F 72 " distance=2.03 Simple disulfide: pdb=" SG CYS F 100 " - pdb=" SG CYS F 122 " distance=2.03 Simple disulfide: pdb=" SG CYS F 177 " - pdb=" SG CYS F 207 " distance=2.04 Simple disulfide: pdb=" SG CYS F 234 " - pdb=" SG CYS F 256 " distance=2.03 Simple disulfide: pdb=" SG CYS F 297 " - pdb=" SG CYS F 309 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 322 " distance=2.03 Simple disulfide: pdb=" SG CYS F 316 " - pdb=" SG CYS F 331 " distance=2.04 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 ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA L 3 " - " MAN L 4 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA L 3 " - " MAN L 5 " " BMA Q 3 " - " MAN Q 5 " " BMA T 3 " - " MAN T 5 " BETA1-3 " BMA N 3 " - " BMA N 4 " " BMA V 3 " - " BMA V 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " 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 L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1004 " - " ASN A 67 " " NAG A1005 " - " ASN A 73 " " NAG A1006 " - " ASN A 430 " " NAG A1007 " - " ASN A 546 " " NAG A1008 " - " ASN A 751 " " NAG B1003 " - " ASN B 73 " " NAG B1004 " - " ASN B 430 " " NAG C1004 " - " ASN C 73 " " NAG C1005 " - " ASN C 275 " " NAG C1006 " - " ASN C 412 " " NAG C1007 " - " ASN C 751 " " NAG D1005 " - " ASN D 67 " " NAG D1006 " - " ASN D 73 " " NAG E 601 " - " ASN E 311 " " NAG F 602 " - " ASN F 311 " " NAG G 1 " - " ASN A 275 " " NAG H 1 " - " ASN A 378 " " NAG I 1 " - " ASN A 412 " " NAG J 1 " - " ASN B 67 " " NAG K 1 " - " ASN B 275 " " NAG L 1 " - " ASN B 378 " " NAG M 1 " - " ASN B 412 " " NAG N 1 " - " ASN B 546 " " NAG O 1 " - " ASN B 751 " " NAG P 1 " - " ASN C 67 " " NAG Q 1 " - " ASN C 378 " " NAG R 1 " - " ASN C 546 " " NAG S 1 " - " ASN D 275 " " NAG T 1 " - " ASN D 378 " " NAG U 1 " - " ASN D 412 " " NAG V 1 " - " ASN D 546 " " NAG W 1 " - " ASN D 751 " Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.4 seconds 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7456 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 57 sheets defined 39.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.578A pdb=" N VAL A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.934A pdb=" N ASN A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 167 removed outlier: 3.639A pdb=" N GLN A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.882A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 244 removed outlier: 3.519A pdb=" N ALA A 236 " --> pdb=" O HIS A 232 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.515A pdb=" N ALA A 263 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 298 removed outlier: 3.511A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.635A pdb=" N LEU A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.590A pdb=" N ASP A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.607A pdb=" N VAL A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.550A pdb=" N MET A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 630 through 665 removed outlier: 3.943A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 675 Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.613A pdb=" N PHE A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 712 removed outlier: 3.555A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 739 through 746 removed outlier: 3.750A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 749 No H-bonds generated for 'chain 'A' and resid 747 through 749' Processing helix chain 'A' and resid 773 through 788 removed outlier: 4.232A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 821 through 853 removed outlier: 3.541A pdb=" N LEU A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 846 " --> pdb=" O PHE A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 867 removed outlier: 3.604A pdb=" N GLU A 863 " --> pdb=" O SER A 859 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU A 865 " --> pdb=" O MET A 861 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 866 " --> pdb=" O VAL A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.577A pdb=" N VAL B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 102 Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.933A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 167 removed outlier: 3.639A pdb=" N GLN B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.880A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 244 removed outlier: 3.520A pdb=" N ALA B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 removed outlier: 3.515A pdb=" N ALA B 263 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.511A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.636A pdb=" N LEU B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.589A pdb=" N ASP B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.608A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 560 through 584 removed outlier: 3.550A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 575 " --> pdb=" O CYS B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 630 through 659 removed outlier: 3.942A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 647 " --> pdb=" O PHE B 643 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 Processing helix chain 'B' and resid 688 through 697 removed outlier: 3.614A pdb=" N PHE B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 712 removed outlier: 3.556A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 729 Processing helix chain 'B' and resid 739 through 746 removed outlier: 3.750A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 749 No H-bonds generated for 'chain 'B' and resid 747 through 749' Processing helix chain 'B' and resid 773 through 788 removed outlier: 4.232A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 821 through 850 removed outlier: 3.541A pdb=" N LEU B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 846 " --> pdb=" O PHE B 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.577A pdb=" N VAL C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.933A pdb=" N ASN C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 167 removed outlier: 3.639A pdb=" N GLN C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.881A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 244 removed outlier: 3.519A pdb=" N ALA C 236 " --> pdb=" O HIS C 232 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 removed outlier: 3.515A pdb=" N ALA C 263 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 removed outlier: 3.510A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.636A pdb=" N LEU C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.589A pdb=" N ASP C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.608A pdb=" N VAL C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 560 through 584 removed outlier: 3.550A pdb=" N MET C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 568 " --> pdb=" O TRP C 564 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 Processing helix chain 'C' and resid 630 through 665 removed outlier: 3.943A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 647 " --> pdb=" O PHE C 643 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER C 650 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 675 Processing helix chain 'C' and resid 688 through 697 removed outlier: 3.614A pdb=" N PHE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 712 removed outlier: 3.556A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 711 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 729 Processing helix chain 'C' and resid 739 through 746 removed outlier: 3.749A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 749 No H-bonds generated for 'chain 'C' and resid 747 through 749' Processing helix chain 'C' and resid 773 through 788 removed outlier: 4.232A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 794 through 799 Processing helix chain 'C' and resid 821 through 853 removed outlier: 3.541A pdb=" N LEU C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 846 " --> pdb=" O PHE C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 868 removed outlier: 3.855A pdb=" N MET C 861 " --> pdb=" O PHE C 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.577A pdb=" N VAL D 61 " --> pdb=" O PHE D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 102 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.933A pdb=" N ASN D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 167 removed outlier: 3.638A pdb=" N GLN D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.880A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 244 removed outlier: 3.519A pdb=" N ALA D 236 " --> pdb=" O HIS D 232 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 removed outlier: 3.515A pdb=" N ALA D 263 " --> pdb=" O ASP D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 298 removed outlier: 3.510A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.635A pdb=" N LEU D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 Processing helix chain 'D' and resid 461 through 475 removed outlier: 3.590A pdb=" N ASP D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.609A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 560 through 584 removed outlier: 3.549A pdb=" N MET D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 Processing helix chain 'D' and resid 630 through 659 removed outlier: 3.942A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 647 " --> pdb=" O PHE D 643 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER D 650 " --> pdb=" O ILE D 646 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 675 Processing helix chain 'D' and resid 688 through 697 removed outlier: 3.614A pdb=" N PHE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE D 694 " --> pdb=" O THR D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 712 removed outlier: 3.555A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 739 through 746 removed outlier: 3.750A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 749 No H-bonds generated for 'chain 'D' and resid 747 through 749' Processing helix chain 'D' and resid 773 through 788 removed outlier: 4.233A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 794 through 799 Processing helix chain 'D' and resid 821 through 850 removed outlier: 3.540A pdb=" N LEU D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 846 " --> pdb=" O PHE D 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.632A pdb=" N CYS E 100 " --> pdb=" O SER E 97 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG E 101 " --> pdb=" O PHE E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 191 through 196 Processing helix chain 'E' and resid 247 through 251 removed outlier: 3.809A pdb=" N ASN E 250 " --> pdb=" O ALA E 247 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU E 251 " --> pdb=" O ILE E 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 247 through 251' Processing helix chain 'E' and resid 278 through 281 removed outlier: 4.053A pdb=" N ARG E 281 " --> pdb=" O GLU E 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 278 through 281' Processing helix chain 'E' and resid 311 through 315 Processing helix chain 'E' and resid 346 through 372 removed outlier: 4.105A pdb=" N ILE E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR E 354 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE E 363 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 371 " --> pdb=" O LEU E 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.632A pdb=" N CYS F 100 " --> pdb=" O SER F 97 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG F 101 " --> pdb=" O PHE F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'F' and resid 247 through 251 removed outlier: 3.810A pdb=" N ASN F 250 " --> pdb=" O ALA F 247 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU F 251 " --> pdb=" O ILE F 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 247 through 251' Processing helix chain 'F' and resid 278 through 281 removed outlier: 4.054A pdb=" N ARG F 281 " --> pdb=" O GLU F 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 278 through 281' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 346 through 372 removed outlier: 4.104A pdb=" N ILE F 350 " --> pdb=" O THR F 346 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR F 354 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 363 " --> pdb=" O LEU F 359 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS F 371 " --> pdb=" O LEU F 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 43 removed outlier: 6.084A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASP A 79 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLN A 81 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.594A pdb=" N TYR A 176 " --> pdb=" O ARG A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 228 removed outlier: 6.431A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 406 removed outlier: 3.714A pdb=" N ASP A 406 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 436 through 437 removed outlier: 3.700A pdb=" N THR A 437 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA8, first strand: chain 'A' and resid 491 through 492 removed outlier: 3.698A pdb=" N GLN A 497 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AB1, first strand: chain 'A' and resid 535 through 536 removed outlier: 3.706A pdb=" N LEU A 536 " --> pdb=" O LYS A 762 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 736 through 738 removed outlier: 3.863A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 684 through 685 removed outlier: 6.140A pdb=" N ALA A 684 " --> pdb=" O VAL A 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 35 through 43 removed outlier: 6.083A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AB6, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.594A pdb=" N TYR B 176 " --> pdb=" O ARG B 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 225 through 228 removed outlier: 6.432A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 405 through 406 removed outlier: 3.714A pdb=" N ASP B 406 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 432 through 433 Processing sheet with id=AC1, first strand: chain 'B' and resid 436 through 437 removed outlier: 3.699A pdb=" N THR B 437 " --> pdb=" O ARG B 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AC3, first strand: chain 'B' and resid 491 through 492 removed outlier: 3.697A pdb=" N GLN B 497 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AC5, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.707A pdb=" N LEU B 536 " --> pdb=" O LYS B 762 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 736 through 738 removed outlier: 3.864A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 684 through 685 removed outlier: 6.140A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 35 through 43 removed outlier: 6.084A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD1, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.593A pdb=" N TYR C 176 " --> pdb=" O ARG C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 225 through 228 removed outlier: 6.431A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 405 through 406 removed outlier: 3.714A pdb=" N ASP C 406 " --> pdb=" O GLY C 410 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 436 through 437 removed outlier: 3.700A pdb=" N THR C 437 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AD6, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.697A pdb=" N GLN C 497 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AD8, first strand: chain 'C' and resid 535 through 536 removed outlier: 3.707A pdb=" N LEU C 536 " --> pdb=" O LYS C 762 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 736 through 738 removed outlier: 3.864A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 684 through 685 removed outlier: 6.140A pdb=" N ALA C 684 " --> pdb=" O VAL C 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 35 through 43 removed outlier: 6.084A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 130 through 131 Processing sheet with id=AE4, first strand: chain 'D' and resid 175 through 176 removed outlier: 3.593A pdb=" N TYR D 176 " --> pdb=" O ARG D 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 225 through 228 removed outlier: 6.431A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 405 through 406 removed outlier: 3.713A pdb=" N ASP D 406 " --> pdb=" O GLY D 410 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 436 through 437 removed outlier: 3.699A pdb=" N THR D 437 " --> pdb=" O ARG D 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AE9, first strand: chain 'D' and resid 491 through 492 removed outlier: 3.697A pdb=" N GLN D 497 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AF2, first strand: chain 'D' and resid 535 through 536 removed outlier: 3.706A pdb=" N LEU D 536 " --> pdb=" O LYS D 762 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 736 through 738 removed outlier: 3.863A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 684 through 685 removed outlier: 6.140A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.907A pdb=" N MET E 137 " --> pdb=" O LEU E 76 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 178 through 181 removed outlier: 5.937A pdb=" N PHE E 179 " --> pdb=" O THR E 210 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS E 212 " --> pdb=" O PHE E 179 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU E 181 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS E 207 " --> pdb=" O MET E 274 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA E 253 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 185 through 189 removed outlier: 3.994A pdb=" N GLY E 186 " --> pdb=" O PHE E 289 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE E 289 " --> pdb=" O GLY E 186 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 185 through 189 removed outlier: 3.994A pdb=" N GLY E 186 " --> pdb=" O PHE E 289 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE E 289 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ARG E 284 " --> pdb=" O TYR E 226 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR E 226 " --> pdb=" O ARG E 284 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG E 286 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.907A pdb=" N MET F 137 " --> pdb=" O LEU F 76 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 178 through 181 removed outlier: 5.937A pdb=" N PHE F 179 " --> pdb=" O THR F 210 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS F 212 " --> pdb=" O PHE F 179 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU F 181 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS F 207 " --> pdb=" O MET F 274 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA F 253 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 185 through 189 removed outlier: 3.994A pdb=" N GLY F 186 " --> pdb=" O PHE F 289 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE F 289 " --> pdb=" O GLY F 186 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 185 through 189 removed outlier: 3.994A pdb=" N GLY F 186 " --> pdb=" O PHE F 289 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE F 289 " --> pdb=" O GLY F 186 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG F 284 " --> pdb=" O TYR F 226 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR F 226 " --> pdb=" O ARG F 284 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG F 286 " --> pdb=" O LEU F 224 " (cutoff:3.500A) 1010 hydrogen bonds defined for protein. 2898 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.92 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5271 1.31 - 1.44: 9237 1.44 - 1.57: 19182 1.57 - 1.70: 38 1.70 - 1.83: 322 Bond restraints: 34050 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.513 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C1 NAG A1007 " pdb=" O5 NAG A1007 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C21 POV C1003 " pdb=" O21 POV C1003 " ideal model delta sigma weight residual 1.330 1.427 -0.097 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C ILE F 174 " pdb=" N PRO F 175 " ideal model delta sigma weight residual 1.334 1.448 -0.114 2.34e-02 1.83e+03 2.36e+01 ... (remaining 34045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 44650 3.10 - 6.20: 1036 6.20 - 9.30: 190 9.30 - 12.40: 62 12.40 - 15.50: 12 Bond angle restraints: 45950 Sorted by residual: angle pdb=" O CYS A 804 " pdb=" C CYS A 804 " pdb=" N PRO A 805 " ideal model delta sigma weight residual 121.32 108.24 13.08 1.15e+00 7.56e-01 1.29e+02 angle pdb=" C PRO F 295 " pdb=" N PRO F 296 " pdb=" CA PRO F 296 " ideal model delta sigma weight residual 119.84 108.95 10.89 1.25e+00 6.40e-01 7.58e+01 angle pdb=" C PRO E 295 " pdb=" N PRO E 296 " pdb=" CA PRO E 296 " ideal model delta sigma weight residual 119.84 109.00 10.84 1.25e+00 6.40e-01 7.53e+01 angle pdb=" C ILE E 174 " pdb=" CA ILE E 174 " pdb=" CB ILE E 174 " ideal model delta sigma weight residual 110.85 119.53 -8.68 1.15e+00 7.56e-01 5.70e+01 angle pdb=" N PRO A 805 " pdb=" CA PRO A 805 " pdb=" C PRO A 805 " ideal model delta sigma weight residual 112.47 127.97 -15.50 2.06e+00 2.36e-01 5.66e+01 ... (remaining 45945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.74: 20608 33.74 - 67.48: 575 67.48 - 101.22: 183 101.22 - 134.97: 72 134.97 - 168.71: 2 Dihedral angle restraints: 21440 sinusoidal: 9848 harmonic: 11592 Sorted by residual: dihedral pdb=" CA TYR E 62 " pdb=" C TYR E 62 " pdb=" N PRO E 63 " pdb=" CA PRO E 63 " ideal model delta harmonic sigma weight residual -180.00 -58.02 -121.98 0 5.00e+00 4.00e-02 5.95e+02 dihedral pdb=" CA TYR F 62 " pdb=" C TYR F 62 " pdb=" N PRO F 63 " pdb=" CA PRO F 63 " ideal model delta harmonic sigma weight residual -180.00 -58.12 -121.88 0 5.00e+00 4.00e-02 5.94e+02 dihedral pdb=" CA ILE E 174 " pdb=" C ILE E 174 " pdb=" N PRO E 175 " pdb=" CA PRO E 175 " ideal model delta harmonic sigma weight residual -180.00 -88.33 -91.67 0 5.00e+00 4.00e-02 3.36e+02 ... (remaining 21437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 5133 0.189 - 0.377: 58 0.377 - 0.566: 7 0.566 - 0.754: 2 0.754 - 0.943: 3 Chirality restraints: 5203 Sorted by residual: chirality pdb=" C1 NAG C1005 " pdb=" ND2 ASN C 275 " pdb=" C2 NAG C1005 " pdb=" O5 NAG C1005 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" CB ILE E 174 " pdb=" CA ILE E 174 " pdb=" CG1 ILE E 174 " pdb=" CG2 ILE E 174 " both_signs ideal model delta sigma weight residual False 2.64 1.71 0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 67 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.73e+01 ... (remaining 5200 not shown) Planarity restraints: 5719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 804 " 0.090 2.00e-02 2.50e+03 1.69e-01 2.85e+02 pdb=" C CYS A 804 " -0.292 2.00e-02 2.50e+03 pdb=" O CYS A 804 " 0.115 2.00e-02 2.50e+03 pdb=" N PRO A 805 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 804 " 0.050 2.00e-02 2.50e+03 9.82e-02 9.64e+01 pdb=" C CYS D 804 " -0.170 2.00e-02 2.50e+03 pdb=" O CYS D 804 " 0.064 2.00e-02 2.50e+03 pdb=" N PRO D 805 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 804 " 0.042 2.00e-02 2.50e+03 8.19e-02 6.71e+01 pdb=" C CYS C 804 " -0.142 2.00e-02 2.50e+03 pdb=" O CYS C 804 " 0.053 2.00e-02 2.50e+03 pdb=" N PRO C 805 " 0.048 2.00e-02 2.50e+03 ... (remaining 5716 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 8002 2.78 - 3.31: 28112 3.31 - 3.84: 51585 3.84 - 4.37: 61120 4.37 - 4.90: 105153 Nonbonded interactions: 253972 Sorted by model distance: nonbonded pdb=" O THR E 298 " pdb=" OG1 THR E 301 " model vdw 2.255 3.040 nonbonded pdb=" O THR F 298 " pdb=" OG1 THR F 301 " model vdw 2.255 3.040 nonbonded pdb=" O PRO D 407 " pdb=" O4 MAN T 4 " model vdw 2.258 3.040 nonbonded pdb=" OG SER A 834 " pdb=" O SER D 632 " model vdw 2.287 3.040 nonbonded pdb=" OE1 GLU D 440 " pdb=" OH TYR D 488 " model vdw 2.292 3.040 ... (remaining 253967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 850 or resid 1008)) selection = (chain 'B' and (resid 33 through 850 or resid 1003)) selection = (chain 'C' and (resid 33 through 850 or resid 1007)) selection = (chain 'D' and (resid 33 through 850 or resid 1005)) } ncs_group { reference = (chain 'E' and resid 43 through 382) selection = (chain 'F' and resid 43 through 382) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'H' selection = chain 'L' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'N' selection = chain 'V' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.010 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.008 0.114 34138 Z= 0.393 Angle : 1.336 19.336 46192 Z= 0.699 Chirality : 0.064 0.943 5203 Planarity : 0.009 0.169 5687 Dihedral : 18.142 168.707 13918 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.48 % Favored : 90.07 % Rotamer: Outliers : 0.43 % Allowed : 5.11 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 4.71 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.85 (0.09), residues: 3986 helix: -4.44 (0.05), residues: 1488 sheet: -3.32 (0.20), residues: 572 loop : -3.54 (0.11), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 273 TYR 0.034 0.002 TYR A 733 PHE 0.021 0.002 PHE B 735 TRP 0.028 0.002 TRP D 353 HIS 0.014 0.002 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00798 (34050) covalent geometry : angle 1.27138 (45950) SS BOND : bond 0.00392 ( 22) SS BOND : angle 1.65057 ( 44) hydrogen bonds : bond 0.30190 ( 1006) hydrogen bonds : angle 10.11852 ( 2898) link_ALPHA1-3 : bond 0.01331 ( 4) link_ALPHA1-3 : angle 2.61759 ( 12) link_ALPHA1-6 : bond 0.01239 ( 4) link_ALPHA1-6 : angle 3.45224 ( 12) link_BETA1-3 : bond 0.00924 ( 2) link_BETA1-3 : angle 2.28738 ( 6) link_BETA1-4 : bond 0.01991 ( 24) link_BETA1-4 : angle 5.04227 ( 72) link_NAG-ASN : bond 0.01472 ( 32) link_NAG-ASN : angle 7.90746 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 943 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TYR cc_start: 0.7409 (m-80) cc_final: 0.7183 (m-80) REVERT: A 141 ASN cc_start: 0.8763 (t160) cc_final: 0.8169 (t0) REVERT: A 196 ASN cc_start: 0.8455 (t0) cc_final: 0.7954 (t0) REVERT: A 260 ASP cc_start: 0.8246 (m-30) cc_final: 0.7991 (m-30) REVERT: A 360 MET cc_start: 0.8622 (tpt) cc_final: 0.8402 (tpp) REVERT: A 376 THR cc_start: 0.8530 (t) cc_final: 0.8047 (m) REVERT: A 514 VAL cc_start: 0.9162 (t) cc_final: 0.8682 (m) REVERT: A 604 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7373 (t0) REVERT: A 626 LEU cc_start: 0.9172 (mt) cc_final: 0.8881 (mt) REVERT: A 827 LEU cc_start: 0.8753 (tp) cc_final: 0.8447 (tt) REVERT: A 863 GLU cc_start: 0.5850 (pt0) cc_final: 0.5196 (tp30) REVERT: A 867 MET cc_start: 0.7388 (mtm) cc_final: 0.7004 (mtm) REVERT: B 84 ASN cc_start: 0.8538 (t0) cc_final: 0.8172 (t0) REVERT: B 187 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7937 (mp0) REVERT: B 360 MET cc_start: 0.9027 (tpt) cc_final: 0.8670 (tpt) REVERT: B 400 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6996 (mt-10) REVERT: B 451 LYS cc_start: 0.8737 (pmmt) cc_final: 0.8205 (pttp) REVERT: B 482 LEU cc_start: 0.9022 (mt) cc_final: 0.8786 (mt) REVERT: B 589 TRP cc_start: 0.8334 (m100) cc_final: 0.7870 (m100) REVERT: B 794 MET cc_start: 0.8856 (mtt) cc_final: 0.8641 (mtp) REVERT: B 844 TYR cc_start: 0.7235 (t80) cc_final: 0.6962 (t80) REVERT: C 209 LYS cc_start: 0.8272 (mttt) cc_final: 0.7802 (tttm) REVERT: C 251 TYR cc_start: 0.7774 (m-80) cc_final: 0.7360 (m-80) REVERT: C 271 TYR cc_start: 0.7755 (m-80) cc_final: 0.7523 (m-80) REVERT: C 337 PHE cc_start: 0.7570 (t80) cc_final: 0.6665 (t80) REVERT: C 355 PHE cc_start: 0.7458 (m-80) cc_final: 0.7215 (m-80) REVERT: C 360 MET cc_start: 0.9084 (tpt) cc_final: 0.8802 (tpp) REVERT: C 397 GLU cc_start: 0.7153 (mp0) cc_final: 0.6890 (tm-30) REVERT: C 434 ILE cc_start: 0.8333 (pt) cc_final: 0.8110 (pt) REVERT: C 437 THR cc_start: 0.8962 (t) cc_final: 0.8757 (m) REVERT: C 609 LEU cc_start: 0.8636 (tp) cc_final: 0.7882 (mt) REVERT: D 241 GLN cc_start: 0.8369 (mt0) cc_final: 0.8143 (mt0) REVERT: D 271 TYR cc_start: 0.8070 (m-80) cc_final: 0.7749 (m-80) REVERT: D 437 THR cc_start: 0.9022 (t) cc_final: 0.8791 (m) REVERT: D 501 MET cc_start: 0.7886 (mtm) cc_final: 0.7623 (mtp) REVERT: D 646 ILE cc_start: 0.8202 (mm) cc_final: 0.8002 (mt) REVERT: D 794 MET cc_start: 0.8013 (mtt) cc_final: 0.7773 (mtt) REVERT: E 243 ASP cc_start: 0.6931 (t70) cc_final: 0.6615 (t0) REVERT: F 98 PHE cc_start: 0.6657 (t80) cc_final: 0.5981 (t80) REVERT: F 152 PHE cc_start: 0.7926 (p90) cc_final: 0.7064 (p90) REVERT: F 282 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7773 (tp) outliers start: 15 outliers final: 2 residues processed: 955 average time/residue: 0.2234 time to fit residues: 333.2442 Evaluate side-chains 485 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 481 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 282 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 495 ASN A 604 ASN A 747 GLN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN B 604 ASN B 819 ASN C 137 GLN C 141 ASN C 350 HIS C 381 ASN C 495 ASN C 497 GLN C 499 ASN C 549 ASN C 726 GLN C 749 ASN C 792 HIS D 81 GLN D 141 ASN D 350 HIS D 381 ASN D 495 ASN D 792 HIS D 819 ASN E 250 ASN E 307 ASN E 321 ASN E 329 ASN F 203 GLN F 305 HIS F 369 GLN F 372 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.163915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.124488 restraints weight = 52820.031| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.09 r_work: 0.3365 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34138 Z= 0.161 Angle : 0.819 18.379 46192 Z= 0.393 Chirality : 0.049 0.371 5203 Planarity : 0.006 0.091 5687 Dihedral : 19.437 153.382 6322 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.35 % Favored : 91.42 % Rotamer: Outliers : 2.81 % Allowed : 11.54 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 3.53 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.20 (0.11), residues: 3986 helix: -2.27 (0.10), residues: 1526 sheet: -3.06 (0.21), residues: 549 loop : -3.13 (0.12), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 748 TYR 0.031 0.002 TYR D 195 PHE 0.032 0.002 PHE B 555 TRP 0.021 0.001 TRP C 353 HIS 0.010 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00346 (34050) covalent geometry : angle 0.77189 (45950) SS BOND : bond 0.00638 ( 22) SS BOND : angle 2.65466 ( 44) hydrogen bonds : bond 0.04907 ( 1006) hydrogen bonds : angle 5.14059 ( 2898) link_ALPHA1-3 : bond 0.01799 ( 4) link_ALPHA1-3 : angle 1.93488 ( 12) link_ALPHA1-6 : bond 0.01684 ( 4) link_ALPHA1-6 : angle 2.74560 ( 12) link_BETA1-3 : bond 0.01002 ( 2) link_BETA1-3 : angle 2.47954 ( 6) link_BETA1-4 : bond 0.00955 ( 24) link_BETA1-4 : angle 3.41339 ( 72) link_NAG-ASN : bond 0.01028 ( 32) link_NAG-ASN : angle 4.85323 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 526 time to evaluate : 1.037 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 137 GLN cc_start: 0.7630 (tp-100) cc_final: 0.7346 (mm-40) REVERT: A 196 ASN cc_start: 0.8727 (t0) cc_final: 0.8110 (t0) REVERT: A 245 MET cc_start: 0.8126 (mpp) cc_final: 0.7683 (mtm) REVERT: A 260 ASP cc_start: 0.8378 (m-30) cc_final: 0.8016 (m-30) REVERT: A 298 MET cc_start: 0.7458 (ppp) cc_final: 0.7197 (ppp) REVERT: A 413 MET cc_start: 0.7960 (mmt) cc_final: 0.7714 (mmt) REVERT: A 428 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5495 (tp) REVERT: A 479 GLU cc_start: 0.6807 (tm-30) cc_final: 0.5754 (pp20) REVERT: A 565 MET cc_start: 0.8361 (mmt) cc_final: 0.8105 (mmm) REVERT: A 733 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6791 (t80) REVERT: A 851 GLN cc_start: 0.6717 (tt0) cc_final: 0.5003 (mp10) REVERT: A 854 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6452 (ptmm) REVERT: B 62 ASN cc_start: 0.8409 (m-40) cc_final: 0.8174 (m-40) REVERT: B 99 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8437 (mp) REVERT: B 187 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8099 (mp0) REVERT: B 400 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 451 LYS cc_start: 0.8663 (pmmt) cc_final: 0.8165 (pttp) REVERT: B 453 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5508 (tm) REVERT: B 581 ILE cc_start: 0.8508 (mm) cc_final: 0.8277 (mp) REVERT: B 589 TRP cc_start: 0.8442 (m100) cc_final: 0.7723 (m100) REVERT: B 611 SER cc_start: 0.9180 (m) cc_final: 0.8594 (t) REVERT: B 661 VAL cc_start: 0.8850 (t) cc_final: 0.8527 (m) REVERT: C 209 LYS cc_start: 0.8551 (mttt) cc_final: 0.7995 (tttm) REVERT: C 251 TYR cc_start: 0.8055 (m-80) cc_final: 0.7813 (m-80) REVERT: C 397 GLU cc_start: 0.7235 (mp0) cc_final: 0.6984 (tm-30) REVERT: C 590 TYR cc_start: 0.6840 (p90) cc_final: 0.6472 (p90) REVERT: D 209 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7568 (mmmt) REVERT: D 271 TYR cc_start: 0.8573 (m-80) cc_final: 0.8254 (m-80) REVERT: D 437 THR cc_start: 0.9106 (t) cc_final: 0.8648 (m) REVERT: D 612 PHE cc_start: 0.8230 (m-80) cc_final: 0.7982 (m-80) REVERT: D 629 LYS cc_start: 0.8502 (ptpp) cc_final: 0.8250 (ptmm) REVERT: D 646 ILE cc_start: 0.8649 (mm) cc_final: 0.8436 (mt) REVERT: D 677 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: D 794 MET cc_start: 0.8257 (mtt) cc_final: 0.8030 (mtm) REVERT: E 93 TYR cc_start: 0.7640 (t80) cc_final: 0.7319 (t80) REVERT: F 152 PHE cc_start: 0.7993 (p90) cc_final: 0.7465 (p90) REVERT: F 167 LEU cc_start: 0.7165 (pp) cc_final: 0.6921 (pp) REVERT: F 252 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7971 (mptt) REVERT: F 282 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7905 (tp) REVERT: F 307 ASN cc_start: 0.8135 (t0) cc_final: 0.7761 (t0) outliers start: 98 outliers final: 42 residues processed: 600 average time/residue: 0.1879 time to fit residues: 187.2452 Evaluate side-chains 468 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 417 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 456 ASN Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 456 ASN Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 381 ASN Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 456 ASN Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 677 GLN Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 73 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 350 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 356 optimal weight: 3.9990 chunk 309 optimal weight: 0.8980 chunk 326 optimal weight: 8.9990 chunk 119 optimal weight: 0.2980 chunk 180 optimal weight: 0.7980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 165 GLN C 350 HIS C 381 ASN C 818 GLN D 381 ASN D 749 ASN E 237 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN F 305 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.163763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.124615 restraints weight = 52707.312| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.18 r_work: 0.3358 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34138 Z= 0.133 Angle : 0.746 13.752 46192 Z= 0.352 Chirality : 0.047 0.398 5203 Planarity : 0.005 0.103 5687 Dihedral : 17.382 144.005 6320 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.85 % Favored : 91.95 % Rotamer: Outliers : 2.21 % Allowed : 14.07 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 4.12 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.12), residues: 3986 helix: -0.83 (0.12), residues: 1528 sheet: -2.94 (0.21), residues: 544 loop : -2.89 (0.12), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 184 TYR 0.020 0.001 TYR B 587 PHE 0.022 0.001 PHE D 476 TRP 0.025 0.001 TRP E 138 HIS 0.007 0.001 HIS E 305 Details of bonding type rmsd covalent geometry : bond 0.00275 (34050) covalent geometry : angle 0.69737 (45950) SS BOND : bond 0.00754 ( 22) SS BOND : angle 3.13087 ( 44) hydrogen bonds : bond 0.03971 ( 1006) hydrogen bonds : angle 4.40670 ( 2898) link_ALPHA1-3 : bond 0.02296 ( 4) link_ALPHA1-3 : angle 2.60694 ( 12) link_ALPHA1-6 : bond 0.02036 ( 4) link_ALPHA1-6 : angle 2.69692 ( 12) link_BETA1-3 : bond 0.01097 ( 2) link_BETA1-3 : angle 2.35014 ( 6) link_BETA1-4 : bond 0.01020 ( 24) link_BETA1-4 : angle 3.24618 ( 72) link_NAG-ASN : bond 0.00808 ( 32) link_NAG-ASN : angle 4.50595 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 494 time to evaluate : 1.208 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 137 GLN cc_start: 0.7651 (tp-100) cc_final: 0.7366 (mm-40) REVERT: A 196 ASN cc_start: 0.8751 (t0) cc_final: 0.8148 (t0) REVERT: A 218 MET cc_start: 0.8403 (mtp) cc_final: 0.8153 (mtp) REVERT: A 245 MET cc_start: 0.8005 (mpp) cc_final: 0.7620 (mtm) REVERT: A 260 ASP cc_start: 0.8417 (m-30) cc_final: 0.8026 (m-30) REVERT: A 428 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5561 (tp) REVERT: A 434 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.6945 (pt) REVERT: A 469 GLU cc_start: 0.8171 (tt0) cc_final: 0.7732 (tp30) REVERT: A 479 GLU cc_start: 0.6786 (tm-30) cc_final: 0.5726 (pp20) REVERT: A 565 MET cc_start: 0.8320 (mmt) cc_final: 0.8091 (mmm) REVERT: A 733 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6880 (t80) REVERT: A 851 GLN cc_start: 0.6704 (tt0) cc_final: 0.5090 (mp10) REVERT: B 184 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8149 (mtm180) REVERT: B 187 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8129 (mp0) REVERT: B 400 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7852 (mt-10) REVERT: B 451 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8277 (tttm) REVERT: B 453 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5518 (tm) REVERT: B 589 TRP cc_start: 0.8404 (m100) cc_final: 0.7663 (m100) REVERT: B 611 SER cc_start: 0.9167 (m) cc_final: 0.8718 (t) REVERT: C 209 LYS cc_start: 0.8623 (mttt) cc_final: 0.8130 (tttm) REVERT: C 566 TYR cc_start: 0.8534 (m-10) cc_final: 0.8331 (m-10) REVERT: C 743 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7901 (tt0) REVERT: D 209 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7509 (mmmt) REVERT: D 437 THR cc_start: 0.9125 (t) cc_final: 0.8685 (m) REVERT: D 469 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7676 (tt0) REVERT: D 629 LYS cc_start: 0.8480 (ptpp) cc_final: 0.8219 (ptmm) REVERT: D 709 MET cc_start: 0.8231 (mtp) cc_final: 0.7932 (mtm) REVERT: E 203 GLN cc_start: 0.7767 (tp40) cc_final: 0.6966 (pt0) REVERT: E 243 ASP cc_start: 0.8206 (t0) cc_final: 0.7861 (t70) REVERT: F 93 TYR cc_start: 0.6792 (t80) cc_final: 0.6452 (t80) REVERT: F 141 PHE cc_start: 0.6923 (t80) cc_final: 0.6698 (t80) REVERT: F 282 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7959 (tp) REVERT: F 307 ASN cc_start: 0.8159 (t0) cc_final: 0.7687 (t0) REVERT: F 365 SER cc_start: 0.9042 (m) cc_final: 0.8750 (p) outliers start: 77 outliers final: 42 residues processed: 546 average time/residue: 0.1962 time to fit residues: 176.2711 Evaluate side-chains 480 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 431 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 456 ASN Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 804 CYS Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 260 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 0.7980 chunk 391 optimal weight: 2.9990 chunk 269 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 67 optimal weight: 0.0170 chunk 64 optimal weight: 6.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS B 381 ASN ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN C 136 HIS C 350 HIS C 622 GLN C 749 ASN D 367 HIS D 749 ASN ** E 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 GLN F 104 HIS F 203 GLN F 321 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.162737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123436 restraints weight = 52447.866| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.15 r_work: 0.3342 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34138 Z= 0.130 Angle : 0.708 12.412 46192 Z= 0.333 Chirality : 0.046 0.337 5203 Planarity : 0.005 0.089 5687 Dihedral : 16.065 143.650 6320 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.10 % Favored : 91.75 % Rotamer: Outliers : 2.56 % Allowed : 14.44 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.13), residues: 3986 helix: -0.09 (0.13), residues: 1534 sheet: -2.83 (0.21), residues: 571 loop : -2.76 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 354 TYR 0.015 0.001 TYR B 86 PHE 0.022 0.001 PHE F 285 TRP 0.027 0.001 TRP E 138 HIS 0.007 0.001 HIS E 305 Details of bonding type rmsd covalent geometry : bond 0.00279 (34050) covalent geometry : angle 0.66573 (45950) SS BOND : bond 0.00343 ( 22) SS BOND : angle 2.11592 ( 44) hydrogen bonds : bond 0.03455 ( 1006) hydrogen bonds : angle 4.14092 ( 2898) link_ALPHA1-3 : bond 0.02329 ( 4) link_ALPHA1-3 : angle 2.63607 ( 12) link_ALPHA1-6 : bond 0.02054 ( 4) link_ALPHA1-6 : angle 2.79807 ( 12) link_BETA1-3 : bond 0.00927 ( 2) link_BETA1-3 : angle 2.20817 ( 6) link_BETA1-4 : bond 0.00913 ( 24) link_BETA1-4 : angle 3.15146 ( 72) link_NAG-ASN : bond 0.00894 ( 32) link_NAG-ASN : angle 4.15829 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 462 time to evaluate : 1.097 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 137 GLN cc_start: 0.7689 (tp-100) cc_final: 0.7445 (mm-40) REVERT: A 196 ASN cc_start: 0.8768 (t0) cc_final: 0.8172 (t0) REVERT: A 245 MET cc_start: 0.8070 (mpp) cc_final: 0.7657 (mtm) REVERT: A 260 ASP cc_start: 0.8394 (m-30) cc_final: 0.7982 (m-30) REVERT: A 428 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5597 (tp) REVERT: A 434 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7289 (pt) REVERT: A 469 GLU cc_start: 0.8184 (tt0) cc_final: 0.7940 (tp30) REVERT: A 479 GLU cc_start: 0.6793 (tm-30) cc_final: 0.5757 (pp20) REVERT: A 565 MET cc_start: 0.8323 (mmt) cc_final: 0.8092 (mmm) REVERT: A 670 SER cc_start: 0.8329 (t) cc_final: 0.8036 (p) REVERT: A 680 ILE cc_start: 0.6910 (OUTLIER) cc_final: 0.6559 (pt) REVERT: A 733 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.7144 (t80) REVERT: A 851 GLN cc_start: 0.6716 (tt0) cc_final: 0.5220 (mp10) REVERT: A 863 GLU cc_start: 0.7758 (tp30) cc_final: 0.7232 (tt0) REVERT: B 99 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8613 (mp) REVERT: B 154 SER cc_start: 0.8337 (m) cc_final: 0.8099 (p) REVERT: B 180 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8336 (m) REVERT: B 184 ARG cc_start: 0.8724 (mtm-85) cc_final: 0.7803 (mtm-85) REVERT: B 187 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8097 (mp0) REVERT: B 400 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7903 (mt-10) REVERT: B 453 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5451 (tm) REVERT: B 611 SER cc_start: 0.9205 (m) cc_final: 0.8774 (t) REVERT: B 664 MET cc_start: 0.8470 (mtp) cc_final: 0.8253 (mtp) REVERT: C 209 LYS cc_start: 0.8636 (mttt) cc_final: 0.8157 (tttm) REVERT: C 367 HIS cc_start: 0.8224 (m90) cc_final: 0.7807 (m90) REVERT: C 566 TYR cc_start: 0.8551 (m-10) cc_final: 0.8325 (m-10) REVERT: C 590 TYR cc_start: 0.6789 (p90) cc_final: 0.6340 (p90) REVERT: C 682 TYR cc_start: 0.7357 (m-80) cc_final: 0.7149 (m-80) REVERT: C 743 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7903 (tt0) REVERT: D 209 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7495 (mmmt) REVERT: D 437 THR cc_start: 0.9125 (t) cc_final: 0.8731 (m) REVERT: D 469 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7583 (tt0) REVERT: D 691 MET cc_start: 0.8311 (tmm) cc_final: 0.8071 (tmm) REVERT: E 101 ARG cc_start: 0.8351 (ptt180) cc_final: 0.7825 (ptt90) REVERT: E 136 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.5290 (m-10) REVERT: E 203 GLN cc_start: 0.7720 (tp40) cc_final: 0.6944 (pt0) REVERT: E 243 ASP cc_start: 0.8230 (t0) cc_final: 0.7944 (t70) REVERT: E 298 THR cc_start: 0.5461 (p) cc_final: 0.5078 (t) REVERT: E 333 GLU cc_start: 0.6864 (mp0) cc_final: 0.5050 (pt0) REVERT: F 89 ASP cc_start: 0.6478 (t0) cc_final: 0.6262 (p0) REVERT: F 141 PHE cc_start: 0.6824 (t80) cc_final: 0.6390 (t80) REVERT: F 166 TYR cc_start: 0.5994 (p90) cc_final: 0.5774 (p90) REVERT: F 167 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6293 (pp) REVERT: F 282 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7913 (tp) REVERT: F 307 ASN cc_start: 0.8269 (t0) cc_final: 0.7739 (t0) REVERT: F 365 SER cc_start: 0.8954 (m) cc_final: 0.8712 (p) outliers start: 89 outliers final: 47 residues processed: 527 average time/residue: 0.1828 time to fit residues: 162.0487 Evaluate side-chains 478 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 420 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain B residue 804 CYS Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 190 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 177 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 130 optimal weight: 0.0270 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS C 818 GLN E 305 HIS F 192 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119621 restraints weight = 52129.364| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.09 r_work: 0.3291 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34138 Z= 0.128 Angle : 0.701 12.091 46192 Z= 0.326 Chirality : 0.046 0.360 5203 Planarity : 0.005 0.079 5687 Dihedral : 15.094 141.919 6320 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.85 % Favored : 92.02 % Rotamer: Outliers : 2.67 % Allowed : 14.33 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.13), residues: 3986 helix: 0.42 (0.14), residues: 1530 sheet: -2.70 (0.21), residues: 563 loop : -2.66 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 66 TYR 0.015 0.001 TYR B 86 PHE 0.023 0.001 PHE F 285 TRP 0.026 0.001 TRP E 138 HIS 0.025 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00277 (34050) covalent geometry : angle 0.65633 (45950) SS BOND : bond 0.00343 ( 22) SS BOND : angle 2.60304 ( 44) hydrogen bonds : bond 0.03273 ( 1006) hydrogen bonds : angle 4.00530 ( 2898) link_ALPHA1-3 : bond 0.02617 ( 4) link_ALPHA1-3 : angle 2.88667 ( 12) link_ALPHA1-6 : bond 0.02016 ( 4) link_ALPHA1-6 : angle 2.83794 ( 12) link_BETA1-3 : bond 0.01321 ( 2) link_BETA1-3 : angle 2.34638 ( 6) link_BETA1-4 : bond 0.00891 ( 24) link_BETA1-4 : angle 3.18411 ( 72) link_NAG-ASN : bond 0.01054 ( 32) link_NAG-ASN : angle 4.13926 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 436 time to evaluate : 1.129 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 196 ASN cc_start: 0.8773 (t0) cc_final: 0.8181 (t0) REVERT: A 245 MET cc_start: 0.8091 (mpp) cc_final: 0.7706 (mtm) REVERT: A 260 ASP cc_start: 0.8455 (m-30) cc_final: 0.8036 (m-30) REVERT: A 428 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5558 (tp) REVERT: A 565 MET cc_start: 0.8373 (mmt) cc_final: 0.8146 (mmm) REVERT: A 670 SER cc_start: 0.8329 (t) cc_final: 0.8022 (p) REVERT: A 733 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.7327 (t80) REVERT: A 851 GLN cc_start: 0.6810 (tt0) cc_final: 0.5357 (mp10) REVERT: A 863 GLU cc_start: 0.7337 (tp30) cc_final: 0.7093 (tt0) REVERT: B 78 TYR cc_start: 0.7981 (p90) cc_final: 0.7731 (p90) REVERT: B 99 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8588 (mp) REVERT: B 112 SER cc_start: 0.9054 (OUTLIER) cc_final: 0.8628 (t) REVERT: B 154 SER cc_start: 0.8333 (m) cc_final: 0.8111 (p) REVERT: B 187 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8087 (mp0) REVERT: B 400 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7935 (mt-10) REVERT: B 611 SER cc_start: 0.9237 (m) cc_final: 0.8838 (t) REVERT: B 664 MET cc_start: 0.8478 (mtp) cc_final: 0.8188 (mtp) REVERT: C 209 LYS cc_start: 0.8641 (mttt) cc_final: 0.8219 (tttm) REVERT: C 566 TYR cc_start: 0.8530 (m-10) cc_final: 0.8276 (m-10) REVERT: C 590 TYR cc_start: 0.6751 (p90) cc_final: 0.6106 (p90) REVERT: C 743 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7955 (tt0) REVERT: D 55 LEU cc_start: 0.8890 (tp) cc_final: 0.8645 (mt) REVERT: D 262 PHE cc_start: 0.8439 (t80) cc_final: 0.7994 (p90) REVERT: D 437 THR cc_start: 0.9142 (t) cc_final: 0.8740 (m) REVERT: D 458 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7452 (ptt-90) REVERT: D 469 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7662 (tt0) REVERT: D 691 MET cc_start: 0.8312 (tmm) cc_final: 0.8068 (tmm) REVERT: E 72 CYS cc_start: 0.2899 (OUTLIER) cc_final: 0.2536 (m) REVERT: E 101 ARG cc_start: 0.8227 (ptt180) cc_final: 0.7631 (ptt90) REVERT: E 148 GLU cc_start: 0.6899 (tp30) cc_final: 0.6681 (tp30) REVERT: E 243 ASP cc_start: 0.8187 (t0) cc_final: 0.7984 (t70) REVERT: E 298 THR cc_start: 0.5789 (p) cc_final: 0.5439 (t) REVERT: E 333 GLU cc_start: 0.6767 (mp0) cc_final: 0.5026 (pt0) REVERT: E 359 LEU cc_start: 0.8646 (mt) cc_final: 0.8164 (mt) REVERT: F 166 TYR cc_start: 0.6084 (p90) cc_final: 0.5761 (p90) REVERT: F 167 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6120 (pp) REVERT: F 282 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7887 (tp) REVERT: F 307 ASN cc_start: 0.8266 (t0) cc_final: 0.7721 (t0) REVERT: F 365 SER cc_start: 0.8963 (m) cc_final: 0.8737 (p) outliers start: 93 outliers final: 52 residues processed: 498 average time/residue: 0.2006 time to fit residues: 166.8197 Evaluate side-chains 468 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 408 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 223 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 chunk 293 optimal weight: 0.0970 chunk 315 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 318 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS C 726 GLN C 818 GLN ** E 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN F 305 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.158327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.118738 restraints weight = 52450.452| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.99 r_work: 0.3271 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 34138 Z= 0.162 Angle : 0.702 11.737 46192 Z= 0.328 Chirality : 0.046 0.327 5203 Planarity : 0.005 0.082 5687 Dihedral : 14.354 136.531 6320 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.55 % Favored : 91.32 % Rotamer: Outliers : 2.81 % Allowed : 14.47 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.13), residues: 3986 helix: 0.69 (0.14), residues: 1528 sheet: -2.63 (0.21), residues: 602 loop : -2.63 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 349 TYR 0.018 0.001 TYR E 324 PHE 0.029 0.002 PHE E 112 TRP 0.025 0.001 TRP E 138 HIS 0.007 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00372 (34050) covalent geometry : angle 0.66314 (45950) SS BOND : bond 0.00495 ( 22) SS BOND : angle 2.18942 ( 44) hydrogen bonds : bond 0.03373 ( 1006) hydrogen bonds : angle 3.97104 ( 2898) link_ALPHA1-3 : bond 0.02559 ( 4) link_ALPHA1-3 : angle 2.84828 ( 12) link_ALPHA1-6 : bond 0.01888 ( 4) link_ALPHA1-6 : angle 2.84661 ( 12) link_BETA1-3 : bond 0.00736 ( 2) link_BETA1-3 : angle 2.15458 ( 6) link_BETA1-4 : bond 0.00886 ( 24) link_BETA1-4 : angle 2.95088 ( 72) link_NAG-ASN : bond 0.00909 ( 32) link_NAG-ASN : angle 3.93394 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 432 time to evaluate : 1.098 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 196 ASN cc_start: 0.8771 (t0) cc_final: 0.8188 (t0) REVERT: A 245 MET cc_start: 0.8101 (mpp) cc_final: 0.7825 (mtm) REVERT: A 260 ASP cc_start: 0.8501 (m-30) cc_final: 0.8100 (m-30) REVERT: A 428 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5524 (tp) REVERT: A 479 GLU cc_start: 0.6890 (tm-30) cc_final: 0.5984 (pp20) REVERT: A 565 MET cc_start: 0.8396 (mmt) cc_final: 0.8177 (mmm) REVERT: A 670 SER cc_start: 0.8338 (t) cc_final: 0.8082 (p) REVERT: A 851 GLN cc_start: 0.6715 (tt0) cc_final: 0.5349 (mp10) REVERT: A 863 GLU cc_start: 0.7352 (tp30) cc_final: 0.6926 (tt0) REVERT: B 78 TYR cc_start: 0.8042 (p90) cc_final: 0.7824 (p90) REVERT: B 99 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8636 (mp) REVERT: B 112 SER cc_start: 0.9128 (OUTLIER) cc_final: 0.8752 (t) REVERT: B 187 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7992 (mp0) REVERT: B 400 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7984 (mt-10) REVERT: B 611 SER cc_start: 0.9212 (m) cc_final: 0.8839 (t) REVERT: C 566 TYR cc_start: 0.8601 (m-10) cc_final: 0.8390 (m-10) REVERT: C 696 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8416 (ttpt) REVERT: C 743 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8046 (tt0) REVERT: D 170 LYS cc_start: 0.8689 (mptt) cc_final: 0.8285 (mttp) REVERT: D 262 PHE cc_start: 0.8440 (t80) cc_final: 0.7987 (p90) REVERT: D 469 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7813 (tt0) REVERT: D 718 VAL cc_start: 0.7941 (OUTLIER) cc_final: 0.7700 (p) REVERT: E 72 CYS cc_start: 0.2648 (OUTLIER) cc_final: 0.2008 (m) REVERT: E 101 ARG cc_start: 0.8202 (ptt180) cc_final: 0.7577 (ptt90) REVERT: E 148 GLU cc_start: 0.7042 (tp30) cc_final: 0.6829 (tp30) REVERT: E 203 GLN cc_start: 0.7711 (tp40) cc_final: 0.6901 (pt0) REVERT: E 298 THR cc_start: 0.5898 (p) cc_final: 0.5534 (t) REVERT: E 333 GLU cc_start: 0.6896 (mp0) cc_final: 0.5096 (pt0) REVERT: F 141 PHE cc_start: 0.7026 (t80) cc_final: 0.6529 (t80) REVERT: F 166 TYR cc_start: 0.6048 (p90) cc_final: 0.5690 (p90) REVERT: F 282 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7899 (tp) REVERT: F 307 ASN cc_start: 0.8397 (t0) cc_final: 0.7882 (t0) REVERT: F 365 SER cc_start: 0.8992 (m) cc_final: 0.8730 (p) outliers start: 98 outliers final: 54 residues processed: 493 average time/residue: 0.2011 time to fit residues: 165.1548 Evaluate side-chains 457 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 397 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 347 HIS Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 156 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 310 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 166 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 253 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 252 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 ASN B 350 HIS C 350 HIS C 456 ASN D 335 GLN E 82 GLN ** E 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119223 restraints weight = 52511.531| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.17 r_work: 0.3280 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34138 Z= 0.126 Angle : 0.683 11.728 46192 Z= 0.319 Chirality : 0.045 0.309 5203 Planarity : 0.005 0.083 5687 Dihedral : 13.869 132.401 6320 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.08 % Favored : 91.87 % Rotamer: Outliers : 2.33 % Allowed : 15.33 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.13), residues: 3986 helix: 0.97 (0.14), residues: 1527 sheet: -2.54 (0.21), residues: 593 loop : -2.55 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 66 TYR 0.018 0.001 TYR E 324 PHE 0.033 0.001 PHE F 152 TRP 0.021 0.001 TRP E 138 HIS 0.010 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00276 (34050) covalent geometry : angle 0.64504 (45950) SS BOND : bond 0.00417 ( 22) SS BOND : angle 2.14987 ( 44) hydrogen bonds : bond 0.03138 ( 1006) hydrogen bonds : angle 3.86368 ( 2898) link_ALPHA1-3 : bond 0.02688 ( 4) link_ALPHA1-3 : angle 3.01191 ( 12) link_ALPHA1-6 : bond 0.02003 ( 4) link_ALPHA1-6 : angle 2.85765 ( 12) link_BETA1-3 : bond 0.00784 ( 2) link_BETA1-3 : angle 2.12364 ( 6) link_BETA1-4 : bond 0.00883 ( 24) link_BETA1-4 : angle 2.87170 ( 72) link_NAG-ASN : bond 0.00927 ( 32) link_NAG-ASN : angle 3.80548 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 409 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.8750 (t0) cc_final: 0.8184 (t0) REVERT: A 245 MET cc_start: 0.8132 (mpp) cc_final: 0.7737 (mtt) REVERT: A 260 ASP cc_start: 0.8494 (m-30) cc_final: 0.8103 (m-30) REVERT: A 428 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5532 (tp) REVERT: A 479 GLU cc_start: 0.6872 (tm-30) cc_final: 0.6030 (pp20) REVERT: A 565 MET cc_start: 0.8395 (mmt) cc_final: 0.8169 (mmm) REVERT: A 670 SER cc_start: 0.8252 (t) cc_final: 0.8036 (p) REVERT: A 851 GLN cc_start: 0.6700 (tt0) cc_final: 0.5378 (mp10) REVERT: A 863 GLU cc_start: 0.7444 (tp30) cc_final: 0.7033 (tt0) REVERT: B 78 TYR cc_start: 0.8026 (p90) cc_final: 0.7825 (p90) REVERT: B 99 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8634 (mp) REVERT: B 112 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8787 (t) REVERT: B 187 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7966 (mp0) REVERT: B 400 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8004 (mt-10) REVERT: B 611 SER cc_start: 0.9214 (m) cc_final: 0.8839 (t) REVERT: B 722 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7996 (mp0) REVERT: C 566 TYR cc_start: 0.8588 (m-10) cc_final: 0.8322 (m-10) REVERT: C 613 TRP cc_start: 0.7489 (t-100) cc_final: 0.7004 (t-100) REVERT: C 696 LYS cc_start: 0.8878 (ttpp) cc_final: 0.8415 (ttpt) REVERT: C 743 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8060 (tt0) REVERT: D 170 LYS cc_start: 0.8690 (mptt) cc_final: 0.8292 (mttp) REVERT: D 262 PHE cc_start: 0.8429 (t80) cc_final: 0.8033 (p90) REVERT: D 509 LYS cc_start: 0.8481 (mtpm) cc_final: 0.8255 (mttt) REVERT: D 718 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7609 (p) REVERT: E 72 CYS cc_start: 0.2410 (OUTLIER) cc_final: 0.1878 (m) REVERT: E 101 ARG cc_start: 0.8178 (ptt180) cc_final: 0.7921 (ptt180) REVERT: E 203 GLN cc_start: 0.7719 (tp40) cc_final: 0.6890 (pt0) REVERT: E 243 ASP cc_start: 0.8430 (t70) cc_final: 0.7742 (t0) REVERT: E 333 GLU cc_start: 0.6856 (mp0) cc_final: 0.5127 (pt0) REVERT: E 378 MET cc_start: 0.3860 (mmt) cc_final: 0.3466 (mmm) REVERT: F 166 TYR cc_start: 0.6071 (p90) cc_final: 0.5766 (p90) REVERT: F 167 LEU cc_start: 0.6197 (pp) cc_final: 0.5922 (pp) REVERT: F 282 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7891 (tp) REVERT: F 307 ASN cc_start: 0.8400 (t0) cc_final: 0.8140 (t0) REVERT: F 365 SER cc_start: 0.8979 (m) cc_final: 0.8727 (p) outliers start: 81 outliers final: 55 residues processed: 461 average time/residue: 0.1947 time to fit residues: 151.4700 Evaluate side-chains 446 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 385 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 605 ASN Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 487 LYS Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 353 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 351 optimal weight: 10.0000 chunk 296 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 354 optimal weight: 1.9990 chunk 214 optimal weight: 0.6980 chunk 370 optimal weight: 20.0000 chunk 143 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN B 350 HIS ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 350 HIS C 456 ASN ** E 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.157597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118119 restraints weight = 52651.076| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.97 r_work: 0.3293 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34138 Z= 0.166 Angle : 0.701 11.794 46192 Z= 0.328 Chirality : 0.046 0.315 5203 Planarity : 0.005 0.086 5687 Dihedral : 13.517 124.181 6320 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.03 % Favored : 90.92 % Rotamer: Outliers : 2.47 % Allowed : 15.33 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3986 helix: 1.05 (0.14), residues: 1529 sheet: -2.52 (0.21), residues: 600 loop : -2.50 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 66 TYR 0.020 0.001 TYR F 121 PHE 0.027 0.001 PHE F 152 TRP 0.013 0.001 TRP E 138 HIS 0.004 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00386 (34050) covalent geometry : angle 0.66466 (45950) SS BOND : bond 0.00398 ( 22) SS BOND : angle 2.00226 ( 44) hydrogen bonds : bond 0.03278 ( 1006) hydrogen bonds : angle 3.93031 ( 2898) link_ALPHA1-3 : bond 0.02597 ( 4) link_ALPHA1-3 : angle 3.02750 ( 12) link_ALPHA1-6 : bond 0.01960 ( 4) link_ALPHA1-6 : angle 2.78813 ( 12) link_BETA1-3 : bond 0.00731 ( 2) link_BETA1-3 : angle 2.22408 ( 6) link_BETA1-4 : bond 0.00847 ( 24) link_BETA1-4 : angle 2.86159 ( 72) link_NAG-ASN : bond 0.00884 ( 32) link_NAG-ASN : angle 3.83592 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 401 time to evaluate : 1.336 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 196 ASN cc_start: 0.8724 (t0) cc_final: 0.8177 (t0) REVERT: A 245 MET cc_start: 0.8173 (mpp) cc_final: 0.7632 (mtt) REVERT: A 260 ASP cc_start: 0.8433 (m-30) cc_final: 0.8061 (m-30) REVERT: A 428 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5423 (tp) REVERT: A 479 GLU cc_start: 0.6993 (tm-30) cc_final: 0.6173 (pp20) REVERT: A 565 MET cc_start: 0.8376 (mmt) cc_final: 0.8169 (mmm) REVERT: A 818 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7716 (pp30) REVERT: A 851 GLN cc_start: 0.6780 (tt0) cc_final: 0.5471 (mp10) REVERT: A 852 LEU cc_start: 0.7699 (tp) cc_final: 0.7475 (mt) REVERT: A 863 GLU cc_start: 0.7631 (tp30) cc_final: 0.7075 (tt0) REVERT: B 99 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8734 (mp) REVERT: B 112 SER cc_start: 0.9067 (OUTLIER) cc_final: 0.8805 (t) REVERT: B 187 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7937 (mp0) REVERT: B 400 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7963 (mt-10) REVERT: B 569 LEU cc_start: 0.8728 (tp) cc_final: 0.8439 (tt) REVERT: B 611 SER cc_start: 0.9223 (m) cc_final: 0.8891 (t) REVERT: B 633 THR cc_start: 0.8658 (p) cc_final: 0.8374 (t) REVERT: C 566 TYR cc_start: 0.8623 (m-10) cc_final: 0.8402 (m-10) REVERT: C 613 TRP cc_start: 0.7469 (t-100) cc_final: 0.7055 (t-100) REVERT: C 696 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8464 (ttpp) REVERT: C 743 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8043 (tt0) REVERT: D 170 LYS cc_start: 0.8691 (mptt) cc_final: 0.8337 (mttp) REVERT: D 262 PHE cc_start: 0.8436 (t80) cc_final: 0.8061 (p90) REVERT: D 718 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7665 (p) REVERT: D 848 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7243 (mmmt) REVERT: E 72 CYS cc_start: 0.2359 (OUTLIER) cc_final: 0.1901 (m) REVERT: E 101 ARG cc_start: 0.8143 (ptt180) cc_final: 0.7859 (ptt180) REVERT: E 243 ASP cc_start: 0.8318 (t70) cc_final: 0.7606 (t0) REVERT: E 275 TRP cc_start: 0.8259 (t-100) cc_final: 0.7948 (t-100) REVERT: E 298 THR cc_start: 0.6088 (p) cc_final: 0.5743 (t) REVERT: E 333 GLU cc_start: 0.6810 (mp0) cc_final: 0.4992 (pt0) REVERT: F 166 TYR cc_start: 0.5968 (p90) cc_final: 0.5672 (p90) REVERT: F 167 LEU cc_start: 0.6106 (pp) cc_final: 0.5811 (pp) REVERT: F 282 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7897 (tp) REVERT: F 365 SER cc_start: 0.8986 (m) cc_final: 0.8762 (p) outliers start: 86 outliers final: 62 residues processed: 456 average time/residue: 0.1956 time to fit residues: 150.3889 Evaluate side-chains 446 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 376 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 605 ASN Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 487 LYS Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 848 LYS Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 347 HIS Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 21 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 276 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 377 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 379 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS C 818 GLN ** E 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** 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 = 0.4006 r_free = 0.4006 target = 0.157816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118033 restraints weight = 52535.085| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.99 r_work: 0.3263 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34138 Z= 0.141 Angle : 0.705 18.944 46192 Z= 0.327 Chirality : 0.046 0.431 5203 Planarity : 0.005 0.086 5687 Dihedral : 13.202 116.500 6320 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.40 % Favored : 91.55 % Rotamer: Outliers : 2.30 % Allowed : 15.76 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.14), residues: 3986 helix: 1.19 (0.14), residues: 1529 sheet: -2.46 (0.21), residues: 587 loop : -2.44 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 66 TYR 0.019 0.001 TYR E 324 PHE 0.030 0.001 PHE F 152 TRP 0.016 0.001 TRP E 138 HIS 0.004 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00321 (34050) covalent geometry : angle 0.65770 (45950) SS BOND : bond 0.00422 ( 22) SS BOND : angle 2.24484 ( 44) hydrogen bonds : bond 0.03114 ( 1006) hydrogen bonds : angle 3.88980 ( 2898) link_ALPHA1-3 : bond 0.02791 ( 4) link_ALPHA1-3 : angle 3.13602 ( 12) link_ALPHA1-6 : bond 0.01969 ( 4) link_ALPHA1-6 : angle 2.76637 ( 12) link_BETA1-3 : bond 0.00662 ( 2) link_BETA1-3 : angle 2.21244 ( 6) link_BETA1-4 : bond 0.00922 ( 24) link_BETA1-4 : angle 2.82716 ( 72) link_NAG-ASN : bond 0.00885 ( 32) link_NAG-ASN : angle 4.61126 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 395 time to evaluate : 1.293 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 196 ASN cc_start: 0.8721 (t0) cc_final: 0.8153 (t0) REVERT: A 245 MET cc_start: 0.8134 (mpp) cc_final: 0.7667 (mtt) REVERT: A 260 ASP cc_start: 0.8480 (m-30) cc_final: 0.8094 (m-30) REVERT: A 428 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.5478 (tp) REVERT: A 479 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6122 (pp20) REVERT: A 565 MET cc_start: 0.8415 (mmt) cc_final: 0.8204 (mmm) REVERT: A 851 GLN cc_start: 0.6728 (tt0) cc_final: 0.5446 (mp10) REVERT: A 852 LEU cc_start: 0.7623 (tp) cc_final: 0.7410 (mt) REVERT: A 863 GLU cc_start: 0.7579 (tp30) cc_final: 0.7014 (tt0) REVERT: B 99 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8672 (mp) REVERT: B 112 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8849 (t) REVERT: B 187 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7893 (mp0) REVERT: B 400 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7978 (mt-10) REVERT: B 569 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8423 (tt) REVERT: B 611 SER cc_start: 0.9221 (m) cc_final: 0.8895 (t) REVERT: B 633 THR cc_start: 0.8646 (p) cc_final: 0.8346 (t) REVERT: C 346 GLN cc_start: 0.7413 (pm20) cc_final: 0.7109 (pm20) REVERT: C 566 TYR cc_start: 0.8597 (m-10) cc_final: 0.8370 (m-10) REVERT: C 613 TRP cc_start: 0.7445 (t-100) cc_final: 0.7042 (t-100) REVERT: C 696 LYS cc_start: 0.8891 (ttpp) cc_final: 0.8458 (ttpp) REVERT: C 743 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8008 (tt0) REVERT: D 170 LYS cc_start: 0.8707 (mptt) cc_final: 0.8285 (mttp) REVERT: D 262 PHE cc_start: 0.8454 (t80) cc_final: 0.8043 (p90) REVERT: D 509 LYS cc_start: 0.8395 (mtpm) cc_final: 0.8117 (mttt) REVERT: D 718 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7624 (p) REVERT: D 733 TYR cc_start: 0.8144 (t80) cc_final: 0.7735 (t80) REVERT: D 848 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7230 (mmmt) REVERT: E 72 CYS cc_start: 0.2490 (OUTLIER) cc_final: 0.1751 (m) REVERT: E 101 ARG cc_start: 0.8122 (ptt180) cc_final: 0.7833 (ptt180) REVERT: E 203 GLN cc_start: 0.7663 (tp40) cc_final: 0.6760 (pt0) REVERT: E 243 ASP cc_start: 0.8376 (t70) cc_final: 0.7674 (t0) REVERT: E 275 TRP cc_start: 0.8188 (t-100) cc_final: 0.7913 (t-100) REVERT: E 298 THR cc_start: 0.5879 (p) cc_final: 0.5518 (t) REVERT: E 333 GLU cc_start: 0.6922 (mp0) cc_final: 0.5160 (pt0) REVERT: E 378 MET cc_start: 0.3901 (mmt) cc_final: 0.3619 (mmt) REVERT: F 141 PHE cc_start: 0.7023 (t80) cc_final: 0.6668 (t80) REVERT: F 166 TYR cc_start: 0.5961 (p90) cc_final: 0.5661 (p90) REVERT: F 167 LEU cc_start: 0.6057 (pp) cc_final: 0.5753 (pp) REVERT: F 221 LEU cc_start: 0.8259 (mm) cc_final: 0.8053 (mt) REVERT: F 282 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7904 (tp) REVERT: F 307 ASN cc_start: 0.8417 (t0) cc_final: 0.8171 (t0) REVERT: F 365 SER cc_start: 0.8989 (m) cc_final: 0.8767 (p) outliers start: 80 outliers final: 64 residues processed: 445 average time/residue: 0.1862 time to fit residues: 140.2844 Evaluate side-chains 451 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 379 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 605 ASN Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 487 LYS Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 848 LYS Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 347 HIS Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 332 optimal weight: 5.9990 chunk 396 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 247 optimal weight: 3.9990 chunk 249 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 357 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN B 350 HIS ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS ** E 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** 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 = 0.4002 r_free = 0.4002 target = 0.157384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116884 restraints weight = 52719.935| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.19 r_work: 0.3237 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34138 Z= 0.148 Angle : 0.710 17.982 46192 Z= 0.330 Chirality : 0.046 0.329 5203 Planarity : 0.005 0.087 5687 Dihedral : 12.832 107.506 6320 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.86 % Favored : 91.09 % Rotamer: Outliers : 2.27 % Allowed : 16.08 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.14), residues: 3986 helix: 1.28 (0.14), residues: 1529 sheet: -2.41 (0.21), residues: 584 loop : -2.37 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 66 TYR 0.023 0.001 TYR A 733 PHE 0.031 0.001 PHE F 285 TRP 0.014 0.001 TRP E 138 HIS 0.004 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00340 (34050) covalent geometry : angle 0.66257 (45950) SS BOND : bond 0.00480 ( 22) SS BOND : angle 2.20176 ( 44) hydrogen bonds : bond 0.03116 ( 1006) hydrogen bonds : angle 3.87596 ( 2898) link_ALPHA1-3 : bond 0.02820 ( 4) link_ALPHA1-3 : angle 3.18306 ( 12) link_ALPHA1-6 : bond 0.01921 ( 4) link_ALPHA1-6 : angle 2.71882 ( 12) link_BETA1-3 : bond 0.00675 ( 2) link_BETA1-3 : angle 2.30412 ( 6) link_BETA1-4 : bond 0.00841 ( 24) link_BETA1-4 : angle 2.79503 ( 72) link_NAG-ASN : bond 0.00965 ( 32) link_NAG-ASN : angle 4.68841 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 395 time to evaluate : 1.131 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 196 ASN cc_start: 0.8715 (t0) cc_final: 0.8132 (t0) REVERT: A 245 MET cc_start: 0.8134 (mpp) cc_final: 0.7658 (mtt) REVERT: A 260 ASP cc_start: 0.8506 (m-30) cc_final: 0.8129 (m-30) REVERT: A 428 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5585 (tp) REVERT: A 479 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6148 (pp20) REVERT: A 492 ASP cc_start: 0.8287 (t70) cc_final: 0.7949 (t0) REVERT: A 565 MET cc_start: 0.8449 (mmt) cc_final: 0.8247 (mmm) REVERT: A 584 PHE cc_start: 0.8014 (t80) cc_final: 0.7672 (t80) REVERT: A 851 GLN cc_start: 0.6698 (tt0) cc_final: 0.5452 (mp10) REVERT: A 863 GLU cc_start: 0.7514 (tp30) cc_final: 0.6876 (tt0) REVERT: B 99 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8735 (mp) REVERT: B 112 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8875 (t) REVERT: B 187 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7919 (mp0) REVERT: B 400 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8070 (mt-10) REVERT: B 569 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8374 (tt) REVERT: B 611 SER cc_start: 0.9233 (m) cc_final: 0.8915 (t) REVERT: B 633 THR cc_start: 0.8692 (p) cc_final: 0.8398 (t) REVERT: C 346 GLN cc_start: 0.7360 (pm20) cc_final: 0.7124 (pm20) REVERT: C 566 TYR cc_start: 0.8597 (m-10) cc_final: 0.8370 (m-10) REVERT: C 613 TRP cc_start: 0.7490 (t-100) cc_final: 0.7036 (t-100) REVERT: C 669 ASP cc_start: 0.7971 (t70) cc_final: 0.7158 (t0) REVERT: C 743 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8063 (tt0) REVERT: D 170 LYS cc_start: 0.8741 (mptt) cc_final: 0.8299 (mttp) REVERT: D 262 PHE cc_start: 0.8534 (t80) cc_final: 0.8078 (p90) REVERT: D 509 LYS cc_start: 0.8397 (mtpm) cc_final: 0.8088 (mttt) REVERT: D 718 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7669 (p) REVERT: D 733 TYR cc_start: 0.8138 (t80) cc_final: 0.7740 (t80) REVERT: D 848 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6475 (tppt) REVERT: E 72 CYS cc_start: 0.2566 (OUTLIER) cc_final: 0.1894 (m) REVERT: E 203 GLN cc_start: 0.7694 (tp40) cc_final: 0.6760 (pt0) REVERT: E 243 ASP cc_start: 0.8370 (t70) cc_final: 0.7663 (t0) REVERT: E 298 THR cc_start: 0.5984 (p) cc_final: 0.5599 (t) REVERT: E 333 GLU cc_start: 0.6971 (mp0) cc_final: 0.5209 (pt0) REVERT: E 378 MET cc_start: 0.3942 (mmt) cc_final: 0.3605 (mmt) REVERT: F 141 PHE cc_start: 0.7044 (t80) cc_final: 0.6508 (t80) REVERT: F 166 TYR cc_start: 0.5961 (p90) cc_final: 0.5657 (p90) REVERT: F 167 LEU cc_start: 0.6024 (pp) cc_final: 0.5724 (pp) REVERT: F 282 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.7998 (tp) REVERT: F 365 SER cc_start: 0.8981 (m) cc_final: 0.8757 (p) outliers start: 79 outliers final: 65 residues processed: 442 average time/residue: 0.1808 time to fit residues: 135.4337 Evaluate side-chains 449 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 376 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 818 GLN Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 605 ASN Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 487 LYS Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 848 LYS Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 347 HIS Chi-restraints excluded: chain F residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 313 optimal weight: 2.9990 chunk 297 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 357 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 373 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN ** E 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** 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 = 0.4000 r_free = 0.4000 target = 0.157201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116828 restraints weight = 52689.835| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.15 r_work: 0.3248 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.390 34138 Z= 0.203 Angle : 0.838 59.187 46192 Z= 0.416 Chirality : 0.048 0.723 5203 Planarity : 0.005 0.087 5687 Dihedral : 12.831 107.502 6320 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.78 % Favored : 91.19 % Rotamer: Outliers : 2.33 % Allowed : 16.37 % Favored : 81.31 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.14), residues: 3986 helix: 1.28 (0.14), residues: 1529 sheet: -2.41 (0.21), residues: 584 loop : -2.36 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 66 TYR 0.016 0.001 TYR A 733 PHE 0.028 0.001 PHE F 285 TRP 0.013 0.001 TRP E 138 HIS 0.004 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00481 (34050) covalent geometry : angle 0.78728 (45950) SS BOND : bond 0.00689 ( 22) SS BOND : angle 4.81929 ( 44) hydrogen bonds : bond 0.03129 ( 1006) hydrogen bonds : angle 3.87556 ( 2898) link_ALPHA1-3 : bond 0.02722 ( 4) link_ALPHA1-3 : angle 3.20867 ( 12) link_ALPHA1-6 : bond 0.01737 ( 4) link_ALPHA1-6 : angle 2.73706 ( 12) link_BETA1-3 : bond 0.00659 ( 2) link_BETA1-3 : angle 2.30499 ( 6) link_BETA1-4 : bond 0.00835 ( 24) link_BETA1-4 : angle 2.80001 ( 72) link_NAG-ASN : bond 0.00957 ( 32) link_NAG-ASN : angle 4.69518 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8131.99 seconds wall clock time: 140 minutes 18.16 seconds (8418.16 seconds total)