Starting phenix.real_space_refine on Sun Aug 24 02:06:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tys_20584/08_2025/6tys_20584.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tys_20584/08_2025/6tys_20584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6tys_20584/08_2025/6tys_20584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tys_20584/08_2025/6tys_20584.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tys_20584/08_2025/6tys_20584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tys_20584/08_2025/6tys_20584.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.097 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: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 10149 2.51 5 N 2565 2.21 5 O 3252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16059 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3445 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 15, 'TRANS': 431} Chain breaks: 1 Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "B" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3445 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 15, 'TRANS': 431} Chain breaks: 1 Chain: "C" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "E" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3445 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 15, 'TRANS': 431} Chain breaks: 1 Chain: "F" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'BMA': 1, 'MAN': 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'BMA': 1, 'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'BMA': 1, 'MAN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.90, per 1000 atoms: 0.24 Number of scatterers: 16059 At special positions: 0 Unit cell: (145.22, 139.74, 124.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 3252 8.00 N 2565 7.00 C 10149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 119 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.02 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.02 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.05 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.06 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.15 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.09 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 119 " distance=2.04 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.02 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.02 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.05 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.06 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.15 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.09 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 192 " distance=2.04 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 119 " distance=2.04 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 340 " distance=2.02 Simple disulfide: pdb=" SG CYS E 355 " - pdb=" SG CYS E 363 " distance=2.02 Simple disulfide: pdb=" SG CYS E 387 " - pdb=" SG CYS E 392 " distance=2.05 Simple disulfide: pdb=" SG CYS E 394 " - pdb=" SG CYS E 417 " distance=2.06 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.15 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.09 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 ALPHA1-2 " BMA K 1 " - " MAN K 2 " " BMA P 1 " - " MAN P 2 " " BMA T 1 " - " MAN T 2 " ALPHA1-4 " NAG I 2 " - " MAN I 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG Q 2 " - " MAN Q 3 " " NAG R 2 " - " MAN R 3 " " NAG U 2 " - " MAN U 3 " ALPHA1-6 " BMA K 1 " - " MAN K 3 " " BMA P 1 " - " MAN P 3 " " BMA T 1 " - " MAN T 3 " BETA1-4 " NAG A 604 " - " NAG A 605 " " NAG B 604 " - " NAG B 605 " " NAG E 604 " - " NAG E 605 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA K 1 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA P 1 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA T 1 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 604 " - " ASN A 99 " " NAG B 604 " - " ASN B 99 " " NAG E 604 " - " ASN E 99 " " NAG I 1 " - " ASN A 67 " " NAG J 1 " - " ASN A 414 " " NAG M 1 " - " ASN A 464 " " NAG N 1 " - " ASN B 67 " " NAG O 1 " - " ASN B 414 " " NAG Q 1 " - " ASN B 464 " " NAG R 1 " - " ASN E 67 " " NAG S 1 " - " ASN E 414 " " NAG U 1 " - " ASN E 464 " Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 586.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 33 sheets defined 30.7% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 removed outlier: 4.270A pdb=" N LYS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 5.846A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 96 Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 125 through 137 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.736A pdb=" N SER A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 191 through 211 Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 452 through 480 removed outlier: 3.580A pdb=" N ASP A 472 " --> pdb=" O GLN A 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.270A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 5.846A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 96 Proline residue: B 89 - end of helix Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 125 through 137 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 147 through 153 removed outlier: 3.735A pdb=" N SER B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 191 through 211 Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 250 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 452 through 480 removed outlier: 3.580A pdb=" N ASP B 472 " --> pdb=" O GLN B 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 29 through 37 removed outlier: 4.270A pdb=" N LYS E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 removed outlier: 5.845A pdb=" N GLN E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR E 72 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 96 Proline residue: E 89 - end of helix Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 125 through 137 Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 147 through 153 removed outlier: 3.735A pdb=" N SER E 153 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 183 Processing helix chain 'E' and resid 184 through 187 Processing helix chain 'E' and resid 191 through 211 Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 233 through 236 Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'E' and resid 250 through 259 Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 349 through 357 Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 437 through 441 Processing helix chain 'E' and resid 452 through 480 removed outlier: 3.580A pdb=" N ASP E 472 " --> pdb=" O GLN E 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 12.870A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.576A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 7.059A pdb=" N MET A 115 " --> pdb=" O SER E 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 393 Processing sheet with id=AA8, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.811A pdb=" N MET H 34 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.798A pdb=" N LYS L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER L 67 " --> pdb=" O LYS L 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.550A pdb=" N GLN L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.550A pdb=" N GLN L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 158 through 162 removed outlier: 12.869A pdb=" N THR B 168 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASP B 56 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL B 338 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS B 45 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N CYS B 340 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS B 47 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.575A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU B 295 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR B 43 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 293 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS B 45 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ALA B 291 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE B 315 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 326 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AB8, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB9, first strand: chain 'B' and resid 392 through 393 Processing sheet with id=AC1, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.811A pdb=" N MET C 34 " --> pdb=" O MET C 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AC4, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.797A pdb=" N LYS D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 67 " --> pdb=" O LYS D 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.550A pdb=" N GLN D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.550A pdb=" N GLN D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 158 through 162 removed outlier: 12.870A pdb=" N THR E 168 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASP E 56 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TYR E 170 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL E 338 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS E 45 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N CYS E 340 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS E 47 " --> pdb=" O CYS E 340 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 264 through 270 removed outlier: 6.575A pdb=" N ILE E 277 " --> pdb=" O ILE E 267 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL E 269 " --> pdb=" O TYR E 275 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR E 275 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE E 284 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASN E 51 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR E 286 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS E 49 " --> pdb=" O THR E 286 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU E 295 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR E 43 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE E 293 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS E 45 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ALA E 291 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE E 315 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE E 326 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AD1, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.811A pdb=" N MET F 34 " --> pdb=" O MET F 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AD4, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.797A pdb=" N LYS G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 67 " --> pdb=" O LYS G 70 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.550A pdb=" N GLN G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.550A pdb=" N GLN G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) 748 hydrogen bonds defined for protein. 1911 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: 2.43 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2589 1.27 - 1.41: 3992 1.41 - 1.55: 9255 1.55 - 1.69: 358 1.69 - 1.84: 138 Bond restraints: 16332 Sorted by residual: bond pdb=" C CYS B 355 " pdb=" O CYS B 355 " ideal model delta sigma weight residual 1.236 1.127 0.109 1.16e-02 7.43e+03 8.88e+01 bond pdb=" C CYS E 355 " pdb=" O CYS E 355 " ideal model delta sigma weight residual 1.236 1.127 0.109 1.21e-02 6.83e+03 8.12e+01 bond pdb=" C CYS A 355 " pdb=" O CYS A 355 " ideal model delta sigma weight residual 1.236 1.127 0.109 1.21e-02 6.83e+03 8.07e+01 bond pdb=" C CYS A 331 " pdb=" O CYS A 331 " ideal model delta sigma weight residual 1.236 1.342 -0.106 1.20e-02 6.94e+03 7.84e+01 bond pdb=" C CYS B 331 " pdb=" O CYS B 331 " ideal model delta sigma weight residual 1.236 1.342 -0.106 1.20e-02 6.94e+03 7.80e+01 ... (remaining 16327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 21525 4.85 - 9.70: 609 9.70 - 14.55: 9 14.55 - 19.40: 6 19.40 - 24.25: 3 Bond angle restraints: 22152 Sorted by residual: angle pdb=" N ASN A 217 " pdb=" CA ASN A 217 " pdb=" C ASN A 217 " ideal model delta sigma weight residual 114.04 97.58 16.46 1.24e+00 6.50e-01 1.76e+02 angle pdb=" N ASN B 217 " pdb=" CA ASN B 217 " pdb=" C ASN B 217 " ideal model delta sigma weight residual 114.04 97.60 16.44 1.24e+00 6.50e-01 1.76e+02 angle pdb=" N ASN E 217 " pdb=" CA ASN E 217 " pdb=" C ASN E 217 " ideal model delta sigma weight residual 114.04 97.61 16.43 1.24e+00 6.50e-01 1.76e+02 angle pdb=" CA CYS B 355 " pdb=" C CYS B 355 " pdb=" N LEU B 356 " ideal model delta sigma weight residual 116.79 105.61 11.18 1.28e+00 6.10e-01 7.63e+01 angle pdb=" C PHE A 282 " pdb=" N PRO A 283 " pdb=" CA PRO A 283 " ideal model delta sigma weight residual 120.03 128.23 -8.20 9.90e-01 1.02e+00 6.85e+01 ... (remaining 22147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.00: 10032 22.00 - 43.99: 210 43.99 - 65.99: 99 65.99 - 87.99: 33 87.99 - 109.98: 18 Dihedral angle restraints: 10392 sinusoidal: 4515 harmonic: 5877 Sorted by residual: dihedral pdb=" N CYS E 355 " pdb=" C CYS E 355 " pdb=" CA CYS E 355 " pdb=" CB CYS E 355 " ideal model delta harmonic sigma weight residual 122.80 135.94 -13.14 0 2.50e+00 1.60e-01 2.76e+01 dihedral pdb=" N CYS B 355 " pdb=" C CYS B 355 " pdb=" CA CYS B 355 " pdb=" CB CYS B 355 " ideal model delta harmonic sigma weight residual 122.80 135.93 -13.13 0 2.50e+00 1.60e-01 2.76e+01 dihedral pdb=" N CYS A 355 " pdb=" C CYS A 355 " pdb=" CA CYS A 355 " pdb=" CB CYS A 355 " ideal model delta harmonic sigma weight residual 122.80 135.93 -13.13 0 2.50e+00 1.60e-01 2.76e+01 ... (remaining 10389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2041 0.120 - 0.240: 560 0.240 - 0.361: 90 0.361 - 0.481: 15 0.481 - 0.601: 6 Chirality restraints: 2712 Sorted by residual: chirality pdb=" C1 BMA K 1 " pdb=" O4 NAG J 2 " pdb=" C2 BMA K 1 " pdb=" O5 BMA K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.66e+02 chirality pdb=" C1 BMA P 1 " pdb=" O4 NAG O 2 " pdb=" C2 BMA P 1 " pdb=" O5 BMA P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.66e+02 chirality pdb=" C1 BMA T 1 " pdb=" O4 NAG S 2 " pdb=" C2 BMA T 1 " pdb=" O5 BMA T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.65e+02 ... (remaining 2709 not shown) Planarity restraints: 2745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.148 2.00e-02 2.50e+03 1.38e-01 2.39e+02 pdb=" C7 NAG I 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.225 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " 0.148 2.00e-02 2.50e+03 1.38e-01 2.38e+02 pdb=" C7 NAG R 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " -0.224 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " -0.148 2.00e-02 2.50e+03 1.38e-01 2.37e+02 pdb=" C7 NAG N 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " 0.224 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.121 2.00e-02 2.50e+03 ... (remaining 2742 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5144 2.84 - 3.35: 14484 3.35 - 3.87: 25742 3.87 - 4.38: 30877 4.38 - 4.90: 50802 Nonbonded interactions: 127049 Sorted by model distance: nonbonded pdb=" O4 MAN K 2 " pdb=" O6 MAN K 2 " model vdw 2.321 3.040 nonbonded pdb=" O4 MAN T 2 " pdb=" O6 MAN T 2 " model vdw 2.321 3.040 nonbonded pdb=" O4 MAN P 2 " pdb=" O6 MAN P 2 " model vdw 2.321 3.040 nonbonded pdb=" O5 NAG E 604 " pdb=" O6 NAG E 604 " model vdw 2.356 2.432 nonbonded pdb=" O5 NAG A 604 " pdb=" O6 NAG A 604 " model vdw 2.356 2.432 ... (remaining 127044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = (chain 'I' and resid 3) selection = (chain 'K' and resid 3) selection = (chain 'M' and resid 3) selection = (chain 'N' and resid 3) selection = (chain 'P' and resid 3) selection = (chain 'Q' and resid 3) selection = (chain 'R' and resid 3) selection = (chain 'T' and resid 3) selection = (chain 'U' and resid 3) } ncs_group { reference = chain 'J' selection = chain 'O' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 14.890 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.021 0.131 16395 Z= 1.120 Angle : 1.967 24.245 22317 Z= 1.246 Chirality : 0.113 0.601 2712 Planarity : 0.011 0.138 2733 Dihedral : 13.053 109.984 6552 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.17 % Allowed : 1.36 % Favored : 98.47 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.18), residues: 1998 helix: -0.35 (0.21), residues: 456 sheet: 0.60 (0.21), residues: 546 loop : 1.14 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 72 TYR 0.057 0.009 TYR A 46 PHE 0.028 0.006 PHE H 105 TRP 0.041 0.010 TRP F 104 HIS 0.009 0.003 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.02053 (16332) covalent geometry : angle 1.94898 (22152) SS BOND : bond 0.04771 ( 24) SS BOND : angle 3.06560 ( 48) hydrogen bonds : bond 0.19110 ( 721) hydrogen bonds : angle 7.79761 ( 1911) link_ALPHA1-2 : bond 0.10578 ( 3) link_ALPHA1-2 : angle 8.05687 ( 9) link_ALPHA1-4 : bond 0.08669 ( 6) link_ALPHA1-4 : angle 2.81335 ( 18) link_ALPHA1-6 : bond 0.07584 ( 3) link_ALPHA1-6 : angle 2.19531 ( 9) link_BETA1-4 : bond 0.09674 ( 15) link_BETA1-4 : angle 3.92301 ( 45) link_NAG-ASN : bond 0.05243 ( 12) link_NAG-ASN : angle 2.69412 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 430 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8299 (m-30) cc_final: 0.8031 (m-30) REVERT: A 373 VAL cc_start: 0.8906 (t) cc_final: 0.8474 (m) REVERT: H 13 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8451 (mmtm) REVERT: B 84 ASN cc_start: 0.8267 (m110) cc_final: 0.8067 (m-40) REVERT: B 244 ARG cc_start: 0.8203 (mmp80) cc_final: 0.7843 (mmp-170) REVERT: B 443 ILE cc_start: 0.8281 (tp) cc_final: 0.8077 (tt) REVERT: C 13 LYS cc_start: 0.8988 (mtpp) cc_final: 0.8622 (mptt) REVERT: E 82 ARG cc_start: 0.8592 (tpt-90) cc_final: 0.8324 (mmm-85) REVERT: E 254 ASP cc_start: 0.8044 (m-30) cc_final: 0.7806 (m-30) REVERT: E 373 VAL cc_start: 0.8786 (t) cc_final: 0.8341 (m) REVERT: F 13 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8504 (mptt) REVERT: F 79 LEU cc_start: 0.9029 (tp) cc_final: 0.8755 (tp) REVERT: G 52 THR cc_start: 0.8955 (p) cc_final: 0.8680 (t) outliers start: 3 outliers final: 2 residues processed: 433 average time/residue: 0.1178 time to fit residues: 74.8838 Evaluate side-chains 264 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain E residue 99 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 303 ASN H 74 ASN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN B 303 ASN B 372 HIS C 39 GLN D 37 GLN E 302 ASN E 303 ASN E 459 GLN E 469 GLN G 37 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.092543 restraints weight = 24956.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.094903 restraints weight = 16146.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.096502 restraints weight = 12013.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.097610 restraints weight = 9818.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.098270 restraints weight = 8526.431| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16395 Z= 0.195 Angle : 0.835 17.157 22317 Z= 0.407 Chirality : 0.049 0.353 2712 Planarity : 0.004 0.037 2733 Dihedral : 9.540 70.827 2956 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.84 % Allowed : 8.23 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.19), residues: 1998 helix: 1.15 (0.25), residues: 459 sheet: 0.57 (0.20), residues: 600 loop : 0.38 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 353 TYR 0.024 0.002 TYR G 49 PHE 0.021 0.002 PHE D 91 TRP 0.018 0.002 TRP G 32 HIS 0.003 0.002 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00433 (16332) covalent geometry : angle 0.79570 (22152) SS BOND : bond 0.00453 ( 24) SS BOND : angle 2.18229 ( 48) hydrogen bonds : bond 0.06052 ( 721) hydrogen bonds : angle 5.87322 ( 1911) link_ALPHA1-2 : bond 0.03112 ( 3) link_ALPHA1-2 : angle 5.23051 ( 9) link_ALPHA1-4 : bond 0.00862 ( 6) link_ALPHA1-4 : angle 1.39718 ( 18) link_ALPHA1-6 : bond 0.00538 ( 3) link_ALPHA1-6 : angle 1.75446 ( 9) link_BETA1-4 : bond 0.01121 ( 15) link_BETA1-4 : angle 3.95346 ( 45) link_NAG-ASN : bond 0.00633 ( 12) link_NAG-ASN : angle 2.83436 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 310 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7120 (OUTLIER) cc_final: 0.6711 (m110) REVERT: A 348 MET cc_start: 0.8497 (ttm) cc_final: 0.8287 (ttm) REVERT: A 373 VAL cc_start: 0.8855 (t) cc_final: 0.8620 (m) REVERT: H 13 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8263 (mptt) REVERT: H 93 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6914 (mmt) REVERT: L 31 THR cc_start: 0.8854 (p) cc_final: 0.8527 (t) REVERT: B 56 ASP cc_start: 0.8047 (m-30) cc_final: 0.7825 (m-30) REVERT: B 226 MET cc_start: 0.7947 (ttm) cc_final: 0.7684 (ttm) REVERT: B 244 ARG cc_start: 0.8128 (mmp80) cc_final: 0.7693 (mmp-170) REVERT: C 13 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8335 (mptt) REVERT: C 39 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: C 42 GLU cc_start: 0.7978 (mp0) cc_final: 0.7673 (mp0) REVERT: C 95 TYR cc_start: 0.9334 (m-80) cc_final: 0.9045 (m-10) REVERT: D 4 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7705 (mpp) REVERT: D 31 THR cc_start: 0.8723 (p) cc_final: 0.8468 (t) REVERT: E 49 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8652 (tttt) REVERT: E 56 ASP cc_start: 0.7853 (m-30) cc_final: 0.7643 (m-30) REVERT: E 254 ASP cc_start: 0.7913 (m-30) cc_final: 0.7692 (m-30) REVERT: E 394 CYS cc_start: 0.6100 (t) cc_final: 0.5789 (t) REVERT: F 13 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8348 (mptt) REVERT: F 32 TYR cc_start: 0.8723 (m-80) cc_final: 0.8498 (m-80) REVERT: F 117 SER cc_start: 0.8918 (t) cc_final: 0.8507 (p) REVERT: G 15 LEU cc_start: 0.8046 (tt) cc_final: 0.7698 (tt) REVERT: G 21 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.8986 (pt) outliers start: 50 outliers final: 28 residues processed: 343 average time/residue: 0.1352 time to fit residues: 68.5864 Evaluate side-chains 282 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 188 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 372 HIS L 37 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 HIS F 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.084949 restraints weight = 26012.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.087657 restraints weight = 15495.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.089482 restraints weight = 10953.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.090664 restraints weight = 8669.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.091437 restraints weight = 7440.272| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 16395 Z= 0.240 Angle : 0.819 17.326 22317 Z= 0.397 Chirality : 0.050 0.377 2712 Planarity : 0.004 0.044 2733 Dihedral : 8.834 113.166 2952 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % Rotamer: Outliers : 4.20 % Allowed : 9.60 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.19), residues: 1998 helix: 1.20 (0.25), residues: 480 sheet: 0.51 (0.21), residues: 594 loop : -0.12 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 82 TYR 0.020 0.002 TYR E 438 PHE 0.026 0.002 PHE D 91 TRP 0.021 0.003 TRP H 108 HIS 0.004 0.002 HIS E 372 Details of bonding type rmsd covalent geometry : bond 0.00565 (16332) covalent geometry : angle 0.78170 (22152) SS BOND : bond 0.00625 ( 24) SS BOND : angle 2.03516 ( 48) hydrogen bonds : bond 0.05581 ( 721) hydrogen bonds : angle 5.59545 ( 1911) link_ALPHA1-2 : bond 0.03276 ( 3) link_ALPHA1-2 : angle 5.01786 ( 9) link_ALPHA1-4 : bond 0.00844 ( 6) link_ALPHA1-4 : angle 1.33209 ( 18) link_ALPHA1-6 : bond 0.00659 ( 3) link_ALPHA1-6 : angle 1.58292 ( 9) link_BETA1-4 : bond 0.01338 ( 15) link_BETA1-4 : angle 3.81496 ( 45) link_NAG-ASN : bond 0.00618 ( 12) link_NAG-ASN : angle 2.87534 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 262 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7108 (OUTLIER) cc_final: 0.6721 (m110) REVERT: A 226 MET cc_start: 0.8416 (ttm) cc_final: 0.8148 (ttp) REVERT: H 13 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8304 (mptt) REVERT: H 82 GLN cc_start: 0.8314 (tp40) cc_final: 0.8079 (tp40) REVERT: H 93 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6982 (mmt) REVERT: L 31 THR cc_start: 0.8805 (p) cc_final: 0.8431 (t) REVERT: B 84 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7924 (m-40) REVERT: B 98 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8194 (ttmm) REVERT: B 226 MET cc_start: 0.8112 (ttm) cc_final: 0.7546 (ttm) REVERT: B 244 ARG cc_start: 0.8165 (mmp80) cc_final: 0.7837 (mmp-170) REVERT: B 336 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7644 (ttm-80) REVERT: B 411 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7878 (tmm) REVERT: C 13 LYS cc_start: 0.8919 (mtpp) cc_final: 0.8392 (mptt) REVERT: C 33 ASP cc_start: 0.8463 (p0) cc_final: 0.7972 (p0) REVERT: C 44 ARG cc_start: 0.7977 (tpt-90) cc_final: 0.7732 (ttp-170) REVERT: C 82 GLN cc_start: 0.8032 (tp40) cc_final: 0.7776 (tp40) REVERT: C 95 TYR cc_start: 0.9347 (m-80) cc_final: 0.9054 (m-10) REVERT: D 31 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8314 (t) REVERT: E 49 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8709 (tttt) REVERT: E 254 ASP cc_start: 0.8281 (m-30) cc_final: 0.7912 (m-30) REVERT: F 13 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8427 (mptt) REVERT: F 32 TYR cc_start: 0.8816 (m-80) cc_final: 0.8568 (m-80) REVERT: F 33 ASP cc_start: 0.8205 (p0) cc_final: 0.7711 (p0) REVERT: F 46 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6754 (mt-10) REVERT: F 82 GLN cc_start: 0.8138 (tp40) cc_final: 0.7892 (tp40) REVERT: G 31 THR cc_start: 0.8596 (p) cc_final: 0.8297 (t) outliers start: 74 outliers final: 50 residues processed: 311 average time/residue: 0.1266 time to fit residues: 57.5984 Evaluate side-chains 287 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 60 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN L 6 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN F 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106326 restraints weight = 24603.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109471 restraints weight = 13983.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111510 restraints weight = 9784.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112815 restraints weight = 7756.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113643 restraints weight = 6674.195| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16395 Z= 0.204 Angle : 0.754 14.149 22317 Z= 0.362 Chirality : 0.048 0.335 2712 Planarity : 0.004 0.041 2733 Dihedral : 8.571 104.998 2952 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.20 % Allowed : 10.68 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.19), residues: 1998 helix: 1.63 (0.25), residues: 462 sheet: 0.49 (0.21), residues: 594 loop : -0.34 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 336 TYR 0.019 0.002 TYR A 438 PHE 0.021 0.002 PHE D 91 TRP 0.017 0.002 TRP F 104 HIS 0.003 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00481 (16332) covalent geometry : angle 0.71101 (22152) SS BOND : bond 0.00499 ( 24) SS BOND : angle 1.73818 ( 48) hydrogen bonds : bond 0.04950 ( 721) hydrogen bonds : angle 5.31448 ( 1911) link_ALPHA1-2 : bond 0.03011 ( 3) link_ALPHA1-2 : angle 4.76833 ( 9) link_ALPHA1-4 : bond 0.00791 ( 6) link_ALPHA1-4 : angle 1.38793 ( 18) link_ALPHA1-6 : bond 0.00588 ( 3) link_ALPHA1-6 : angle 1.65081 ( 9) link_BETA1-4 : bond 0.01318 ( 15) link_BETA1-4 : angle 3.86440 ( 45) link_NAG-ASN : bond 0.00286 ( 12) link_NAG-ASN : angle 3.30427 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 240 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6766 (OUTLIER) cc_final: 0.6470 (m110) REVERT: A 375 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7804 (mtt-85) REVERT: A 463 MET cc_start: 0.7715 (ttm) cc_final: 0.7296 (ptm) REVERT: H 13 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8381 (mptt) REVERT: H 50 MET cc_start: 0.8457 (ttt) cc_final: 0.8124 (ttt) REVERT: L 20 THR cc_start: 0.9038 (m) cc_final: 0.8767 (p) REVERT: L 31 THR cc_start: 0.8731 (p) cc_final: 0.8385 (t) REVERT: L 89 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8943 (tm-30) REVERT: B 84 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7880 (m-40) REVERT: B 98 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8306 (ttmm) REVERT: C 13 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8423 (mptt) REVERT: C 33 ASP cc_start: 0.8331 (p0) cc_final: 0.7885 (p0) REVERT: C 42 GLU cc_start: 0.7803 (mp0) cc_final: 0.7488 (mp0) REVERT: C 82 GLN cc_start: 0.7960 (tp40) cc_final: 0.7681 (tp40) REVERT: C 95 TYR cc_start: 0.9267 (m-80) cc_final: 0.9022 (m-10) REVERT: D 31 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8354 (t) REVERT: E 49 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8753 (tttt) REVERT: F 13 LYS cc_start: 0.9093 (mtpp) cc_final: 0.8455 (mptt) REVERT: F 32 TYR cc_start: 0.8786 (m-80) cc_final: 0.8529 (m-10) REVERT: F 33 ASP cc_start: 0.8211 (p0) cc_final: 0.7743 (p0) REVERT: F 46 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6709 (mt-10) REVERT: F 82 GLN cc_start: 0.8055 (tp40) cc_final: 0.7847 (tp40) REVERT: G 20 THR cc_start: 0.8703 (p) cc_final: 0.8482 (p) REVERT: G 21 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9062 (pt) REVERT: G 31 THR cc_start: 0.8565 (p) cc_final: 0.8312 (t) outliers start: 74 outliers final: 56 residues processed: 291 average time/residue: 0.1310 time to fit residues: 56.1232 Evaluate side-chains 291 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 228 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 139 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 165 optimal weight: 0.1980 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 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN H 99 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107568 restraints weight = 24545.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110680 restraints weight = 13992.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112769 restraints weight = 9778.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.114098 restraints weight = 7758.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114838 restraints weight = 6679.587| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16395 Z= 0.145 Angle : 0.670 12.673 22317 Z= 0.321 Chirality : 0.046 0.318 2712 Planarity : 0.004 0.043 2733 Dihedral : 8.658 109.484 2952 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.86 % Allowed : 11.41 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.19), residues: 1998 helix: 1.87 (0.25), residues: 462 sheet: 0.60 (0.21), residues: 588 loop : -0.39 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 336 TYR 0.017 0.001 TYR G 49 PHE 0.017 0.002 PHE D 91 TRP 0.018 0.002 TRP C 104 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00326 (16332) covalent geometry : angle 0.63060 (22152) SS BOND : bond 0.00390 ( 24) SS BOND : angle 1.18595 ( 48) hydrogen bonds : bond 0.04227 ( 721) hydrogen bonds : angle 4.98031 ( 1911) link_ALPHA1-2 : bond 0.02799 ( 3) link_ALPHA1-2 : angle 4.63161 ( 9) link_ALPHA1-4 : bond 0.00771 ( 6) link_ALPHA1-4 : angle 1.39368 ( 18) link_ALPHA1-6 : bond 0.00631 ( 3) link_ALPHA1-6 : angle 1.47941 ( 9) link_BETA1-4 : bond 0.01270 ( 15) link_BETA1-4 : angle 3.74345 ( 45) link_NAG-ASN : bond 0.00320 ( 12) link_NAG-ASN : angle 2.70417 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 251 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.5957 (OUTLIER) cc_final: 0.5753 (m110) REVERT: A 115 MET cc_start: 0.7412 (mtp) cc_final: 0.7178 (mtp) REVERT: A 180 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8140 (p0) REVERT: A 388 ILE cc_start: 0.8983 (tt) cc_final: 0.8753 (tt) REVERT: A 412 ILE cc_start: 0.8886 (mt) cc_final: 0.8674 (mt) REVERT: A 458 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.8137 (p) REVERT: H 13 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8453 (mptt) REVERT: H 50 MET cc_start: 0.8313 (ttt) cc_final: 0.7968 (ttt) REVERT: L 20 THR cc_start: 0.9059 (m) cc_final: 0.8790 (p) REVERT: L 31 THR cc_start: 0.8690 (p) cc_final: 0.8339 (t) REVERT: L 89 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8426 (pp30) REVERT: B 49 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8712 (tttt) REVERT: B 84 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7860 (m-40) REVERT: B 98 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8194 (ttmm) REVERT: B 138 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6703 (mpp) REVERT: C 13 LYS cc_start: 0.8959 (mtpp) cc_final: 0.8448 (mptt) REVERT: C 18 LEU cc_start: 0.8920 (tp) cc_final: 0.8701 (tp) REVERT: C 32 TYR cc_start: 0.8658 (m-80) cc_final: 0.8085 (m-80) REVERT: C 33 ASP cc_start: 0.8349 (p0) cc_final: 0.7882 (p0) REVERT: C 42 GLU cc_start: 0.8025 (mp0) cc_final: 0.7669 (mp0) REVERT: C 82 GLN cc_start: 0.7951 (tp40) cc_final: 0.7635 (tp40) REVERT: C 95 TYR cc_start: 0.9299 (m-80) cc_final: 0.8997 (m-10) REVERT: D 31 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8303 (t) REVERT: E 49 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8725 (tttt) REVERT: F 13 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8473 (mptt) REVERT: F 32 TYR cc_start: 0.8691 (m-80) cc_final: 0.8462 (m-80) REVERT: F 33 ASP cc_start: 0.8145 (p0) cc_final: 0.7701 (p0) REVERT: F 46 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6625 (mt-10) REVERT: G 20 THR cc_start: 0.8683 (p) cc_final: 0.8471 (p) REVERT: G 21 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9005 (pt) REVERT: G 31 THR cc_start: 0.8503 (p) cc_final: 0.8234 (t) outliers start: 68 outliers final: 45 residues processed: 299 average time/residue: 0.1187 time to fit residues: 52.4870 Evaluate side-chains 283 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 227 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 40 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 303 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108391 restraints weight = 24386.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111600 restraints weight = 13892.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113665 restraints weight = 9713.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114986 restraints weight = 7700.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115867 restraints weight = 6626.808| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16395 Z= 0.135 Angle : 0.656 12.699 22317 Z= 0.313 Chirality : 0.046 0.323 2712 Planarity : 0.004 0.043 2733 Dihedral : 8.476 114.515 2952 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.15 % Allowed : 12.04 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.19), residues: 1998 helix: 2.03 (0.26), residues: 462 sheet: 0.68 (0.21), residues: 588 loop : -0.41 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 336 TYR 0.016 0.001 TYR G 49 PHE 0.017 0.001 PHE D 91 TRP 0.017 0.002 TRP C 104 HIS 0.009 0.002 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00304 (16332) covalent geometry : angle 0.61784 (22152) SS BOND : bond 0.00343 ( 24) SS BOND : angle 1.01618 ( 48) hydrogen bonds : bond 0.03938 ( 721) hydrogen bonds : angle 4.75847 ( 1911) link_ALPHA1-2 : bond 0.02674 ( 3) link_ALPHA1-2 : angle 4.37236 ( 9) link_ALPHA1-4 : bond 0.00760 ( 6) link_ALPHA1-4 : angle 1.41100 ( 18) link_ALPHA1-6 : bond 0.00601 ( 3) link_ALPHA1-6 : angle 1.42658 ( 9) link_BETA1-4 : bond 0.01274 ( 15) link_BETA1-4 : angle 3.79928 ( 45) link_NAG-ASN : bond 0.00451 ( 12) link_NAG-ASN : angle 2.44538 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 250 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6630 (OUTLIER) cc_final: 0.6273 (m110) REVERT: A 180 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8227 (p0) REVERT: A 388 ILE cc_start: 0.8995 (tt) cc_final: 0.8716 (tp) REVERT: A 412 ILE cc_start: 0.8866 (mt) cc_final: 0.8660 (mt) REVERT: A 458 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8218 (p) REVERT: H 13 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8483 (mptt) REVERT: H 50 MET cc_start: 0.8254 (ttt) cc_final: 0.7890 (ttt) REVERT: H 82 GLN cc_start: 0.8059 (tp40) cc_final: 0.7769 (tp40) REVERT: L 20 THR cc_start: 0.9067 (m) cc_final: 0.8791 (p) REVERT: L 89 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8410 (pp30) REVERT: B 49 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8707 (tttt) REVERT: B 84 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7865 (m-40) REVERT: B 98 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8177 (ttmm) REVERT: B 138 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6728 (mpp) REVERT: B 177 ASP cc_start: 0.7652 (p0) cc_final: 0.7328 (p0) REVERT: B 411 MET cc_start: 0.8007 (tmm) cc_final: 0.7746 (tmm) REVERT: C 13 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8489 (mptt) REVERT: C 18 LEU cc_start: 0.8973 (tp) cc_final: 0.8738 (tp) REVERT: C 32 TYR cc_start: 0.8647 (m-80) cc_final: 0.8140 (m-80) REVERT: C 33 ASP cc_start: 0.8259 (p0) cc_final: 0.7803 (p0) REVERT: C 42 GLU cc_start: 0.7924 (mp0) cc_final: 0.7587 (mp0) REVERT: C 82 GLN cc_start: 0.7779 (tp40) cc_final: 0.7518 (tp40) REVERT: C 95 TYR cc_start: 0.9257 (m-80) cc_final: 0.8981 (m-10) REVERT: F 13 LYS cc_start: 0.9094 (mtpp) cc_final: 0.8436 (mptt) REVERT: F 32 TYR cc_start: 0.8637 (m-80) cc_final: 0.8424 (m-80) REVERT: F 33 ASP cc_start: 0.8202 (p0) cc_final: 0.7762 (p0) REVERT: G 20 THR cc_start: 0.8655 (p) cc_final: 0.8423 (p) REVERT: G 21 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9015 (pt) REVERT: G 31 THR cc_start: 0.8475 (p) cc_final: 0.8201 (t) outliers start: 73 outliers final: 50 residues processed: 299 average time/residue: 0.1351 time to fit residues: 59.4348 Evaluate side-chains 286 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 13 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN H 99 GLN B 180 ASN E 303 ASN F 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.083370 restraints weight = 25966.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.085889 restraints weight = 15822.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.087580 restraints weight = 11397.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.088703 restraints weight = 9173.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.089371 restraints weight = 7920.149| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16395 Z= 0.245 Angle : 0.728 12.647 22317 Z= 0.352 Chirality : 0.048 0.341 2712 Planarity : 0.004 0.041 2733 Dihedral : 8.382 111.565 2952 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.92 % Allowed : 12.95 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.19), residues: 1998 helix: 1.86 (0.26), residues: 462 sheet: 0.65 (0.21), residues: 594 loop : -0.60 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 353 TYR 0.020 0.002 TYR A 438 PHE 0.023 0.002 PHE D 91 TRP 0.016 0.002 TRP F 108 HIS 0.005 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00592 (16332) covalent geometry : angle 0.69437 (22152) SS BOND : bond 0.00536 ( 24) SS BOND : angle 1.28603 ( 48) hydrogen bonds : bond 0.04679 ( 721) hydrogen bonds : angle 4.99486 ( 1911) link_ALPHA1-2 : bond 0.02565 ( 3) link_ALPHA1-2 : angle 4.04934 ( 9) link_ALPHA1-4 : bond 0.00832 ( 6) link_ALPHA1-4 : angle 1.43549 ( 18) link_ALPHA1-6 : bond 0.00533 ( 3) link_ALPHA1-6 : angle 1.48608 ( 9) link_BETA1-4 : bond 0.01200 ( 15) link_BETA1-4 : angle 3.79217 ( 45) link_NAG-ASN : bond 0.00319 ( 12) link_NAG-ASN : angle 2.51550 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 231 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8549 (mtp) cc_final: 0.7806 (mtp) REVERT: A 99 ASN cc_start: 0.6623 (OUTLIER) cc_final: 0.6280 (m110) REVERT: A 388 ILE cc_start: 0.9019 (tt) cc_final: 0.8787 (tt) REVERT: A 412 ILE cc_start: 0.8909 (mt) cc_final: 0.8703 (mt) REVERT: A 458 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8371 (p) REVERT: H 13 LYS cc_start: 0.9112 (mtpp) cc_final: 0.8494 (mptt) REVERT: H 33 ASP cc_start: 0.8515 (p0) cc_final: 0.7934 (p0) REVERT: H 50 MET cc_start: 0.8436 (ttt) cc_final: 0.8030 (ttt) REVERT: H 82 GLN cc_start: 0.8075 (tp40) cc_final: 0.7758 (tp40) REVERT: L 20 THR cc_start: 0.9063 (m) cc_final: 0.8795 (p) REVERT: L 89 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8394 (pp30) REVERT: B 84 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7917 (m-40) REVERT: B 98 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8388 (ttmm) REVERT: B 138 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6845 (mpp) REVERT: B 177 ASP cc_start: 0.7777 (p0) cc_final: 0.7459 (p0) REVERT: B 238 ASN cc_start: 0.8498 (t0) cc_final: 0.8271 (t0) REVERT: C 13 LYS cc_start: 0.9030 (mtpp) cc_final: 0.8489 (mptt) REVERT: C 32 TYR cc_start: 0.8532 (m-80) cc_final: 0.7965 (m-80) REVERT: C 33 ASP cc_start: 0.8363 (p0) cc_final: 0.7819 (p0) REVERT: C 42 GLU cc_start: 0.8027 (mp0) cc_final: 0.7669 (mp0) REVERT: C 95 TYR cc_start: 0.9239 (m-80) cc_final: 0.9031 (m-10) REVERT: F 13 LYS cc_start: 0.9139 (mtpp) cc_final: 0.8448 (mptt) REVERT: F 32 TYR cc_start: 0.8780 (m-80) cc_final: 0.8513 (m-10) REVERT: F 33 ASP cc_start: 0.8258 (p0) cc_final: 0.7759 (p0) REVERT: F 46 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6771 (mt-10) REVERT: F 82 GLN cc_start: 0.7752 (tp40) cc_final: 0.7545 (tp40) REVERT: F 107 TYR cc_start: 0.8466 (m-80) cc_final: 0.8126 (m-10) REVERT: G 31 THR cc_start: 0.8572 (p) cc_final: 0.8350 (t) outliers start: 69 outliers final: 59 residues processed: 281 average time/residue: 0.1170 time to fit residues: 48.6954 Evaluate side-chains 291 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 12 optimal weight: 0.5980 chunk 162 optimal weight: 0.0870 chunk 187 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN H 99 GLN B 29 HIS E 303 ASN F 39 GLN F 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.097838 restraints weight = 25307.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100745 restraints weight = 15291.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.102675 restraints weight = 11065.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103908 restraints weight = 8936.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104770 restraints weight = 7756.038| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16395 Z= 0.133 Angle : 0.662 12.759 22317 Z= 0.316 Chirality : 0.046 0.334 2712 Planarity : 0.004 0.043 2733 Dihedral : 8.228 113.216 2952 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.75 % Allowed : 13.57 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.19), residues: 1998 helix: 1.96 (0.25), residues: 462 sheet: 0.65 (0.22), residues: 588 loop : -0.58 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 336 TYR 0.016 0.001 TYR G 49 PHE 0.015 0.001 PHE D 91 TRP 0.016 0.001 TRP C 104 HIS 0.007 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00299 (16332) covalent geometry : angle 0.62500 (22152) SS BOND : bond 0.00349 ( 24) SS BOND : angle 1.00438 ( 48) hydrogen bonds : bond 0.03969 ( 721) hydrogen bonds : angle 4.76675 ( 1911) link_ALPHA1-2 : bond 0.02432 ( 3) link_ALPHA1-2 : angle 3.97572 ( 9) link_ALPHA1-4 : bond 0.00790 ( 6) link_ALPHA1-4 : angle 1.46146 ( 18) link_ALPHA1-6 : bond 0.00598 ( 3) link_ALPHA1-6 : angle 1.37999 ( 9) link_BETA1-4 : bond 0.01275 ( 15) link_BETA1-4 : angle 3.83907 ( 45) link_NAG-ASN : bond 0.00465 ( 12) link_NAG-ASN : angle 2.47137 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 237 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6574 (OUTLIER) cc_final: 0.6223 (m110) REVERT: A 348 MET cc_start: 0.8392 (ttm) cc_final: 0.8076 (ttm) REVERT: A 388 ILE cc_start: 0.8990 (tt) cc_final: 0.8697 (tp) REVERT: A 458 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.8250 (p) REVERT: H 13 LYS cc_start: 0.9093 (mtpp) cc_final: 0.8502 (mptt) REVERT: H 33 ASP cc_start: 0.8476 (p0) cc_final: 0.7921 (p0) REVERT: H 50 MET cc_start: 0.8232 (ttt) cc_final: 0.7864 (ttt) REVERT: H 82 GLN cc_start: 0.8049 (tp40) cc_final: 0.7745 (tp40) REVERT: L 6 GLN cc_start: 0.8617 (tt0) cc_final: 0.8305 (tt0) REVERT: L 20 THR cc_start: 0.9058 (m) cc_final: 0.8668 (p) REVERT: L 89 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8506 (pp30) REVERT: B 49 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8701 (tttt) REVERT: B 84 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7872 (m-40) REVERT: B 98 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8200 (ttmm) REVERT: C 13 LYS cc_start: 0.9002 (mtpp) cc_final: 0.8505 (mptt) REVERT: C 18 LEU cc_start: 0.9024 (tp) cc_final: 0.8789 (tp) REVERT: C 32 TYR cc_start: 0.8545 (m-80) cc_final: 0.7898 (m-80) REVERT: C 33 ASP cc_start: 0.8282 (p0) cc_final: 0.7788 (p0) REVERT: C 42 GLU cc_start: 0.7932 (mp0) cc_final: 0.7620 (mp0) REVERT: C 95 TYR cc_start: 0.9198 (m-80) cc_final: 0.8982 (m-10) REVERT: F 13 LYS cc_start: 0.9117 (mtpp) cc_final: 0.8459 (mptt) REVERT: F 33 ASP cc_start: 0.8216 (p0) cc_final: 0.7769 (p0) REVERT: F 82 GLN cc_start: 0.7724 (tp40) cc_final: 0.7522 (tp40) REVERT: G 31 THR cc_start: 0.8509 (p) cc_final: 0.8293 (t) outliers start: 66 outliers final: 54 residues processed: 279 average time/residue: 0.1155 time to fit residues: 47.8158 Evaluate side-chains 284 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 67 optimal weight: 2.9990 chunk 57 optimal weight: 0.0270 chunk 119 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 183 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN F 39 GLN F 99 GLN G 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105845 restraints weight = 24657.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109006 restraints weight = 14048.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111064 restraints weight = 9821.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112396 restraints weight = 7798.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113285 restraints weight = 6700.044| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16395 Z= 0.129 Angle : 0.651 12.835 22317 Z= 0.309 Chirality : 0.045 0.327 2712 Planarity : 0.004 0.044 2733 Dihedral : 8.075 114.045 2952 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.29 % Allowed : 14.20 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.19), residues: 1998 helix: 2.02 (0.25), residues: 462 sheet: 0.65 (0.22), residues: 588 loop : -0.57 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 336 TYR 0.016 0.001 TYR G 49 PHE 0.014 0.001 PHE D 91 TRP 0.017 0.001 TRP C 104 HIS 0.008 0.002 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00288 (16332) covalent geometry : angle 0.61343 (22152) SS BOND : bond 0.00329 ( 24) SS BOND : angle 0.95542 ( 48) hydrogen bonds : bond 0.03708 ( 721) hydrogen bonds : angle 4.66476 ( 1911) link_ALPHA1-2 : bond 0.02315 ( 3) link_ALPHA1-2 : angle 3.75505 ( 9) link_ALPHA1-4 : bond 0.00796 ( 6) link_ALPHA1-4 : angle 1.42137 ( 18) link_ALPHA1-6 : bond 0.00626 ( 3) link_ALPHA1-6 : angle 1.36835 ( 9) link_BETA1-4 : bond 0.01275 ( 15) link_BETA1-4 : angle 3.85296 ( 45) link_NAG-ASN : bond 0.00514 ( 12) link_NAG-ASN : angle 2.46556 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6367 (OUTLIER) cc_final: 0.6082 (m110) REVERT: A 244 ARG cc_start: 0.8354 (mmp80) cc_final: 0.8007 (mmp80) REVERT: A 388 ILE cc_start: 0.8929 (tt) cc_final: 0.8626 (tp) REVERT: A 470 SER cc_start: 0.7549 (m) cc_final: 0.7295 (t) REVERT: H 13 LYS cc_start: 0.9079 (mtpp) cc_final: 0.8499 (mptt) REVERT: H 33 ASP cc_start: 0.8436 (p0) cc_final: 0.7837 (p0) REVERT: H 50 MET cc_start: 0.8200 (ttt) cc_final: 0.7771 (ttt) REVERT: H 82 GLN cc_start: 0.8047 (tp40) cc_final: 0.7736 (tp40) REVERT: L 89 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8349 (pp30) REVERT: B 84 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7843 (m-40) REVERT: B 98 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8270 (ttmm) REVERT: B 258 GLU cc_start: 0.7878 (tp30) cc_final: 0.6990 (tp30) REVERT: C 13 LYS cc_start: 0.9032 (mtpp) cc_final: 0.8525 (mptt) REVERT: C 32 TYR cc_start: 0.8556 (m-80) cc_final: 0.7877 (m-80) REVERT: C 33 ASP cc_start: 0.8348 (p0) cc_final: 0.7812 (p0) REVERT: C 42 GLU cc_start: 0.7925 (mp0) cc_final: 0.7610 (mp0) REVERT: C 95 TYR cc_start: 0.9236 (m-80) cc_final: 0.9007 (m-10) REVERT: E 470 SER cc_start: 0.7315 (m) cc_final: 0.6925 (p) REVERT: F 13 LYS cc_start: 0.9106 (mtpp) cc_final: 0.8459 (mptt) REVERT: F 33 ASP cc_start: 0.8309 (p0) cc_final: 0.7793 (p0) REVERT: F 107 TYR cc_start: 0.8391 (m-80) cc_final: 0.8108 (m-10) REVERT: G 31 THR cc_start: 0.8487 (p) cc_final: 0.8237 (t) outliers start: 58 outliers final: 51 residues processed: 280 average time/residue: 0.1227 time to fit residues: 50.2043 Evaluate side-chains 282 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 49 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN F 99 GLN G 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.084064 restraints weight = 25809.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.086662 restraints weight = 15524.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.088362 restraints weight = 11080.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.089510 restraints weight = 8913.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.090284 restraints weight = 7686.555| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16395 Z= 0.242 Angle : 0.732 12.852 22317 Z= 0.353 Chirality : 0.048 0.341 2712 Planarity : 0.004 0.041 2733 Dihedral : 8.100 112.097 2952 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.52 % Allowed : 14.25 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.19), residues: 1998 helix: 1.88 (0.25), residues: 462 sheet: 0.53 (0.22), residues: 579 loop : -0.60 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 336 TYR 0.021 0.002 TYR A 438 PHE 0.021 0.002 PHE D 91 TRP 0.015 0.002 TRP H 108 HIS 0.007 0.002 HIS E 29 Details of bonding type rmsd covalent geometry : bond 0.00588 (16332) covalent geometry : angle 0.69886 (22152) SS BOND : bond 0.00504 ( 24) SS BOND : angle 1.32253 ( 48) hydrogen bonds : bond 0.04628 ( 721) hydrogen bonds : angle 4.93912 ( 1911) link_ALPHA1-2 : bond 0.02225 ( 3) link_ALPHA1-2 : angle 3.35108 ( 9) link_ALPHA1-4 : bond 0.00866 ( 6) link_ALPHA1-4 : angle 1.44800 ( 18) link_ALPHA1-6 : bond 0.00559 ( 3) link_ALPHA1-6 : angle 1.44446 ( 9) link_BETA1-4 : bond 0.01236 ( 15) link_BETA1-4 : angle 3.84422 ( 45) link_NAG-ASN : bond 0.00380 ( 12) link_NAG-ASN : angle 2.52415 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6823 (OUTLIER) cc_final: 0.6461 (m110) REVERT: A 244 ARG cc_start: 0.8338 (mmp80) cc_final: 0.7984 (mmp80) REVERT: A 388 ILE cc_start: 0.9016 (tt) cc_final: 0.8782 (tt) REVERT: H 13 LYS cc_start: 0.9135 (mtpp) cc_final: 0.8499 (mptt) REVERT: H 33 ASP cc_start: 0.8580 (p0) cc_final: 0.7890 (p0) REVERT: H 50 MET cc_start: 0.8463 (ttt) cc_final: 0.8077 (ttt) REVERT: H 82 GLN cc_start: 0.8065 (tp40) cc_final: 0.7739 (tp40) REVERT: L 89 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8960 (tm-30) REVERT: B 84 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7907 (m-40) REVERT: B 98 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8221 (ttmm) REVERT: B 238 ASN cc_start: 0.8552 (t0) cc_final: 0.8308 (t0) REVERT: C 13 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8506 (mptt) REVERT: C 32 TYR cc_start: 0.8666 (m-80) cc_final: 0.7963 (m-80) REVERT: C 33 ASP cc_start: 0.8361 (p0) cc_final: 0.7783 (p0) REVERT: C 42 GLU cc_start: 0.7977 (mp0) cc_final: 0.7687 (mp0) REVERT: C 95 TYR cc_start: 0.9265 (m-80) cc_final: 0.8954 (m-10) REVERT: F 13 LYS cc_start: 0.9168 (mtpp) cc_final: 0.8489 (mptt) REVERT: F 33 ASP cc_start: 0.8268 (p0) cc_final: 0.7713 (p0) REVERT: F 107 TYR cc_start: 0.8454 (m-80) cc_final: 0.8120 (m-10) outliers start: 62 outliers final: 56 residues processed: 266 average time/residue: 0.1281 time to fit residues: 49.9198 Evaluate side-chains 279 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 219 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 124 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 180 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104741 restraints weight = 24523.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107859 restraints weight = 14004.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109909 restraints weight = 9829.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111246 restraints weight = 7801.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112009 restraints weight = 6705.924| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16395 Z= 0.134 Angle : 0.668 12.951 22317 Z= 0.317 Chirality : 0.046 0.334 2712 Planarity : 0.004 0.044 2733 Dihedral : 8.000 113.886 2952 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.29 % Allowed : 14.88 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.19), residues: 1998 helix: 1.98 (0.25), residues: 462 sheet: 0.56 (0.22), residues: 588 loop : -0.67 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 336 TYR 0.018 0.001 TYR G 49 PHE 0.015 0.001 PHE D 91 TRP 0.016 0.002 TRP C 104 HIS 0.008 0.001 HIS E 29 Details of bonding type rmsd covalent geometry : bond 0.00304 (16332) covalent geometry : angle 0.63285 (22152) SS BOND : bond 0.00348 ( 24) SS BOND : angle 0.96485 ( 48) hydrogen bonds : bond 0.03881 ( 721) hydrogen bonds : angle 4.72766 ( 1911) link_ALPHA1-2 : bond 0.02128 ( 3) link_ALPHA1-2 : angle 3.30804 ( 9) link_ALPHA1-4 : bond 0.00814 ( 6) link_ALPHA1-4 : angle 1.45846 ( 18) link_ALPHA1-6 : bond 0.00641 ( 3) link_ALPHA1-6 : angle 1.33967 ( 9) link_BETA1-4 : bond 0.01265 ( 15) link_BETA1-4 : angle 3.86324 ( 45) link_NAG-ASN : bond 0.00476 ( 12) link_NAG-ASN : angle 2.46790 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2444.55 seconds wall clock time: 43 minutes 5.14 seconds (2585.14 seconds total)