Starting phenix.real_space_refine on Sat Sep 12 13:45:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6tys_20584/09_2026/6tys_20584.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tys_20584/09_2026/6tys_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6tys_20584/09_2026/6tys_20584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tys_20584/09_2026/6tys_20584.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6tys_20584/09_2026/6tys_20584.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6tys_20584/09_2026/6tys_20584.cif" model { file = "/net/cci-nas-00/data/ceres_data/6tys_20584/09_2026/6tys_20584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tys_20584/09_2026/6tys_20584.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 4.15, per 1000 atoms: 0.26 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: 1.35 Conformation dependent library (CDL) restraints added in 667.6 milliseconds 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: 0.61 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: 3.10 Time building geometry restraints manager: 1.68 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 - 17.90: 9252 17.90 - 35.79: 231 35.79 - 53.69: 78 53.69 - 71.58: 18 71.58 - 89.48: 24 Dihedral angle restraints: 9603 sinusoidal: 3726 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 9600 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: 0.05 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.600 Find NCS groups from input model: 0.500 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: 0.020 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 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 : 11.192 89.479 5763 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 are 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/Z covalent geometry : bond 0.02053 / 1.10 (16332) covalent geometry : angle 1.94898 / 1.24 (22152) SS BOND : bond 0.04771 / 2.80 ( 24) SS BOND : angle 3.06560 / 1.99 ( 48) hydrogen bonds : bond 0.19110 / 12.69 ( 721) hydrogen bonds : angle 7.79761 / 5.43 ( 1911) link_ALPHA1-2 : bond 0.10578 / 4.89 ( 3) link_ALPHA1-2 : angle 8.05687 / 4.11 ( 9) link_ALPHA1-4 : bond 0.08669 / 4.57 ( 6) link_ALPHA1-4 : angle 2.81335 / 1.41 ( 18) link_ALPHA1-6 : bond 0.07584 / 3.50 ( 3) link_ALPHA1-6 : angle 2.19531 / 1.18 ( 9) link_BETA1-4 : bond 0.09674 / 5.34 ( 15) link_BETA1-4 : angle 3.92301 / 3.07 ( 45) link_NAG-ASN : bond 0.05243 / 2.91 ( 12) link_NAG-ASN : angle 2.69412 / 1.86 ( 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 : 0.610 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: 0.8884 (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: 0.7807 (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: 0.8503 (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: 0.1326 time to fit residues: 85.2334 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 : 0.651 ------------------------------------------------------------------------------- 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... ** 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103413 restraints weight = 23774.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.105652 restraints weight = 15521.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107111 restraints weight = 11577.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108015 restraints weight = 9504.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108777 restraints weight = 8332.250| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16395 Z= 0.191 Angle : 0.836 16.383 22317 Z= 0.406 Chirality : 0.049 0.351 2712 Planarity : 0.004 0.037 2733 Dihedral : 5.267 56.365 2167 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.78 % Allowed : 8.35 % Favored : 88.87 % 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 are not related in a simple way. whole: 0.85 (0.19), residues: 1998 helix: 1.23 (0.25), residues: 459 sheet: 0.59 (0.20), residues: 600 loop : 0.37 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 353 TYR 0.025 0.002 TYR G 49 PHE 0.020 0.002 PHE D 91 TRP 0.019 0.002 TRP G 32 HIS 0.003 0.001 HIS B 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (16332) covalent geometry : angle 0.79948 / 0.40 (22152) SS BOND : bond 0.00236 / 0.15 ( 24) SS BOND : angle 2.11491 / 1.53 ( 48) hydrogen bonds : bond 0.06054 / 3.93 ( 721) hydrogen bonds : angle 5.91803 / 4.18 ( 1911) link_ALPHA1-2 : bond 0.02907 / 1.35 ( 3) link_ALPHA1-2 : angle 4.95702 / 2.52 ( 9) link_ALPHA1-4 : bond 0.00899 / 0.48 ( 6) link_ALPHA1-4 : angle 1.41528 / 0.74 ( 18) link_ALPHA1-6 : bond 0.00674 / 0.31 ( 3) link_ALPHA1-6 : angle 1.75838 / 0.94 ( 9) link_BETA1-4 : bond 0.01232 / 0.66 ( 15) link_BETA1-4 : angle 3.81195 / 3.03 ( 45) link_NAG-ASN : bond 0.01003 / 0.50 ( 12) link_NAG-ASN : angle 2.75996 / 1.74 ( 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 350 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 301 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7204 (OUTLIER) cc_final: 0.6954 (m110) REVERT: A 348 MET cc_start: 0.8394 (ttm) cc_final: 0.8189 (ttm) REVERT: A 373 VAL cc_start: 0.8831 (t) cc_final: 0.8587 (m) REVERT: H 13 LYS cc_start: 0.8803 (mtpp) cc_final: 0.8313 (mptt) REVERT: H 93 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6867 (mmt) REVERT: L 31 THR cc_start: 0.8855 (p) cc_final: 0.8550 (t) REVERT: B 56 ASP cc_start: 0.7982 (m-30) cc_final: 0.7746 (m-30) REVERT: B 226 MET cc_start: 0.7935 (ttm) cc_final: 0.7516 (ttm) REVERT: C 13 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8344 (mptt) REVERT: C 39 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: C 42 GLU cc_start: 0.7853 (mp0) cc_final: 0.7621 (mp0) REVERT: C 95 TYR cc_start: 0.9305 (m-80) cc_final: 0.8989 (m-10) REVERT: D 31 THR cc_start: 0.8731 (p) cc_final: 0.8500 (t) REVERT: E 49 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8605 (tttt) REVERT: E 56 ASP cc_start: 0.7949 (m-30) cc_final: 0.7746 (m-30) REVERT: E 244 ARG cc_start: 0.8184 (mmp80) cc_final: 0.7765 (mmp80) REVERT: F 13 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8371 (mptt) REVERT: F 32 TYR cc_start: 0.8652 (m-80) cc_final: 0.8432 (m-80) REVERT: F 117 SER cc_start: 0.8805 (t) cc_final: 0.8418 (p) REVERT: G 15 LEU cc_start: 0.8023 (tt) cc_final: 0.7733 (tt) REVERT: G 21 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8979 (pt) outliers start: 49 outliers final: 28 residues processed: 335 average time/residue: 0.1225 time to fit residues: 61.7798 Evaluate side-chains 276 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 40 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN A 372 HIS L 6 GLN L 37 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 = 0.3376 r_free = 0.3376 target = 0.117810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.099324 restraints weight = 24855.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101430 restraints weight = 16769.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102855 restraints weight = 12795.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.103761 restraints weight = 10630.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.104495 restraints weight = 9384.560| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16395 Z= 0.172 Angle : 0.759 17.647 22317 Z= 0.363 Chirality : 0.047 0.346 2712 Planarity : 0.004 0.039 2733 Dihedral : 4.732 24.405 2163 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.70 % Favored : 97.20 % Rotamer: Outliers : 3.80 % Allowed : 10.11 % Favored : 86.09 % 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 are not related in a simple way. whole: 0.67 (0.19), residues: 1998 helix: 1.31 (0.25), residues: 480 sheet: 0.55 (0.20), residues: 600 loop : 0.02 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 82 TYR 0.018 0.001 TYR G 49 PHE 0.020 0.002 PHE D 91 TRP 0.017 0.002 TRP F 104 HIS 0.004 0.001 HIS B 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (16332) covalent geometry : angle 0.72140 / 0.35 (22152) SS BOND : bond 0.00718 / 0.53 ( 24) SS BOND : angle 2.12764 / 1.63 ( 48) hydrogen bonds : bond 0.05047 / 3.30 ( 721) hydrogen bonds : angle 5.46501 / 3.87 ( 1911) link_ALPHA1-2 : bond 0.02830 / 1.30 ( 3) link_ALPHA1-2 : angle 4.87925 / 2.48 ( 9) link_ALPHA1-4 : bond 0.00822 / 0.43 ( 6) link_ALPHA1-4 : angle 1.31374 / 0.70 ( 18) link_ALPHA1-6 : bond 0.00661 / 0.31 ( 3) link_ALPHA1-6 : angle 1.41990 / 0.77 ( 9) link_BETA1-4 : bond 0.01337 / 0.75 ( 15) link_BETA1-4 : angle 3.71653 / 2.99 ( 45) link_NAG-ASN : bond 0.00512 / 0.26 ( 12) link_NAG-ASN : angle 2.53562 / 1.56 ( 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 344 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 277 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.6757 (m110) REVERT: A 180 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8277 (p0) REVERT: A 226 MET cc_start: 0.8269 (ttm) cc_final: 0.8040 (ttp) REVERT: A 373 VAL cc_start: 0.8880 (t) cc_final: 0.8653 (m) REVERT: H 13 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8407 (mptt) REVERT: H 93 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6780 (mmt) REVERT: L 31 THR cc_start: 0.8744 (p) cc_final: 0.8443 (t) REVERT: B 56 ASP cc_start: 0.7835 (m-30) cc_final: 0.7608 (m-30) REVERT: B 98 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8260 (ttmm) REVERT: B 226 MET cc_start: 0.7991 (ttm) cc_final: 0.7511 (ttm) REVERT: C 13 LYS cc_start: 0.8714 (mtpp) cc_final: 0.8441 (mptt) REVERT: C 33 ASP cc_start: 0.7991 (p0) cc_final: 0.7690 (p0) REVERT: C 95 TYR cc_start: 0.9173 (m-80) cc_final: 0.8858 (m-10) REVERT: D 31 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8473 (t) REVERT: E 49 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8635 (tttt) REVERT: F 13 LYS cc_start: 0.8952 (mtpp) cc_final: 0.8486 (mptt) REVERT: F 32 TYR cc_start: 0.8544 (m-80) cc_final: 0.8328 (m-80) REVERT: F 33 ASP cc_start: 0.7987 (p0) cc_final: 0.7696 (p0) REVERT: F 117 SER cc_start: 0.8902 (t) cc_final: 0.8601 (p) outliers start: 67 outliers final: 40 residues processed: 317 average time/residue: 0.1313 time to fit residues: 61.8545 Evaluate side-chains 289 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 124 THR Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 366 GLU 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 40 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 107 LYS Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 49 LYS 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 416 THR Chi-restraints excluded: chain B residue 421 VAL 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 31 THR 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 366 GLU 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: 0.6980 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 372 HIS D 6 GLN F 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.097379 restraints weight = 25416.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100407 restraints weight = 15270.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102376 restraints weight = 10943.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103694 restraints weight = 8826.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104480 restraints weight = 7635.443| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16395 Z= 0.143 Angle : 0.699 15.329 22317 Z= 0.332 Chirality : 0.048 0.487 2712 Planarity : 0.004 0.041 2733 Dihedral : 4.491 29.449 2163 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.07 % Allowed : 11.13 % Favored : 85.80 % 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 are not related in a simple way. whole: 0.72 (0.19), residues: 1998 helix: 1.59 (0.25), residues: 480 sheet: 0.62 (0.21), residues: 597 loop : -0.14 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 336 TYR 0.015 0.001 TYR A 438 PHE 0.018 0.001 PHE D 91 TRP 0.017 0.002 TRP F 104 HIS 0.003 0.001 HIS E 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (16332) covalent geometry : angle 0.66014 / 0.32 (22152) SS BOND : bond 0.00530 / 0.28 ( 24) SS BOND : angle 1.50777 / 0.90 ( 48) hydrogen bonds : bond 0.04351 / 2.84 ( 721) hydrogen bonds : angle 5.11298 / 3.62 ( 1911) link_ALPHA1-2 : bond 0.02685 / 1.24 ( 3) link_ALPHA1-2 : angle 4.62399 / 2.35 ( 9) link_ALPHA1-4 : bond 0.00750 / 0.39 ( 6) link_ALPHA1-4 : angle 1.34323 / 0.71 ( 18) link_ALPHA1-6 : bond 0.00537 / 0.25 ( 3) link_ALPHA1-6 : angle 1.44372 / 0.78 ( 9) link_BETA1-4 : bond 0.01392 / 0.77 ( 15) link_BETA1-4 : angle 3.70607 / 3.03 ( 45) link_NAG-ASN : bond 0.00498 / 0.28 ( 12) link_NAG-ASN : angle 2.73639 / 1.80 ( 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 313 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 259 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.5867 (OUTLIER) cc_final: 0.5634 (m110) REVERT: A 348 MET cc_start: 0.8548 (ttm) cc_final: 0.8303 (ttm) REVERT: A 375 ARG cc_start: 0.7872 (mtt-85) cc_final: 0.7602 (mtt-85) REVERT: A 463 MET cc_start: 0.7652 (ttm) cc_final: 0.7345 (ptm) REVERT: H 13 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8314 (mptt) REVERT: H 50 MET cc_start: 0.8469 (ttt) cc_final: 0.8113 (ttt) REVERT: H 93 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6898 (mmt) REVERT: L 31 THR cc_start: 0.8702 (p) cc_final: 0.8319 (t) REVERT: B 49 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8819 (tttt) REVERT: B 98 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8054 (ttmm) REVERT: C 13 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8344 (mptt) REVERT: C 33 ASP cc_start: 0.8329 (p0) cc_final: 0.7858 (p0) REVERT: C 82 GLN cc_start: 0.7869 (tp40) cc_final: 0.7627 (tp40) REVERT: D 31 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8412 (t) REVERT: E 49 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8764 (tttt) REVERT: F 13 LYS cc_start: 0.9085 (mtpp) cc_final: 0.8438 (mptt) REVERT: F 32 TYR cc_start: 0.8647 (m-80) cc_final: 0.8434 (m-80) REVERT: F 33 ASP cc_start: 0.8212 (p0) cc_final: 0.7792 (p0) REVERT: F 117 SER cc_start: 0.9195 (t) cc_final: 0.8835 (p) REVERT: G 21 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.9008 (pt) outliers start: 54 outliers final: 40 residues processed: 296 average time/residue: 0.1275 time to fit residues: 56.3821 Evaluate side-chains 283 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 416 THR Chi-restraints excluded: chain A residue 421 VAL 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 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 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 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 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 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 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 E residue 49 LYS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 139 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 51 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 81 optimal weight: 0.0050 chunk 145 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 165 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN E 372 HIS F 39 GLN F 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.128405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106620 restraints weight = 24801.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.109651 restraints weight = 14572.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111632 restraints weight = 10372.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112913 restraints weight = 8310.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113768 restraints weight = 7179.857| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16395 Z= 0.125 Angle : 0.641 12.400 22317 Z= 0.307 Chirality : 0.046 0.331 2712 Planarity : 0.004 0.043 2733 Dihedral : 4.295 22.802 2163 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.35 % Allowed : 11.64 % Favored : 85.01 % 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 are not related in a simple way. whole: 0.82 (0.19), residues: 1998 helix: 1.81 (0.25), residues: 480 sheet: 0.68 (0.21), residues: 597 loop : -0.16 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 336 TYR 0.015 0.001 TYR G 49 PHE 0.016 0.001 PHE D 91 TRP 0.017 0.002 TRP F 104 HIS 0.003 0.001 HIS E 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (16332) covalent geometry : angle 0.60314 / 0.30 (22152) SS BOND : bond 0.00422 / 0.21 ( 24) SS BOND : angle 1.29755 / 0.82 ( 48) hydrogen bonds : bond 0.03897 / 2.55 ( 721) hydrogen bonds : angle 4.79480 / 3.40 ( 1911) link_ALPHA1-2 : bond 0.02439 / 1.13 ( 3) link_ALPHA1-2 : angle 4.45493 / 2.27 ( 9) link_ALPHA1-4 : bond 0.00741 / 0.39 ( 6) link_ALPHA1-4 : angle 1.35881 / 0.72 ( 18) link_ALPHA1-6 : bond 0.00484 / 0.22 ( 3) link_ALPHA1-6 : angle 1.42537 / 0.77 ( 9) link_BETA1-4 : bond 0.01301 / 0.72 ( 15) link_BETA1-4 : angle 3.66625 / 3.01 ( 45) link_NAG-ASN : bond 0.00357 / 0.21 ( 12) link_NAG-ASN : angle 2.37954 / 1.52 ( 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 320 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 261 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.5719 (OUTLIER) cc_final: 0.5485 (m110) REVERT: A 180 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7923 (p0) REVERT: A 375 ARG cc_start: 0.7953 (mtt-85) cc_final: 0.7656 (mtt-85) REVERT: A 388 ILE cc_start: 0.8986 (tt) cc_final: 0.8738 (tp) REVERT: H 13 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8385 (mptt) REVERT: H 50 MET cc_start: 0.8333 (ttt) cc_final: 0.7910 (ttt) REVERT: H 93 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6919 (tpp) REVERT: L 20 THR cc_start: 0.9050 (m) cc_final: 0.8753 (p) REVERT: L 31 THR cc_start: 0.8697 (p) cc_final: 0.8327 (t) REVERT: L 89 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8792 (tm-30) REVERT: B 49 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8649 (tttt) REVERT: B 98 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8243 (ttmm) REVERT: B 138 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6686 (mpp) REVERT: B 244 ARG cc_start: 0.8355 (mmp80) cc_final: 0.8067 (mmp80) REVERT: C 13 LYS cc_start: 0.8793 (mtpp) cc_final: 0.8333 (mptt) REVERT: C 32 TYR cc_start: 0.8531 (m-80) cc_final: 0.7992 (m-80) REVERT: C 33 ASP cc_start: 0.8158 (p0) cc_final: 0.7765 (p0) REVERT: C 42 GLU cc_start: 0.7817 (mp0) cc_final: 0.7456 (mp0) REVERT: D 31 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8393 (t) REVERT: E 49 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8651 (tttt) REVERT: F 13 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8488 (mptt) REVERT: F 32 TYR cc_start: 0.8481 (m-80) cc_final: 0.8188 (m-80) REVERT: F 33 ASP cc_start: 0.8155 (p0) cc_final: 0.7756 (p0) REVERT: G 21 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9141 (pt) outliers start: 59 outliers final: 43 residues processed: 304 average time/residue: 0.1318 time to fit residues: 59.5944 Evaluate side-chains 287 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 234 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 40 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 60 SER 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 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 324 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 421 VAL 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 31 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 49 LYS Chi-restraints excluded: chain E residue 114 ILE 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 419 THR Chi-restraints excluded: chain E residue 421 VAL 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 48 VAL 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: 2.9990 chunk 26 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 67 optimal weight: 0.0040 chunk 82 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN A 303 ASN H 39 GLN L 38 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107437 restraints weight = 24448.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110608 restraints weight = 13927.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112684 restraints weight = 9735.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113988 restraints weight = 7709.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114855 restraints weight = 6635.043| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16395 Z= 0.181 Angle : 0.679 12.623 22317 Z= 0.330 Chirality : 0.047 0.343 2712 Planarity : 0.004 0.042 2733 Dihedral : 4.385 22.035 2163 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.69 % Allowed : 12.72 % Favored : 83.59 % 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 are not related in a simple way. whole: 0.85 (0.19), residues: 1998 helix: 2.09 (0.26), residues: 462 sheet: 0.78 (0.22), residues: 591 loop : -0.31 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 336 TYR 0.018 0.001 TYR E 438 PHE 0.021 0.002 PHE D 91 TRP 0.015 0.002 TRP C 104 HIS 0.002 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (16332) covalent geometry : angle 0.64496 / 0.32 (22152) SS BOND : bond 0.00435 / 0.26 ( 24) SS BOND : angle 1.31338 / 0.87 ( 48) hydrogen bonds : bond 0.04309 / 2.82 ( 721) hydrogen bonds : angle 4.84942 / 3.43 ( 1911) link_ALPHA1-2 : bond 0.02193 / 1.01 ( 3) link_ALPHA1-2 : angle 4.16468 / 2.13 ( 9) link_ALPHA1-4 : bond 0.00733 / 0.38 ( 6) link_ALPHA1-4 : angle 1.40305 / 0.74 ( 18) link_ALPHA1-6 : bond 0.00348 / 0.16 ( 3) link_ALPHA1-6 : angle 1.52088 / 0.82 ( 9) link_BETA1-4 : bond 0.01280 / 0.71 ( 15) link_BETA1-4 : angle 3.64925 / 3.01 ( 45) link_NAG-ASN : bond 0.00337 / 0.20 ( 12) link_NAG-ASN : angle 2.14474 / 1.43 ( 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 311 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 246 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.5549 (OUTLIER) cc_final: 0.5266 (m110) REVERT: A 180 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8288 (p0) REVERT: A 244 ARG cc_start: 0.8339 (mmp80) cc_final: 0.8102 (mmp80) REVERT: A 388 ILE cc_start: 0.9004 (tt) cc_final: 0.8765 (tt) REVERT: H 13 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8370 (mmtm) REVERT: H 50 MET cc_start: 0.8364 (ttt) cc_final: 0.8036 (ttt) REVERT: H 82 GLN cc_start: 0.8095 (tp40) cc_final: 0.7776 (tp40) REVERT: H 93 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6806 (mmt) REVERT: L 20 THR cc_start: 0.9061 (m) cc_final: 0.8785 (p) REVERT: L 31 THR cc_start: 0.8716 (p) cc_final: 0.8333 (t) REVERT: L 89 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8944 (tm-30) REVERT: B 49 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8696 (tttt) REVERT: B 98 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8151 (ttmm) REVERT: B 138 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6535 (mpp) REVERT: C 13 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8444 (mptt) REVERT: C 32 TYR cc_start: 0.8616 (m-80) cc_final: 0.8131 (m-80) REVERT: C 33 ASP cc_start: 0.8341 (p0) cc_final: 0.7887 (p0) REVERT: C 42 GLU cc_start: 0.8075 (mp0) cc_final: 0.7715 (mp0) REVERT: D 31 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8331 (t) REVERT: E 49 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8720 (tttt) REVERT: F 13 LYS cc_start: 0.9169 (mtpp) cc_final: 0.8538 (mptt) REVERT: F 32 TYR cc_start: 0.8628 (m-80) cc_final: 0.8372 (m-80) REVERT: F 33 ASP cc_start: 0.8323 (p0) cc_final: 0.7868 (p0) REVERT: F 107 TYR cc_start: 0.8455 (m-80) cc_final: 0.8081 (m-10) REVERT: G 20 THR cc_start: 0.8635 (p) cc_final: 0.8427 (p) REVERT: G 21 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9051 (pt) REVERT: G 31 THR cc_start: 0.8498 (p) cc_final: 0.8215 (t) outliers start: 65 outliers final: 48 residues processed: 292 average time/residue: 0.1321 time to fit residues: 57.3783 Evaluate side-chains 288 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 230 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 ILE 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 93 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 69 THR 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 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 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 49 LYS Chi-restraints excluded: chain E residue 114 ILE 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 419 THR Chi-restraints excluded: chain E residue 421 VAL 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 48 VAL 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 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 13 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 93 optimal weight: 0.0040 chunk 176 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN G 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.105195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.084269 restraints weight = 25740.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.086809 restraints weight = 15750.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.088492 restraints weight = 11352.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.089613 restraints weight = 9134.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.090403 restraints weight = 7878.518| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16395 Z= 0.222 Angle : 0.710 12.606 22317 Z= 0.345 Chirality : 0.048 0.356 2712 Planarity : 0.004 0.040 2733 Dihedral : 4.483 24.326 2163 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.09 % Allowed : 12.83 % Favored : 83.08 % 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 are not related in a simple way. whole: 0.65 (0.19), residues: 1998 helix: 1.95 (0.26), residues: 462 sheet: 0.71 (0.22), residues: 588 loop : -0.49 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 336 TYR 0.020 0.002 TYR A 438 PHE 0.022 0.002 PHE D 91 TRP 0.015 0.002 TRP C 104 HIS 0.003 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (16332) covalent geometry : angle 0.67775 / 0.34 (22152) SS BOND : bond 0.00470 / 0.28 ( 24) SS BOND : angle 1.49088 / 0.95 ( 48) hydrogen bonds : bond 0.04611 / 3.00 ( 721) hydrogen bonds : angle 4.95158 / 3.51 ( 1911) link_ALPHA1-2 : bond 0.01990 / 0.91 ( 3) link_ALPHA1-2 : angle 3.94774 / 2.03 ( 9) link_ALPHA1-4 : bond 0.00763 / 0.39 ( 6) link_ALPHA1-4 : angle 1.43877 / 0.76 ( 18) link_ALPHA1-6 : bond 0.00305 / 0.14 ( 3) link_ALPHA1-6 : angle 1.53665 / 0.83 ( 9) link_BETA1-4 : bond 0.01236 / 0.69 ( 15) link_BETA1-4 : angle 3.64838 / 3.00 ( 45) link_NAG-ASN : bond 0.00369 / 0.20 ( 12) link_NAG-ASN : angle 2.11962 / 1.37 ( 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 299 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 227 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.5479 (OUTLIER) cc_final: 0.5165 (m110) REVERT: A 244 ARG cc_start: 0.8297 (mmp80) cc_final: 0.8088 (mmp80) REVERT: A 388 ILE cc_start: 0.9026 (tt) cc_final: 0.8792 (tt) REVERT: H 13 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8399 (mmtm) REVERT: H 33 ASP cc_start: 0.8486 (p0) cc_final: 0.7915 (p0) REVERT: H 50 MET cc_start: 0.8386 (ttt) cc_final: 0.7991 (ttt) REVERT: L 20 THR cc_start: 0.9058 (m) cc_final: 0.8844 (p) REVERT: L 31 THR cc_start: 0.8755 (p) cc_final: 0.8376 (t) REVERT: L 89 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8993 (tm-30) REVERT: B 98 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8314 (ttmm) REVERT: B 138 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6799 (mpp) REVERT: B 244 ARG cc_start: 0.8255 (mmp80) cc_final: 0.8003 (mmp80) REVERT: C 13 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8444 (mptt) REVERT: C 32 TYR cc_start: 0.8699 (m-80) cc_final: 0.8081 (m-80) REVERT: C 33 ASP cc_start: 0.8386 (p0) cc_final: 0.7869 (p0) REVERT: C 42 GLU cc_start: 0.8068 (mp0) cc_final: 0.7752 (mp0) REVERT: E 49 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8666 (tttt) REVERT: F 13 LYS cc_start: 0.9210 (mtpp) cc_final: 0.8473 (mptt) REVERT: F 32 TYR cc_start: 0.8734 (m-80) cc_final: 0.8530 (m-80) REVERT: F 33 ASP cc_start: 0.8250 (p0) cc_final: 0.7788 (p0) REVERT: F 46 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6724 (mt-10) REVERT: G 31 THR cc_start: 0.8536 (p) cc_final: 0.8267 (t) outliers start: 72 outliers final: 56 residues processed: 281 average time/residue: 0.1381 time to fit residues: 57.2175 Evaluate side-chains 278 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 217 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain H residue 5 VAL 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 33 LEU Chi-restraints excluded: chain L residue 69 THR 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 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 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 54 LEU 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 462 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL 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 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 12 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3267 r_free = 0.3267 target = 0.107421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.086372 restraints weight = 25653.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.088972 restraints weight = 15337.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.090762 restraints weight = 10930.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.091946 restraints weight = 8698.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.092739 restraints weight = 7452.839| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16395 Z= 0.157 Angle : 0.668 12.701 22317 Z= 0.321 Chirality : 0.046 0.348 2712 Planarity : 0.004 0.042 2733 Dihedral : 4.405 22.812 2163 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.41 % Allowed : 13.91 % 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 are not related in a simple way. whole: 0.64 (0.19), residues: 1998 helix: 2.00 (0.26), residues: 462 sheet: 0.67 (0.22), residues: 588 loop : -0.51 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 336 TYR 0.018 0.001 TYR A 438 PHE 0.017 0.002 PHE D 91 TRP 0.016 0.002 TRP C 104 HIS 0.002 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (16332) covalent geometry : angle 0.63507 / 0.31 (22152) SS BOND : bond 0.00373 / 0.22 ( 24) SS BOND : angle 1.28769 / 0.82 ( 48) hydrogen bonds : bond 0.04146 / 2.70 ( 721) hydrogen bonds : angle 4.79789 / 3.41 ( 1911) link_ALPHA1-2 : bond 0.01971 / 0.91 ( 3) link_ALPHA1-2 : angle 3.82937 / 1.97 ( 9) link_ALPHA1-4 : bond 0.00745 / 0.38 ( 6) link_ALPHA1-4 : angle 1.45501 / 0.77 ( 18) link_ALPHA1-6 : bond 0.00360 / 0.17 ( 3) link_ALPHA1-6 : angle 1.47835 / 0.80 ( 9) link_BETA1-4 : bond 0.01277 / 0.70 ( 15) link_BETA1-4 : angle 3.67075 / 3.03 ( 45) link_NAG-ASN : bond 0.00416 / 0.23 ( 12) link_NAG-ASN : angle 2.10047 / 1.41 ( 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 298 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 238 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.5519 (OUTLIER) cc_final: 0.5265 (m110) REVERT: A 388 ILE cc_start: 0.9008 (tt) cc_final: 0.8769 (tt) REVERT: H 13 LYS cc_start: 0.9039 (mtpp) cc_final: 0.8415 (mptt) REVERT: H 33 ASP cc_start: 0.8501 (p0) cc_final: 0.7926 (p0) REVERT: H 50 MET cc_start: 0.8311 (ttt) cc_final: 0.7962 (ttt) REVERT: L 20 THR cc_start: 0.9081 (m) cc_final: 0.8784 (p) REVERT: L 21 ILE cc_start: 0.9326 (pt) cc_final: 0.9105 (pt) REVERT: L 36 TYR cc_start: 0.9124 (m-80) cc_final: 0.8828 (m-80) REVERT: B 98 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8140 (ttmm) REVERT: B 244 ARG cc_start: 0.8227 (mmp80) cc_final: 0.8007 (mmp80) REVERT: C 13 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8465 (mptt) REVERT: C 32 TYR cc_start: 0.8669 (m-80) cc_final: 0.8020 (m-80) REVERT: C 33 ASP cc_start: 0.8330 (p0) cc_final: 0.7785 (p0) REVERT: C 42 GLU cc_start: 0.7972 (mp0) cc_final: 0.7669 (mp0) REVERT: E 49 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8601 (tttt) REVERT: F 13 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8389 (mptt) REVERT: F 32 TYR cc_start: 0.8660 (m-80) cc_final: 0.8454 (m-80) REVERT: F 33 ASP cc_start: 0.8271 (p0) cc_final: 0.7804 (p0) REVERT: G 21 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9020 (pt) REVERT: G 31 THR cc_start: 0.8546 (p) cc_final: 0.8299 (t) REVERT: G 72 SER cc_start: 0.9242 (p) cc_final: 0.9034 (m) outliers start: 60 outliers final: 50 residues processed: 280 average time/residue: 0.1336 time to fit residues: 55.0968 Evaluate side-chains 281 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 138 MET Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 421 VAL 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 69 THR 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 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 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 54 LEU 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 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 462 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL 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 54 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 67 optimal weight: 4.9990 chunk 57 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 105 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 HIS A 180 ASN A 303 ASN B 29 HIS ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108528 restraints weight = 24434.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111719 restraints weight = 13917.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113793 restraints weight = 9718.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115159 restraints weight = 7689.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116032 restraints weight = 6576.815| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4262 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= 0.126 Angle : 0.644 12.893 22317 Z= 0.308 Chirality : 0.045 0.339 2712 Planarity : 0.004 0.042 2733 Dihedral : 4.266 18.787 2163 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.12 % Allowed : 14.20 % 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 are not related in a simple way. whole: 0.68 (0.19), residues: 1998 helix: 2.08 (0.26), residues: 462 sheet: 0.67 (0.22), residues: 588 loop : -0.49 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 336 TYR 0.016 0.001 TYR G 49 PHE 0.014 0.001 PHE D 91 TRP 0.017 0.002 TRP C 104 HIS 0.010 0.002 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (16332) covalent geometry : angle 0.61115 / 0.30 (22152) SS BOND : bond 0.00331 / 0.19 ( 24) SS BOND : angle 0.98708 / 0.65 ( 48) hydrogen bonds : bond 0.03737 / 2.44 ( 721) hydrogen bonds : angle 4.61887 / 3.28 ( 1911) link_ALPHA1-2 : bond 0.01879 / 0.87 ( 3) link_ALPHA1-2 : angle 3.70116 / 1.90 ( 9) link_ALPHA1-4 : bond 0.00757 / 0.39 ( 6) link_ALPHA1-4 : angle 1.44228 / 0.76 ( 18) link_ALPHA1-6 : bond 0.00391 / 0.18 ( 3) link_ALPHA1-6 : angle 1.44359 / 0.78 ( 9) link_BETA1-4 : bond 0.01275 / 0.70 ( 15) link_BETA1-4 : angle 3.70400 / 3.06 ( 45) link_NAG-ASN : bond 0.00418 / 0.23 ( 12) link_NAG-ASN : angle 1.98877 / 1.33 ( 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 295 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.5889 (OUTLIER) cc_final: 0.5572 (m110) REVERT: A 115 MET cc_start: 0.7409 (mtp) cc_final: 0.7149 (ttt) REVERT: A 388 ILE cc_start: 0.8983 (tt) cc_final: 0.8705 (tp) REVERT: A 470 SER cc_start: 0.7541 (m) cc_final: 0.7279 (t) REVERT: H 13 LYS cc_start: 0.9021 (mtpp) cc_final: 0.8420 (mptt) REVERT: H 33 ASP cc_start: 0.8507 (p0) cc_final: 0.7939 (p0) REVERT: H 50 MET cc_start: 0.8196 (ttt) cc_final: 0.7816 (ttt) REVERT: H 110 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7871 (mm-40) REVERT: L 6 GLN cc_start: 0.8528 (tt0) cc_final: 0.8243 (tt0) REVERT: L 20 THR cc_start: 0.9082 (m) cc_final: 0.8652 (p) REVERT: L 36 TYR cc_start: 0.9151 (m-80) cc_final: 0.8886 (m-80) REVERT: B 98 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8129 (ttmm) REVERT: C 13 LYS cc_start: 0.8950 (mtpp) cc_final: 0.8496 (mptt) REVERT: C 19 LYS cc_start: 0.8873 (tttm) cc_final: 0.8644 (tttm) REVERT: C 32 TYR cc_start: 0.8650 (m-80) cc_final: 0.7952 (m-80) REVERT: C 33 ASP cc_start: 0.8235 (p0) cc_final: 0.7717 (p0) REVERT: C 42 GLU cc_start: 0.7928 (mp0) cc_final: 0.7726 (mp0) REVERT: E 49 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8424 (tttt) REVERT: E 470 SER cc_start: 0.7343 (m) cc_final: 0.6913 (p) REVERT: F 13 LYS cc_start: 0.9089 (mtpp) cc_final: 0.8393 (mptt) REVERT: F 33 ASP cc_start: 0.8327 (p0) cc_final: 0.7844 (p0) REVERT: G 21 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9056 (pt) REVERT: G 31 THR cc_start: 0.8502 (p) cc_final: 0.8248 (t) outliers start: 55 outliers final: 50 residues processed: 279 average time/residue: 0.1304 time to fit residues: 54.3082 Evaluate side-chains 278 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 224 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 124 THR Chi-restraints excluded: chain A residue 138 MET 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 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 33 LEU Chi-restraints excluded: chain L residue 69 THR 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 72 THR 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 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 54 LEU 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 462 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 58 VAL 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: 2.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 0.0070 chunk 150 optimal weight: 0.3980 chunk 134 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN B 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099158 restraints weight = 25140.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102073 restraints weight = 15176.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103953 restraints weight = 10964.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105210 restraints weight = 8883.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105982 restraints weight = 7711.125| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16395 Z= 0.131 Angle : 0.647 12.957 22317 Z= 0.310 Chirality : 0.045 0.338 2712 Planarity : 0.004 0.042 2733 Dihedral : 4.236 20.808 2163 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.01 % Allowed : 14.54 % Favored : 82.45 % 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 are not related in a simple way. whole: 0.67 (0.19), residues: 1998 helix: 2.10 (0.25), residues: 462 sheet: 0.67 (0.22), residues: 588 loop : -0.51 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 336 TYR 0.016 0.001 TYR G 49 PHE 0.015 0.001 PHE D 91 TRP 0.017 0.001 TRP C 104 HIS 0.007 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (16332) covalent geometry : angle 0.61490 / 0.30 (22152) SS BOND : bond 0.00321 / 0.18 ( 24) SS BOND : angle 0.98255 / 0.64 ( 48) hydrogen bonds : bond 0.03748 / 2.46 ( 721) hydrogen bonds : angle 4.57675 / 3.26 ( 1911) link_ALPHA1-2 : bond 0.01844 / 0.86 ( 3) link_ALPHA1-2 : angle 3.59672 / 1.84 ( 9) link_ALPHA1-4 : bond 0.00740 / 0.38 ( 6) link_ALPHA1-4 : angle 1.42483 / 0.76 ( 18) link_ALPHA1-6 : bond 0.00364 / 0.17 ( 3) link_ALPHA1-6 : angle 1.44937 / 0.78 ( 9) link_BETA1-4 : bond 0.01288 / 0.71 ( 15) link_BETA1-4 : angle 3.68362 / 3.05 ( 45) link_NAG-ASN : bond 0.00501 / 0.26 ( 12) link_NAG-ASN : angle 1.98740 / 1.33 ( 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 283 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.6014 (OUTLIER) cc_final: 0.5709 (m110) REVERT: A 388 ILE cc_start: 0.8947 (tt) cc_final: 0.8656 (tp) REVERT: A 470 SER cc_start: 0.7496 (m) cc_final: 0.7243 (t) REVERT: H 13 LYS cc_start: 0.9011 (mtpp) cc_final: 0.8383 (mptt) REVERT: H 33 ASP cc_start: 0.8498 (p0) cc_final: 0.7939 (p0) REVERT: H 50 MET cc_start: 0.8211 (ttt) cc_final: 0.7804 (ttt) REVERT: L 6 GLN cc_start: 0.8602 (tt0) cc_final: 0.8359 (tt0) REVERT: L 36 TYR cc_start: 0.9148 (m-80) cc_final: 0.8875 (m-80) REVERT: B 98 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7871 (ttmm) REVERT: C 13 LYS cc_start: 0.9005 (mtpp) cc_final: 0.8531 (mptt) REVERT: C 19 LYS cc_start: 0.8831 (tttm) cc_final: 0.8581 (tttm) REVERT: C 32 TYR cc_start: 0.8534 (m-80) cc_final: 0.7839 (m-80) REVERT: C 33 ASP cc_start: 0.8231 (p0) cc_final: 0.7739 (p0) REVERT: C 42 GLU cc_start: 0.7947 (mp0) cc_final: 0.7623 (mp0) REVERT: E 49 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8452 (tttt) REVERT: E 470 SER cc_start: 0.7385 (m) cc_final: 0.6995 (p) REVERT: F 13 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8456 (mptt) REVERT: F 33 ASP cc_start: 0.8300 (p0) cc_final: 0.7824 (p0) REVERT: F 107 TYR cc_start: 0.8381 (m-80) cc_final: 0.8051 (m-10) REVERT: G 21 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9094 (pt) REVERT: G 31 THR cc_start: 0.8514 (p) cc_final: 0.8268 (t) outliers start: 53 outliers final: 48 residues processed: 267 average time/residue: 0.1322 time to fit residues: 52.2876 Evaluate side-chains 278 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 226 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 124 THR Chi-restraints excluded: chain A residue 138 MET 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 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 33 LEU 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 62 ILE Chi-restraints excluded: chain B residue 72 THR 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 180 ASN 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 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 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 F residue 11 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 58 VAL 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 124 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 159 optimal weight: 0.0470 chunk 29 optimal weight: 2.9990 chunk 163 optimal weight: 0.0870 chunk 27 optimal weight: 0.0980 chunk 180 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.099386 restraints weight = 25180.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102297 restraints weight = 15172.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104203 restraints weight = 10958.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105464 restraints weight = 8853.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106057 restraints weight = 7676.889| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.317 16395 Z= 0.243 Angle : 0.915 59.172 22317 Z= 0.538 Chirality : 0.047 0.691 2712 Planarity : 0.005 0.154 2733 Dihedral : 4.289 24.845 2163 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 3.18 % Allowed : 14.48 % Favored : 82.34 % Cbeta Deviations : 0.11 % 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 are not related in a simple way. whole: 0.67 (0.19), residues: 1998 helix: 2.11 (0.25), residues: 462 sheet: 0.67 (0.22), residues: 588 loop : -0.51 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 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 0.006 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.24 (16332) covalent geometry : angle 0.89398 / 0.53 (22152) SS BOND : bond 0.00320 / 0.18 ( 24) SS BOND : angle 0.95847 / 0.62 ( 48) hydrogen bonds : bond 0.03785 / 2.46 ( 721) hydrogen bonds : angle 4.59190 / 3.28 ( 1911) link_ALPHA1-2 : bond 0.01500 / 0.65 ( 3) link_ALPHA1-2 : angle 3.66331 / 1.90 ( 9) link_ALPHA1-4 : bond 0.00711 / 0.37 ( 6) link_ALPHA1-4 : angle 1.44242 / 0.76 ( 18) link_ALPHA1-6 : bond 0.00396 / 0.18 ( 3) link_ALPHA1-6 : angle 1.46581 / 0.79 ( 9) link_BETA1-4 : bond 0.01117 / 0.52 ( 15) link_BETA1-4 : angle 3.70347 / 3.06 ( 45) link_NAG-ASN : bond 0.00508 / 0.27 ( 12) link_NAG-ASN : angle 1.98355 / 1.33 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2676.35 seconds wall clock time: 47 minutes 18.74 seconds (2838.74 seconds total)