Starting phenix.real_space_refine on Sun May 3 12:12:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzn_48762/05_2026/9mzn_48762.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzn_48762/05_2026/9mzn_48762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mzn_48762/05_2026/9mzn_48762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzn_48762/05_2026/9mzn_48762.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mzn_48762/05_2026/9mzn_48762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzn_48762/05_2026/9mzn_48762.map" } resolution = 3.4 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= 0.003 sd= 0.039 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 68 5.16 5 C 8123 2.51 5 N 2149 2.21 5 O 2444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12784 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3170 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 16, 'TRANS': 382} Chain: "B" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3057 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 15, 'TRANS': 368} Chain: "C" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3170 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 16, 'TRANS': 382} Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.48, per 1000 atoms: 0.27 Number of scatterers: 12784 At special positions: 0 Unit cell: (159, 100.7, 94.34, 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 68 16.00 O 2444 8.00 N 2149 7.00 C 8123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1001 " - " ASN A 412 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 412 " " NAG B1003 " - " ASN B 378 " " NAG C1001 " - " ASN C 412 " " NAG C1002 " - " ASN C 430 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG E 1 " - " ASN A 275 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN B 67 " " NAG H 1 " - " ASN C 378 " " NAG I 1 " - " ASN C 275 " " NAG J 1 " - " ASN C 67 " " NAG K 1 " - " ASN D 67 " " NAG L 1 " - " ASN D 378 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 561.7 milliseconds 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2950 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 13 sheets defined 41.0% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.797A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 removed outlier: 4.168A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.675A pdb=" N ALA A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 266 through 273 removed outlier: 3.514A pdb=" N ARG A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR A 271 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.551A pdb=" N SER A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 Processing helix chain 'A' and resid 356 through 365 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.323A pdb=" N LEU A 428 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 429 " --> pdb=" O ASP A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 88 through 101 Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.726A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 231 through 245 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 300 Processing helix chain 'B' and resid 317 through 337 removed outlier: 3.524A pdb=" N GLN B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 111 through 126 Processing helix chain 'C' and resid 152 through 168 removed outlier: 4.405A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 185 removed outlier: 4.135A pdb=" N ILE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 231 through 245 removed outlier: 4.028A pdb=" N MET C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.734A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 Processing helix chain 'C' and resid 317 through 337 removed outlier: 3.777A pdb=" N PHE C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 365 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 101 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.979A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 4.068A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 185 removed outlier: 4.344A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 246 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 266 through 271 removed outlier: 4.692A pdb=" N TYR D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 300 Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.523A pdb=" N GLN D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 83 removed outlier: 9.742A pdb=" N ALA A 105 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ARG A 37 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N PHE A 107 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLY A 39 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 203 removed outlier: 3.708A pdb=" N TYR A 176 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 279 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.943A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 406 removed outlier: 4.082A pdb=" N ASP A 406 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 75 through 83 removed outlier: 5.846A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N PHE B 107 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLY B 39 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.342A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 279 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 389 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR B 404 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 83 removed outlier: 6.521A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N PHE C 107 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY C 39 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.579A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N PHE C 279 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE C 256 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU C 389 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR C 404 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 74 through 83 removed outlier: 7.214A pdb=" N HIS D 34 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR D 77 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D 41 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.063A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N PHE D 279 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N PHE D 256 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU D 389 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR D 404 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 369 through 370 502 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4047 1.34 - 1.46: 2297 1.46 - 1.58: 6602 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 13066 Sorted by residual: bond pdb=" CB TRP A 296 " pdb=" CG TRP A 296 " ideal model delta sigma weight residual 1.498 1.542 -0.044 3.10e-02 1.04e+03 2.01e+00 bond pdb=" CA ASP D 260 " pdb=" CB ASP D 260 " ideal model delta sigma weight residual 1.532 1.563 -0.030 2.23e-02 2.01e+03 1.87e+00 bond pdb=" CB ARG C 68 " pdb=" CG ARG C 68 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.43e+00 bond pdb=" C LYS C 212 " pdb=" N PRO C 213 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.20e-02 6.94e+03 1.38e+00 bond pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta sigma weight residual 1.527 1.547 -0.020 1.75e-02 3.27e+03 1.31e+00 ... (remaining 13061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 17432 2.14 - 4.28: 217 4.28 - 6.42: 28 6.42 - 8.56: 10 8.56 - 10.70: 3 Bond angle restraints: 17690 Sorted by residual: angle pdb=" C SER D 47 " pdb=" CA SER D 47 " pdb=" CB SER D 47 " ideal model delta sigma weight residual 116.54 111.28 5.26 1.15e+00 7.56e-01 2.09e+01 angle pdb=" CB MET B 248 " pdb=" CG MET B 248 " pdb=" SD MET B 248 " ideal model delta sigma weight residual 112.70 123.40 -10.70 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CB MET A 248 " pdb=" CG MET A 248 " pdb=" SD MET A 248 " ideal model delta sigma weight residual 112.70 122.69 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CB ARG C 68 " pdb=" CG ARG C 68 " pdb=" CD ARG C 68 " ideal model delta sigma weight residual 111.30 118.94 -7.64 2.30e+00 1.89e-01 1.10e+01 angle pdb=" C2 NAG F 1 " pdb=" N2 NAG F 1 " pdb=" C7 NAG F 1 " ideal model delta sigma weight residual 124.56 134.16 -9.60 3.00e+00 1.11e-01 1.02e+01 ... (remaining 17685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 7081 17.74 - 35.47: 847 35.47 - 53.21: 180 53.21 - 70.95: 22 70.95 - 88.68: 16 Dihedral angle restraints: 8146 sinusoidal: 3583 harmonic: 4563 Sorted by residual: dihedral pdb=" CB CYS C 96 " pdb=" SG CYS C 96 " pdb=" SG CYS C 347 " pdb=" CB CYS C 347 " ideal model delta sinusoidal sigma weight residual 93.00 169.39 -76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 347 " pdb=" CB CYS A 347 " ideal model delta sinusoidal sigma weight residual -86.00 -141.34 55.34 1 1.00e+01 1.00e-02 4.14e+01 dihedral pdb=" CA ALA B 191 " pdb=" C ALA B 191 " pdb=" N PRO B 192 " pdb=" CA PRO B 192 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 8143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1658 0.047 - 0.095: 297 0.095 - 0.142: 79 0.142 - 0.190: 2 0.190 - 0.237: 5 Chirality restraints: 2041 Sorted by residual: chirality pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" N2 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.25 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C3 NAG I 1 " pdb=" C2 NAG I 1 " pdb=" C4 NAG I 1 " pdb=" O3 NAG I 1 " both_signs ideal model delta sigma weight residual False 2.45 2.23 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE A 424 " pdb=" CA ILE A 424 " pdb=" CG1 ILE A 424 " pdb=" CG2 ILE A 424 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2038 not shown) Planarity restraints: 2241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 169 " -0.039 2.00e-02 2.50e+03 2.97e-02 2.21e+01 pdb=" CG TRP A 169 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP A 169 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 169 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 169 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 169 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 169 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 169 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 169 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 169 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 304 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO D 305 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 305 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 305 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 337 " 0.011 2.00e-02 2.50e+03 1.28e-02 2.88e+00 pdb=" CG PHE A 337 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 337 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 337 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 337 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 337 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 337 " -0.002 2.00e-02 2.50e+03 ... (remaining 2238 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 6914 3.00 - 3.48: 12892 3.48 - 3.95: 20323 3.95 - 4.43: 23320 4.43 - 4.90: 37061 Nonbonded interactions: 100510 Sorted by model distance: nonbonded pdb=" O THR D 257 " pdb=" OG1 THR D 257 " model vdw 2.526 3.040 nonbonded pdb=" O THR C 257 " pdb=" OG1 THR C 257 " model vdw 2.545 3.040 nonbonded pdb=" C ASP B 87 " pdb=" OD1 ASP B 87 " model vdw 2.588 3.270 nonbonded pdb=" O SER D 110 " pdb=" OG SER D 110 " model vdw 2.590 3.040 nonbonded pdb=" C4 NAG I 1 " pdb=" O5 NAG I 2 " model vdw 2.605 2.776 ... (remaining 100505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 415 or resid 1001)) selection = (chain 'B' and (resid 33 through 415 or resid 1003)) selection = (chain 'C' and (resid 33 through 415 or resid 1001)) selection = (chain 'D' and (resid 33 through 415 or resid 1002)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.340 Find NCS groups from input model: 0.370 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: 0.000 Load rotamer database and sin/cos tables:1.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 0.003 0.044 13094 Z= 0.123 Angle : 0.614 10.704 17770 Z= 0.309 Chirality : 0.041 0.237 2041 Planarity : 0.003 0.053 2225 Dihedral : 15.362 88.684 5184 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.53 % Allowed : 16.73 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.21), residues: 1557 helix: 0.30 (0.21), residues: 570 sheet: -1.33 (0.34), residues: 263 loop : -1.41 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 354 TYR 0.013 0.001 TYR A 78 PHE 0.030 0.001 PHE A 337 TRP 0.079 0.002 TRP A 169 HIS 0.018 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00274 (13066) covalent geometry : angle 0.59819 (17690) SS BOND : bond 0.00288 ( 4) SS BOND : angle 0.75520 ( 8) hydrogen bonds : bond 0.21166 ( 502) hydrogen bonds : angle 7.04067 ( 1446) link_BETA1-4 : bond 0.00675 ( 8) link_BETA1-4 : angle 2.16443 ( 24) link_NAG-ASN : bond 0.00266 ( 16) link_NAG-ASN : angle 2.27530 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.529 Fit side-chains REVERT: A 78 TYR cc_start: 0.8144 (p90) cc_final: 0.7859 (p90) REVERT: A 316 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7175 (mmt) REVERT: B 70 LEU cc_start: 0.8600 (mp) cc_final: 0.8322 (mp) REVERT: B 83 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6719 (pt) REVERT: B 296 TRP cc_start: 0.8901 (t60) cc_final: 0.8276 (t60) REVERT: B 316 MET cc_start: 0.8645 (tpt) cc_final: 0.7858 (tpt) REVERT: B 323 MET cc_start: 0.8593 (mmm) cc_final: 0.8367 (mmm) REVERT: B 355 PHE cc_start: 0.8620 (m-80) cc_final: 0.8412 (m-80) REVERT: C 245 MET cc_start: 0.7814 (pmm) cc_final: 0.7474 (pmm) REVERT: C 265 ASP cc_start: 0.7887 (t0) cc_final: 0.6998 (m-30) REVERT: D 44 TYR cc_start: 0.8812 (t80) cc_final: 0.8422 (t80) REVERT: D 233 GLU cc_start: 0.8657 (mp0) cc_final: 0.8409 (mp0) outliers start: 21 outliers final: 16 residues processed: 195 average time/residue: 0.0880 time to fit residues: 26.8573 Evaluate side-chains 197 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 331 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN D 34 HIS D 350 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.142183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.103168 restraints weight = 18621.668| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.27 r_work: 0.3154 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13094 Z= 0.313 Angle : 0.690 10.648 17770 Z= 0.343 Chirality : 0.045 0.212 2041 Planarity : 0.004 0.055 2225 Dihedral : 7.099 59.584 2227 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.65 % Allowed : 16.73 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.22), residues: 1557 helix: 0.82 (0.21), residues: 573 sheet: -1.30 (0.32), residues: 292 loop : -1.36 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 431 TYR 0.013 0.002 TYR C 78 PHE 0.019 0.002 PHE A 166 TRP 0.047 0.002 TRP A 169 HIS 0.007 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00747 (13066) covalent geometry : angle 0.67374 (17690) SS BOND : bond 0.00326 ( 4) SS BOND : angle 1.32969 ( 8) hydrogen bonds : bond 0.04452 ( 502) hydrogen bonds : angle 5.00212 ( 1446) link_BETA1-4 : bond 0.00641 ( 8) link_BETA1-4 : angle 2.37897 ( 24) link_NAG-ASN : bond 0.00403 ( 16) link_NAG-ASN : angle 2.46249 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 179 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 296 TRP cc_start: 0.7530 (t60) cc_final: 0.7226 (t60) REVERT: B 83 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7191 (tp) REVERT: B 260 ASP cc_start: 0.8644 (t70) cc_final: 0.8328 (t0) REVERT: B 296 TRP cc_start: 0.8984 (t60) cc_final: 0.8085 (t60) REVERT: B 316 MET cc_start: 0.8688 (tpt) cc_final: 0.7891 (tpt) REVERT: B 413 MET cc_start: 0.8705 (ptm) cc_final: 0.8472 (ptm) REVERT: C 245 MET cc_start: 0.8375 (pmm) cc_final: 0.8058 (pmm) REVERT: C 312 LEU cc_start: 0.8258 (mp) cc_final: 0.7993 (mt) REVERT: D 44 TYR cc_start: 0.8811 (t80) cc_final: 0.8418 (t80) REVERT: D 87 ASP cc_start: 0.7784 (t0) cc_final: 0.7371 (t0) REVERT: D 245 MET cc_start: 0.9180 (mmm) cc_final: 0.8597 (mmm) outliers start: 50 outliers final: 35 residues processed: 214 average time/residue: 0.0841 time to fit residues: 28.8690 Evaluate side-chains 202 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 329 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 141 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN C 165 GLN D 34 HIS D 350 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108463 restraints weight = 18570.831| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.36 r_work: 0.3240 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13094 Z= 0.128 Angle : 0.554 9.468 17770 Z= 0.275 Chirality : 0.041 0.223 2041 Planarity : 0.003 0.053 2225 Dihedral : 6.131 59.103 2208 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.29 % Allowed : 17.60 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.22), residues: 1557 helix: 1.08 (0.21), residues: 573 sheet: -1.33 (0.33), residues: 275 loop : -1.27 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 431 TYR 0.013 0.001 TYR C 324 PHE 0.018 0.001 PHE B 337 TRP 0.016 0.001 TRP A 169 HIS 0.006 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00306 (13066) covalent geometry : angle 0.53658 (17690) SS BOND : bond 0.00312 ( 4) SS BOND : angle 1.22017 ( 8) hydrogen bonds : bond 0.03775 ( 502) hydrogen bonds : angle 4.60890 ( 1446) link_BETA1-4 : bond 0.00592 ( 8) link_BETA1-4 : angle 2.16779 ( 24) link_NAG-ASN : bond 0.00273 ( 16) link_NAG-ASN : angle 2.26007 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.448 Fit side-chains REVERT: A 296 TRP cc_start: 0.7636 (t60) cc_final: 0.7112 (t60) REVERT: B 83 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.6844 (pt) REVERT: B 260 ASP cc_start: 0.8430 (t70) cc_final: 0.8146 (t0) REVERT: B 296 TRP cc_start: 0.8945 (t60) cc_final: 0.8040 (t60) REVERT: B 316 MET cc_start: 0.8636 (tpt) cc_final: 0.7855 (tpt) REVERT: B 323 MET cc_start: 0.8673 (mmm) cc_final: 0.7948 (mmm) REVERT: B 331 SER cc_start: 0.9169 (t) cc_final: 0.8587 (p) REVERT: C 245 MET cc_start: 0.8203 (pmm) cc_final: 0.7942 (pmm) REVERT: C 265 ASP cc_start: 0.7996 (t0) cc_final: 0.6686 (p0) REVERT: C 312 LEU cc_start: 0.8267 (mp) cc_final: 0.8033 (mt) REVERT: C 365 GLU cc_start: 0.7925 (pp20) cc_final: 0.7494 (pp20) REVERT: C 368 TRP cc_start: 0.8960 (t60) cc_final: 0.8650 (t60) REVERT: D 44 TYR cc_start: 0.8780 (t80) cc_final: 0.8405 (t80) REVERT: D 87 ASP cc_start: 0.7731 (t0) cc_final: 0.7146 (t0) REVERT: D 245 MET cc_start: 0.9135 (mmm) cc_final: 0.8499 (mmm) REVERT: D 331 SER cc_start: 0.9313 (t) cc_final: 0.8785 (p) outliers start: 45 outliers final: 24 residues processed: 222 average time/residue: 0.0811 time to fit residues: 29.1583 Evaluate side-chains 201 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 289 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 93 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108416 restraints weight = 18596.202| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.36 r_work: 0.3241 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13094 Z= 0.144 Angle : 0.558 9.522 17770 Z= 0.275 Chirality : 0.041 0.220 2041 Planarity : 0.003 0.053 2225 Dihedral : 5.868 59.328 2203 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.92 % Allowed : 19.72 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.22), residues: 1557 helix: 1.17 (0.21), residues: 573 sheet: -1.30 (0.33), residues: 274 loop : -1.30 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 184 TYR 0.012 0.001 TYR C 324 PHE 0.013 0.001 PHE D 89 TRP 0.031 0.001 TRP A 169 HIS 0.006 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00347 (13066) covalent geometry : angle 0.54055 (17690) SS BOND : bond 0.00413 ( 4) SS BOND : angle 1.31652 ( 8) hydrogen bonds : bond 0.03520 ( 502) hydrogen bonds : angle 4.47041 ( 1446) link_BETA1-4 : bond 0.00648 ( 8) link_BETA1-4 : angle 2.13987 ( 24) link_NAG-ASN : bond 0.00251 ( 16) link_NAG-ASN : angle 2.21493 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.487 Fit side-chains REVERT: A 285 GLU cc_start: 0.8257 (pm20) cc_final: 0.7555 (pm20) REVERT: A 296 TRP cc_start: 0.7627 (t60) cc_final: 0.7137 (t60) REVERT: A 316 MET cc_start: 0.8013 (tpp) cc_final: 0.7693 (tpp) REVERT: A 400 GLU cc_start: 0.7780 (pt0) cc_final: 0.7448 (pt0) REVERT: B 83 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6911 (pt) REVERT: B 260 ASP cc_start: 0.8419 (t70) cc_final: 0.8076 (t0) REVERT: B 296 TRP cc_start: 0.8950 (t60) cc_final: 0.8430 (t60) REVERT: B 323 MET cc_start: 0.8697 (mmm) cc_final: 0.7913 (mmm) REVERT: B 331 SER cc_start: 0.9139 (t) cc_final: 0.8552 (p) REVERT: C 245 MET cc_start: 0.8147 (pmm) cc_final: 0.7939 (pmm) REVERT: C 265 ASP cc_start: 0.7962 (t0) cc_final: 0.6680 (p0) REVERT: C 365 GLU cc_start: 0.7937 (pp20) cc_final: 0.7498 (pp20) REVERT: C 368 TRP cc_start: 0.8969 (t60) cc_final: 0.8652 (t60) REVERT: D 44 TYR cc_start: 0.8776 (t80) cc_final: 0.8390 (t80) REVERT: D 87 ASP cc_start: 0.7822 (t0) cc_final: 0.7199 (t0) REVERT: D 245 MET cc_start: 0.9090 (mmm) cc_final: 0.8563 (mmm) REVERT: D 331 SER cc_start: 0.9350 (t) cc_final: 0.8773 (p) outliers start: 40 outliers final: 30 residues processed: 208 average time/residue: 0.0832 time to fit residues: 27.9440 Evaluate side-chains 202 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 289 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN D 34 HIS D 350 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.145337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106429 restraints weight = 18496.537| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.28 r_work: 0.3205 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13094 Z= 0.171 Angle : 0.570 9.549 17770 Z= 0.280 Chirality : 0.041 0.215 2041 Planarity : 0.003 0.053 2225 Dihedral : 5.718 59.048 2202 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.16 % Allowed : 19.43 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1557 helix: 1.20 (0.21), residues: 576 sheet: -1.28 (0.33), residues: 273 loop : -1.35 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.012 0.001 TYR C 252 PHE 0.020 0.001 PHE D 38 TRP 0.016 0.001 TRP A 169 HIS 0.007 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00411 (13066) covalent geometry : angle 0.55362 (17690) SS BOND : bond 0.00818 ( 4) SS BOND : angle 1.15804 ( 8) hydrogen bonds : bond 0.03465 ( 502) hydrogen bonds : angle 4.39807 ( 1446) link_BETA1-4 : bond 0.00634 ( 8) link_BETA1-4 : angle 2.14956 ( 24) link_NAG-ASN : bond 0.00253 ( 16) link_NAG-ASN : angle 2.22399 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 185 time to evaluate : 0.453 Fit side-chains REVERT: A 296 TRP cc_start: 0.8150 (t60) cc_final: 0.7409 (t60) REVERT: A 316 MET cc_start: 0.8431 (tpp) cc_final: 0.7528 (tpp) REVERT: A 400 GLU cc_start: 0.7728 (pt0) cc_final: 0.7414 (pt0) REVERT: B 83 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6788 (pt) REVERT: B 260 ASP cc_start: 0.8578 (t70) cc_final: 0.8220 (t0) REVERT: B 296 TRP cc_start: 0.8951 (t60) cc_final: 0.8438 (t60) REVERT: B 323 MET cc_start: 0.8657 (mmm) cc_final: 0.7903 (mmm) REVERT: B 331 SER cc_start: 0.9187 (t) cc_final: 0.8581 (p) REVERT: C 265 ASP cc_start: 0.7970 (t0) cc_final: 0.6628 (p0) REVERT: C 365 GLU cc_start: 0.7956 (pp20) cc_final: 0.7494 (pp20) REVERT: C 368 TRP cc_start: 0.8995 (t60) cc_final: 0.8642 (t60) REVERT: D 44 TYR cc_start: 0.8768 (t80) cc_final: 0.8370 (t80) REVERT: D 87 ASP cc_start: 0.7773 (t0) cc_final: 0.7117 (t0) REVERT: D 245 MET cc_start: 0.9080 (mmm) cc_final: 0.8590 (mmm) REVERT: D 331 SER cc_start: 0.9301 (t) cc_final: 0.8682 (p) outliers start: 57 outliers final: 40 residues processed: 221 average time/residue: 0.0824 time to fit residues: 29.1659 Evaluate side-chains 212 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 289 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 88 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN D 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108234 restraints weight = 18405.468| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.35 r_work: 0.3237 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13094 Z= 0.138 Angle : 0.565 9.508 17770 Z= 0.276 Chirality : 0.040 0.218 2041 Planarity : 0.003 0.053 2225 Dihedral : 5.562 58.782 2202 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.58 % Allowed : 19.14 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.22), residues: 1557 helix: 1.27 (0.21), residues: 575 sheet: -1.28 (0.33), residues: 273 loop : -1.30 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 198 TYR 0.013 0.001 TYR A 78 PHE 0.012 0.001 PHE D 89 TRP 0.032 0.001 TRP A 169 HIS 0.008 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00331 (13066) covalent geometry : angle 0.54851 (17690) SS BOND : bond 0.00323 ( 4) SS BOND : angle 1.43639 ( 8) hydrogen bonds : bond 0.03340 ( 502) hydrogen bonds : angle 4.33116 ( 1446) link_BETA1-4 : bond 0.00594 ( 8) link_BETA1-4 : angle 2.06684 ( 24) link_NAG-ASN : bond 0.00238 ( 16) link_NAG-ASN : angle 2.16710 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 296 TRP cc_start: 0.8280 (t60) cc_final: 0.7498 (t60) REVERT: A 316 MET cc_start: 0.8495 (tpp) cc_final: 0.7556 (tpp) REVERT: A 400 GLU cc_start: 0.7804 (pt0) cc_final: 0.7489 (pt0) REVERT: B 83 ILE cc_start: 0.7278 (OUTLIER) cc_final: 0.6807 (pt) REVERT: B 260 ASP cc_start: 0.8498 (t70) cc_final: 0.8141 (t0) REVERT: B 296 TRP cc_start: 0.8954 (t60) cc_final: 0.8177 (t60) REVERT: B 316 MET cc_start: 0.8499 (tpt) cc_final: 0.7922 (tpp) REVERT: B 323 MET cc_start: 0.8600 (mmm) cc_final: 0.7888 (mmm) REVERT: B 331 SER cc_start: 0.9185 (t) cc_final: 0.8585 (p) REVERT: C 133 ARG cc_start: 0.8945 (tpp80) cc_final: 0.8703 (mmm-85) REVERT: C 247 MET cc_start: 0.8477 (mtp) cc_final: 0.8226 (mtp) REVERT: C 265 ASP cc_start: 0.7955 (t0) cc_final: 0.6673 (p0) REVERT: C 365 GLU cc_start: 0.7989 (pp20) cc_final: 0.7536 (pp20) REVERT: C 368 TRP cc_start: 0.8974 (t60) cc_final: 0.8675 (t60) REVERT: D 44 TYR cc_start: 0.8772 (t80) cc_final: 0.8385 (t80) REVERT: D 87 ASP cc_start: 0.7833 (t0) cc_final: 0.7168 (t0) REVERT: D 245 MET cc_start: 0.9061 (mmm) cc_final: 0.8626 (mmm) REVERT: D 331 SER cc_start: 0.9326 (t) cc_final: 0.8740 (p) REVERT: D 340 MET cc_start: 0.7838 (tpp) cc_final: 0.7638 (mmt) outliers start: 49 outliers final: 40 residues processed: 209 average time/residue: 0.0825 time to fit residues: 27.6410 Evaluate side-chains 217 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 289 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 117 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN C 136 HIS D 350 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.148410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108772 restraints weight = 18450.406| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.37 r_work: 0.3211 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13094 Z= 0.131 Angle : 0.561 10.030 17770 Z= 0.273 Chirality : 0.040 0.219 2041 Planarity : 0.003 0.053 2225 Dihedral : 5.430 58.669 2202 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.80 % Allowed : 19.50 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1557 helix: 1.30 (0.21), residues: 575 sheet: -1.26 (0.33), residues: 273 loop : -1.28 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 198 TYR 0.014 0.001 TYR A 78 PHE 0.012 0.001 PHE D 337 TRP 0.032 0.001 TRP A 169 HIS 0.016 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00313 (13066) covalent geometry : angle 0.54569 (17690) SS BOND : bond 0.00486 ( 4) SS BOND : angle 1.16077 ( 8) hydrogen bonds : bond 0.03258 ( 502) hydrogen bonds : angle 4.28286 ( 1446) link_BETA1-4 : bond 0.00577 ( 8) link_BETA1-4 : angle 2.01284 ( 24) link_NAG-ASN : bond 0.00223 ( 16) link_NAG-ASN : angle 2.13631 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 169 TRP cc_start: 0.7741 (m100) cc_final: 0.7509 (m100) REVERT: A 296 TRP cc_start: 0.8258 (t60) cc_final: 0.7287 (t60) REVERT: A 316 MET cc_start: 0.8699 (tpp) cc_final: 0.7360 (tpp) REVERT: A 400 GLU cc_start: 0.7776 (pt0) cc_final: 0.7459 (pt0) REVERT: B 83 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6687 (pt) REVERT: B 260 ASP cc_start: 0.8559 (t70) cc_final: 0.8210 (t0) REVERT: B 296 TRP cc_start: 0.8966 (t60) cc_final: 0.8202 (t60) REVERT: B 316 MET cc_start: 0.8521 (tpt) cc_final: 0.7921 (tpp) REVERT: B 323 MET cc_start: 0.8701 (mmm) cc_final: 0.7816 (mmm) REVERT: B 331 SER cc_start: 0.9150 (t) cc_final: 0.8593 (p) REVERT: C 133 ARG cc_start: 0.8945 (tpp80) cc_final: 0.8676 (mmm-85) REVERT: C 265 ASP cc_start: 0.7970 (t0) cc_final: 0.6693 (p0) REVERT: C 365 GLU cc_start: 0.8031 (pp20) cc_final: 0.7586 (pp20) REVERT: C 368 TRP cc_start: 0.8981 (t60) cc_final: 0.8667 (t60) REVERT: D 44 TYR cc_start: 0.8751 (t80) cc_final: 0.8368 (t80) REVERT: D 87 ASP cc_start: 0.7786 (t0) cc_final: 0.7101 (t0) REVERT: D 245 MET cc_start: 0.9009 (mmm) cc_final: 0.8607 (mmm) REVERT: D 331 SER cc_start: 0.9329 (t) cc_final: 0.8751 (p) REVERT: D 340 MET cc_start: 0.7938 (tpp) cc_final: 0.7715 (mmt) outliers start: 52 outliers final: 44 residues processed: 213 average time/residue: 0.0833 time to fit residues: 28.4123 Evaluate side-chains 216 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 289 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 132 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN D 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.150978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111103 restraints weight = 18122.785| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.34 r_work: 0.3238 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13094 Z= 0.125 Angle : 0.556 10.303 17770 Z= 0.270 Chirality : 0.040 0.220 2041 Planarity : 0.003 0.053 2225 Dihedral : 5.315 58.577 2202 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.58 % Allowed : 20.31 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.22), residues: 1557 helix: 1.33 (0.21), residues: 575 sheet: -1.29 (0.34), residues: 268 loop : -1.27 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.014 0.001 TYR A 78 PHE 0.012 0.001 PHE D 337 TRP 0.020 0.001 TRP A 169 HIS 0.008 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00298 (13066) covalent geometry : angle 0.54143 (17690) SS BOND : bond 0.00385 ( 4) SS BOND : angle 1.06929 ( 8) hydrogen bonds : bond 0.03207 ( 502) hydrogen bonds : angle 4.25039 ( 1446) link_BETA1-4 : bond 0.00572 ( 8) link_BETA1-4 : angle 1.98214 ( 24) link_NAG-ASN : bond 0.00221 ( 16) link_NAG-ASN : angle 2.10296 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8976 (ttm) cc_final: 0.8488 (mtp) REVERT: A 296 TRP cc_start: 0.8388 (t60) cc_final: 0.7676 (t60) REVERT: A 400 GLU cc_start: 0.7776 (pt0) cc_final: 0.7455 (pt0) REVERT: B 44 TYR cc_start: 0.8654 (t80) cc_final: 0.8444 (t80) REVERT: B 83 ILE cc_start: 0.6974 (OUTLIER) cc_final: 0.6495 (pt) REVERT: B 260 ASP cc_start: 0.8477 (t70) cc_final: 0.8142 (t0) REVERT: B 296 TRP cc_start: 0.8976 (t60) cc_final: 0.8197 (t60) REVERT: B 316 MET cc_start: 0.8504 (tpt) cc_final: 0.7919 (tpp) REVERT: B 323 MET cc_start: 0.8601 (mmm) cc_final: 0.7926 (mmm) REVERT: B 331 SER cc_start: 0.9098 (t) cc_final: 0.8517 (p) REVERT: C 133 ARG cc_start: 0.8949 (tpp80) cc_final: 0.8697 (mmm-85) REVERT: C 265 ASP cc_start: 0.8046 (t0) cc_final: 0.6781 (p0) REVERT: C 365 GLU cc_start: 0.8082 (pp20) cc_final: 0.7636 (pp20) REVERT: C 368 TRP cc_start: 0.8967 (t60) cc_final: 0.8648 (t60) REVERT: D 44 TYR cc_start: 0.8754 (t80) cc_final: 0.8372 (t80) REVERT: D 87 ASP cc_start: 0.7794 (t0) cc_final: 0.7087 (t0) REVERT: D 245 MET cc_start: 0.9004 (mmm) cc_final: 0.8607 (mmm) outliers start: 49 outliers final: 44 residues processed: 214 average time/residue: 0.0885 time to fit residues: 30.0523 Evaluate side-chains 222 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 259 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.150953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111017 restraints weight = 18362.442| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.36 r_work: 0.3240 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13094 Z= 0.127 Angle : 0.560 10.855 17770 Z= 0.272 Chirality : 0.040 0.219 2041 Planarity : 0.003 0.053 2225 Dihedral : 5.252 58.561 2202 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.58 % Allowed : 20.45 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1557 helix: 1.35 (0.21), residues: 575 sheet: -1.22 (0.34), residues: 267 loop : -1.27 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.015 0.001 TYR A 78 PHE 0.016 0.001 PHE B 38 TRP 0.018 0.001 TRP A 169 HIS 0.008 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00305 (13066) covalent geometry : angle 0.54441 (17690) SS BOND : bond 0.00408 ( 4) SS BOND : angle 1.93373 ( 8) hydrogen bonds : bond 0.03175 ( 502) hydrogen bonds : angle 4.23626 ( 1446) link_BETA1-4 : bond 0.00545 ( 8) link_BETA1-4 : angle 1.93542 ( 24) link_NAG-ASN : bond 0.00212 ( 16) link_NAG-ASN : angle 2.08961 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8971 (ttm) cc_final: 0.8498 (mtp) REVERT: A 296 TRP cc_start: 0.8464 (t60) cc_final: 0.7643 (t60) REVERT: A 400 GLU cc_start: 0.7782 (pt0) cc_final: 0.7462 (pt0) REVERT: B 44 TYR cc_start: 0.8647 (t80) cc_final: 0.8442 (t80) REVERT: B 83 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6493 (pt) REVERT: B 260 ASP cc_start: 0.8524 (t70) cc_final: 0.8179 (t0) REVERT: B 296 TRP cc_start: 0.8981 (t60) cc_final: 0.8202 (t60) REVERT: B 316 MET cc_start: 0.8501 (tpt) cc_final: 0.7913 (tpp) REVERT: B 323 MET cc_start: 0.8605 (mmm) cc_final: 0.7893 (mmm) REVERT: B 331 SER cc_start: 0.9163 (t) cc_final: 0.8530 (p) REVERT: C 133 ARG cc_start: 0.8940 (tpp80) cc_final: 0.8691 (mmm-85) REVERT: C 144 SER cc_start: 0.8926 (p) cc_final: 0.8495 (p) REVERT: C 265 ASP cc_start: 0.7890 (t0) cc_final: 0.6628 (p0) REVERT: C 365 GLU cc_start: 0.8091 (pp20) cc_final: 0.7624 (pp20) REVERT: C 368 TRP cc_start: 0.8964 (t60) cc_final: 0.8656 (t60) REVERT: D 44 TYR cc_start: 0.8752 (t80) cc_final: 0.8370 (t80) REVERT: D 87 ASP cc_start: 0.7764 (t0) cc_final: 0.7064 (t0) REVERT: D 245 MET cc_start: 0.8996 (mmm) cc_final: 0.8633 (mmm) REVERT: D 340 MET cc_start: 0.7923 (tpp) cc_final: 0.7631 (mmt) outliers start: 49 outliers final: 44 residues processed: 213 average time/residue: 0.0837 time to fit residues: 28.4878 Evaluate side-chains 220 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 152 optimal weight: 0.5980 chunk 153 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.151681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.111865 restraints weight = 18328.085| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.36 r_work: 0.3233 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13094 Z= 0.123 Angle : 0.562 11.138 17770 Z= 0.273 Chirality : 0.040 0.219 2041 Planarity : 0.003 0.053 2225 Dihedral : 5.201 58.511 2202 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.29 % Allowed : 20.75 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.22), residues: 1557 helix: 1.38 (0.21), residues: 575 sheet: -1.17 (0.34), residues: 265 loop : -1.29 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 194 TYR 0.016 0.001 TYR A 78 PHE 0.015 0.001 PHE B 38 TRP 0.017 0.001 TRP A 169 HIS 0.008 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00294 (13066) covalent geometry : angle 0.54732 (17690) SS BOND : bond 0.00313 ( 4) SS BOND : angle 1.63718 ( 8) hydrogen bonds : bond 0.03154 ( 502) hydrogen bonds : angle 4.21328 ( 1446) link_BETA1-4 : bond 0.00541 ( 8) link_BETA1-4 : angle 1.91816 ( 24) link_NAG-ASN : bond 0.00221 ( 16) link_NAG-ASN : angle 2.05435 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 TRP cc_start: 0.8510 (t60) cc_final: 0.7657 (t60) REVERT: A 400 GLU cc_start: 0.7732 (pt0) cc_final: 0.7416 (pt0) REVERT: B 44 TYR cc_start: 0.8678 (t80) cc_final: 0.8449 (t80) REVERT: B 83 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6523 (pt) REVERT: B 260 ASP cc_start: 0.8458 (t70) cc_final: 0.8124 (t0) REVERT: B 296 TRP cc_start: 0.8993 (t60) cc_final: 0.8238 (t60) REVERT: B 316 MET cc_start: 0.8522 (tpt) cc_final: 0.7941 (tpp) REVERT: B 323 MET cc_start: 0.8664 (mmm) cc_final: 0.7896 (mmm) REVERT: B 381 ASN cc_start: 0.8390 (t0) cc_final: 0.8148 (t0) REVERT: C 133 ARG cc_start: 0.8917 (tpp80) cc_final: 0.8674 (mmm-85) REVERT: C 144 SER cc_start: 0.8903 (p) cc_final: 0.8468 (p) REVERT: C 265 ASP cc_start: 0.7852 (t0) cc_final: 0.6644 (p0) REVERT: C 365 GLU cc_start: 0.8062 (pp20) cc_final: 0.7629 (pp20) REVERT: C 368 TRP cc_start: 0.8959 (t60) cc_final: 0.8672 (t60) REVERT: C 413 MET cc_start: 0.8561 (mtp) cc_final: 0.8177 (mmm) REVERT: D 44 TYR cc_start: 0.8771 (t80) cc_final: 0.8384 (t80) REVERT: D 87 ASP cc_start: 0.7805 (t0) cc_final: 0.7087 (t0) REVERT: D 245 MET cc_start: 0.8955 (mmm) cc_final: 0.8586 (mmm) REVERT: D 340 MET cc_start: 0.7919 (tpp) cc_final: 0.7626 (mmt) outliers start: 45 outliers final: 42 residues processed: 216 average time/residue: 0.0831 time to fit residues: 28.5686 Evaluate side-chains 223 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 89 optimal weight: 0.5980 chunk 86 optimal weight: 0.0770 chunk 136 optimal weight: 0.7980 chunk 25 optimal weight: 0.0670 chunk 57 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.149947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.111150 restraints weight = 18053.697| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.27 r_work: 0.3295 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13094 Z= 0.108 Angle : 0.551 10.952 17770 Z= 0.268 Chirality : 0.040 0.222 2041 Planarity : 0.003 0.053 2225 Dihedral : 5.088 58.384 2202 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.78 % Allowed : 21.11 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1557 helix: 1.38 (0.21), residues: 575 sheet: -1.11 (0.34), residues: 265 loop : -1.26 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 194 TYR 0.016 0.001 TYR A 78 PHE 0.015 0.001 PHE D 337 TRP 0.015 0.001 TRP A 169 HIS 0.008 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00256 (13066) covalent geometry : angle 0.53690 (17690) SS BOND : bond 0.00308 ( 4) SS BOND : angle 1.42690 ( 8) hydrogen bonds : bond 0.03084 ( 502) hydrogen bonds : angle 4.17609 ( 1446) link_BETA1-4 : bond 0.00537 ( 8) link_BETA1-4 : angle 1.87219 ( 24) link_NAG-ASN : bond 0.00249 ( 16) link_NAG-ASN : angle 2.01480 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2578.87 seconds wall clock time: 45 minutes 16.44 seconds (2716.44 seconds total)