Starting phenix.real_space_refine on Thu Mar 5 08:56:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aln_11818/03_2026/7aln_11818.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aln_11818/03_2026/7aln_11818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7aln_11818/03_2026/7aln_11818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aln_11818/03_2026/7aln_11818.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aln_11818/03_2026/7aln_11818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aln_11818/03_2026/7aln_11818.map" } resolution = 3.77 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 ------------------------------------------------------------------------------- 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= 0.095 sd= 1.311 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: 7 Type Number sf(0) Gaussians Br 3 7.06 5 P 11 5.49 5 Mg 5 5.21 5 S 111 5.16 5 C 13157 2.51 5 N 3502 2.21 5 O 4000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20789 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2890 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2890 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2890 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2890 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2890 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 6058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6058 Classifications: {'peptide': 766} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 740} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.60, per 1000 atoms: 0.22 Number of scatterers: 20789 At special positions: 0 Unit cell: (144.9, 126.27, 191.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 3 34.99 S 111 16.00 P 11 15.00 Mg 5 11.99 O 4000 8.00 N 3502 7.00 C 13157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 258 " distance=2.05 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 258 " distance=2.05 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 258 " distance=2.05 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 258 " distance=2.05 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 258 " distance=2.05 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 850.5 milliseconds 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4828 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 32 sheets defined 47.5% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 113 through 127 removed outlier: 3.977A pdb=" N ARG A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 203 through 218 removed outlier: 3.522A pdb=" N CYS A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.861A pdb=" N ARG A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.648A pdb=" N MET A 306 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 359 through 367 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 113 through 127 removed outlier: 3.976A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 203 through 218 removed outlier: 3.523A pdb=" N CYS B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.861A pdb=" N ARG B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.647A pdb=" N MET B 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 338 through 349 Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 359 through 367 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 79 through 93 Processing helix chain 'C' and resid 113 through 127 removed outlier: 3.976A pdb=" N ARG C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 203 through 218 removed outlier: 3.523A pdb=" N CYS C 218 " --> pdb=" O LYS C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.861A pdb=" N ARG C 255 " --> pdb=" O GLY C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 290 through 296 Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.648A pdb=" N MET C 306 " --> pdb=" O GLY C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 359 through 367 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'D' and resid 56 through 62 Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 113 through 127 removed outlier: 3.976A pdb=" N ARG D 117 " --> pdb=" O PRO D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 146 Processing helix chain 'D' and resid 182 through 198 Processing helix chain 'D' and resid 203 through 218 removed outlier: 3.523A pdb=" N CYS D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.861A pdb=" N ARG D 255 " --> pdb=" O GLY D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 290 through 296 Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.647A pdb=" N MET D 306 " --> pdb=" O GLY D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 322 Processing helix chain 'D' and resid 338 through 349 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 359 through 367 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'E' and resid 56 through 62 Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 113 through 127 removed outlier: 3.976A pdb=" N ARG E 117 " --> pdb=" O PRO E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 146 Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 203 through 218 removed outlier: 3.523A pdb=" N CYS E 218 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 231 Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.861A pdb=" N ARG E 255 " --> pdb=" O GLY E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 274 through 285 Processing helix chain 'E' and resid 290 through 296 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.648A pdb=" N MET E 306 " --> pdb=" O GLY E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 322 Processing helix chain 'E' and resid 338 through 349 Processing helix chain 'E' and resid 352 through 356 Processing helix chain 'E' and resid 359 through 367 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'F' and resid 4 through 15 Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 109 through 123 removed outlier: 3.831A pdb=" N VAL F 113 " --> pdb=" O ASN F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 157 removed outlier: 3.708A pdb=" N THR F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 181 removed outlier: 3.639A pdb=" N CYS F 170 " --> pdb=" O HIS F 166 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 210 Processing helix chain 'F' and resid 219 through 227 Processing helix chain 'F' and resid 227 through 235 removed outlier: 3.918A pdb=" N LEU F 231 " --> pdb=" O ALA F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 297 removed outlier: 3.533A pdb=" N ALA F 297 " --> pdb=" O PHE F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 306 Processing helix chain 'F' and resid 330 through 341 removed outlier: 3.586A pdb=" N GLU F 334 " --> pdb=" O LYS F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 363 Processing helix chain 'F' and resid 385 through 396 Processing helix chain 'F' and resid 399 through 408 Processing helix chain 'F' and resid 424 through 456 removed outlier: 3.745A pdb=" N ARG F 454 " --> pdb=" O HIS F 450 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE F 455 " --> pdb=" O LEU F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 512 removed outlier: 3.542A pdb=" N GLU F 512 " --> pdb=" O LEU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 519 removed outlier: 3.641A pdb=" N GLU F 518 " --> pdb=" O SER F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 533 Processing helix chain 'F' and resid 537 through 548 removed outlier: 3.586A pdb=" N TYR F 541 " --> pdb=" O SER F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 564 Processing helix chain 'F' and resid 596 through 602 removed outlier: 3.778A pdb=" N LYS F 600 " --> pdb=" O SER F 596 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS F 602 " --> pdb=" O LEU F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 615 removed outlier: 3.680A pdb=" N VAL F 612 " --> pdb=" O ASP F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.684A pdb=" N PHE F 625 " --> pdb=" O VAL F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 658 Processing helix chain 'F' and resid 679 through 690 Processing helix chain 'F' and resid 691 through 700 Processing helix chain 'F' and resid 709 through 716 Processing helix chain 'F' and resid 720 through 725 removed outlier: 3.508A pdb=" N ALA F 724 " --> pdb=" O ASP F 720 " (cutoff:3.500A) Processing helix chain 'F' and resid 730 through 742 Processing helix chain 'F' and resid 759 through 767 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.696A pdb=" N LEU A 9 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR A 107 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL A 11 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 134 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 removed outlier: 7.403A pdb=" N VAL A 299 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE A 152 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE A 298 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.697A pdb=" N LEU B 9 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR B 107 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL B 11 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 134 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA8, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AA9, first strand: chain 'B' and resid 170 through 171 removed outlier: 7.404A pdb=" N VAL B 299 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE B 152 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE B 298 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.697A pdb=" N LEU C 9 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR C 107 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N VAL C 11 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR C 134 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 72 through 73 Processing sheet with id=AB5, first strand: chain 'C' and resid 170 through 171 removed outlier: 7.403A pdb=" N VAL C 299 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE C 152 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE C 298 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 239 through 242 Processing sheet with id=AB7, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.696A pdb=" N LEU D 9 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR D 107 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL D 11 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR D 134 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AB9, first strand: chain 'D' and resid 72 through 73 Processing sheet with id=AC1, first strand: chain 'D' and resid 170 through 171 removed outlier: 7.405A pdb=" N VAL D 299 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE D 152 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE D 298 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 239 through 242 Processing sheet with id=AC3, first strand: chain 'E' and resid 30 through 32 removed outlier: 6.696A pdb=" N LEU E 9 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N THR E 107 " --> pdb=" O LEU E 9 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N VAL E 11 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR E 134 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AC5, first strand: chain 'E' and resid 72 through 73 Processing sheet with id=AC6, first strand: chain 'E' and resid 170 through 171 removed outlier: 7.404A pdb=" N VAL E 299 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE E 152 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE E 298 " --> pdb=" O VAL E 331 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 239 through 242 Processing sheet with id=AC8, first strand: chain 'F' and resid 80 through 82 removed outlier: 5.763A pdb=" N GLN F 70 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL F 56 " --> pdb=" O GLN F 70 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 127 through 128 removed outlier: 5.996A pdb=" N THR F 186 " --> pdb=" O HIS F 662 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE F 664 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE F 188 " --> pdb=" O ILE F 664 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N CYS F 666 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER F 190 " --> pdb=" O CYS F 666 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG F 250 " --> pdb=" O ASP F 469 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR F 264 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 236 through 239 removed outlier: 5.930A pdb=" N ALA F 237 " --> pdb=" O ASN F 244 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN F 244 " --> pdb=" O ALA F 237 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN F 242 " --> pdb=" O THR F 239 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 367 through 369 Processing sheet with id=AD3, first strand: chain 'F' and resid 409 through 413 Processing sheet with id=AD4, first strand: chain 'F' and resid 570 through 572 Processing sheet with id=AD5, first strand: chain 'F' and resid 705 through 708 956 hydrogen bonds defined for protein. 2568 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5648 1.33 - 1.46: 5913 1.46 - 1.60: 9460 1.60 - 1.73: 1 1.73 - 1.86: 192 Bond restraints: 21214 Sorted by residual: bond pdb=" O3P SEP F 19 " pdb=" P SEP F 19 " ideal model delta sigma weight residual 1.610 1.516 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" O1P SEP F 19 " pdb=" P SEP F 19 " ideal model delta sigma weight residual 1.610 1.517 0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" O2P SEP F 19 " pdb=" P SEP F 19 " ideal model delta sigma weight residual 1.610 1.517 0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C TYR B 70 " pdb=" N PRO B 71 " ideal model delta sigma weight residual 1.337 1.378 -0.042 9.80e-03 1.04e+04 1.82e+01 bond pdb=" C TYR E 70 " pdb=" N PRO E 71 " ideal model delta sigma weight residual 1.337 1.378 -0.042 9.80e-03 1.04e+04 1.80e+01 ... (remaining 21209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 27815 2.44 - 4.89: 817 4.89 - 7.33: 76 7.33 - 9.77: 3 9.77 - 12.21: 17 Bond angle restraints: 28728 Sorted by residual: angle pdb=" C LYS F 668 " pdb=" N PRO F 669 " pdb=" CA PRO F 669 " ideal model delta sigma weight residual 118.85 126.02 -7.17 1.09e+00 8.42e-01 4.33e+01 angle pdb=" C ALA B 109 " pdb=" N PRO B 110 " pdb=" CA PRO B 110 " ideal model delta sigma weight residual 119.89 125.74 -5.85 1.02e+00 9.61e-01 3.29e+01 angle pdb=" C ALA C 109 " pdb=" N PRO C 110 " pdb=" CA PRO C 110 " ideal model delta sigma weight residual 119.89 125.73 -5.84 1.02e+00 9.61e-01 3.28e+01 angle pdb=" C PRO F 617 " pdb=" N ASN F 618 " pdb=" CA ASN F 618 " ideal model delta sigma weight residual 121.20 128.62 -7.42 1.40e+00 5.10e-01 2.81e+01 angle pdb=" C TYR E 70 " pdb=" N PRO E 71 " pdb=" CA PRO E 71 " ideal model delta sigma weight residual 120.12 125.62 -5.50 1.11e+00 8.12e-01 2.46e+01 ... (remaining 28723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 12739 35.95 - 71.89: 71 71.89 - 107.84: 26 107.84 - 143.78: 39 143.78 - 179.73: 17 Dihedral angle restraints: 12892 sinusoidal: 5363 harmonic: 7529 Sorted by residual: dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 125.73 174.27 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 125.84 174.16 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 128.00 172.00 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 12889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2691 0.083 - 0.166: 460 0.166 - 0.249: 39 0.249 - 0.332: 4 0.332 - 0.415: 6 Chirality restraints: 3200 Sorted by residual: chirality pdb=" C8 9UE C 403 " pdb=" C20 9UE C 403 " pdb=" C7 9UE C 403 " pdb=" N1 9UE C 403 " both_signs ideal model delta sigma weight residual False 2.15 2.56 -0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" C8 9UE E 403 " pdb=" C20 9UE E 403 " pdb=" C7 9UE E 403 " pdb=" N1 9UE E 403 " both_signs ideal model delta sigma weight residual False 2.15 2.55 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C8 9UE A 403 " pdb=" C20 9UE A 403 " pdb=" C7 9UE A 403 " pdb=" N1 9UE A 403 " both_signs ideal model delta sigma weight residual False 2.15 2.55 -0.41 2.00e-01 2.50e+01 4.14e+00 ... (remaining 3197 not shown) Planarity restraints: 3677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 9UE C 403 " -0.216 2.00e-02 2.50e+03 1.80e-01 4.03e+02 pdb=" C11 9UE C 403 " 0.045 2.00e-02 2.50e+03 pdb=" C12 9UE C 403 " -0.146 2.00e-02 2.50e+03 pdb=" N2 9UE C 403 " 0.302 2.00e-02 2.50e+03 pdb=" O4 9UE C 403 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 9UE E 403 " -0.216 2.00e-02 2.50e+03 1.80e-01 4.03e+02 pdb=" C11 9UE E 403 " 0.047 2.00e-02 2.50e+03 pdb=" C12 9UE E 403 " -0.146 2.00e-02 2.50e+03 pdb=" N2 9UE E 403 " 0.302 2.00e-02 2.50e+03 pdb=" O4 9UE E 403 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 9UE A 403 " -0.216 2.00e-02 2.50e+03 1.79e-01 4.01e+02 pdb=" C11 9UE A 403 " 0.047 2.00e-02 2.50e+03 pdb=" C12 9UE A 403 " -0.146 2.00e-02 2.50e+03 pdb=" N2 9UE A 403 " 0.301 2.00e-02 2.50e+03 pdb=" O4 9UE A 403 " 0.014 2.00e-02 2.50e+03 ... (remaining 3674 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 83 2.43 - 3.04: 12025 3.04 - 3.66: 30893 3.66 - 4.28: 48938 4.28 - 4.90: 80411 Nonbonded interactions: 172350 Sorted by model distance: nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.807 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 1.837 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 1.957 2.170 nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.013 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.053 2.170 ... (remaining 172345 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 6 through 402) selection = chain 'B' selection = (chain 'C' and resid 6 through 402) selection = chain 'D' selection = (chain 'E' and resid 6 through 402) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.190 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.015 0.886 21223 Z= 1.231 Angle : 0.985 12.214 28738 Z= 0.538 Chirality : 0.063 0.415 3200 Planarity : 0.009 0.180 3677 Dihedral : 16.152 179.729 8049 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.84 % Rotamer: Outliers : 0.22 % Allowed : 1.86 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -3.95 (0.13), residues: 2599 helix: -3.04 (0.09), residues: 1072 sheet: -2.64 (0.23), residues: 386 loop : -1.97 (0.16), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 241 TYR 0.031 0.003 TYR C 189 PHE 0.031 0.003 PHE F 444 TRP 0.033 0.005 TRP B 341 HIS 0.015 0.003 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00931 (21214) covalent geometry : angle 0.98374 (28728) SS BOND : bond 0.01605 ( 5) SS BOND : angle 2.51924 ( 10) hydrogen bonds : bond 0.15743 ( 956) hydrogen bonds : angle 10.13034 ( 2568) Misc. bond : bond 0.83759 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 543 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS F 768 " (corrupted residue). Skipping it. REVERT: A 218 CYS cc_start: 0.5965 (m) cc_final: 0.5671 (m) REVERT: A 228 MET cc_start: 0.8538 (mmm) cc_final: 0.8186 (tpp) REVERT: B 55 VAL cc_start: 0.9461 (t) cc_final: 0.9145 (p) REVERT: B 206 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6838 (mt-10) REVERT: B 208 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 228 MET cc_start: 0.8603 (mmm) cc_final: 0.8382 (tpp) REVERT: C 191 MET cc_start: 0.8159 (mtm) cc_final: 0.7881 (mtp) REVERT: C 284 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8661 (mtpp) REVERT: C 306 MET cc_start: 0.8656 (mmm) cc_final: 0.8365 (mmt) REVERT: D 45 MET cc_start: 0.8243 (mmm) cc_final: 0.7992 (tpt) REVERT: D 70 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: D 83 MET cc_start: 0.8529 (tpt) cc_final: 0.8123 (tpt) REVERT: D 144 TYR cc_start: 0.8392 (m-80) cc_final: 0.8188 (m-80) REVERT: D 228 MET cc_start: 0.8539 (mmm) cc_final: 0.8263 (tpp) REVERT: E 228 MET cc_start: 0.8530 (mmm) cc_final: 0.7968 (tpp) REVERT: E 356 MET cc_start: 0.8696 (mtt) cc_final: 0.8470 (mtm) REVERT: F 47 ASP cc_start: 0.5421 (t0) cc_final: 0.5217 (m-30) REVERT: F 368 ILE cc_start: 0.8547 (pt) cc_final: 0.8254 (mm) REVERT: F 445 LEU cc_start: 0.8290 (mt) cc_final: 0.7814 (mt) REVERT: F 555 LYS cc_start: 0.7535 (mttt) cc_final: 0.7314 (mttt) REVERT: F 568 ASN cc_start: 0.7650 (p0) cc_final: 0.7214 (t0) REVERT: F 694 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7011 (tp30) REVERT: F 699 ARG cc_start: 0.6529 (tpt170) cc_final: 0.5770 (ttm-80) REVERT: F 714 TYR cc_start: 0.8331 (t80) cc_final: 0.8089 (t80) outliers start: 5 outliers final: 0 residues processed: 548 average time/residue: 0.1764 time to fit residues: 142.6489 Evaluate side-chains 286 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 258 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN F 91 ASN F 182 ASN ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN F 288 HIS F 292 GLN F 341 ASN F 450 HIS ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 479 ASN ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.082711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066483 restraints weight = 57417.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.068590 restraints weight = 27094.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.069972 restraints weight = 15492.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.070797 restraints weight = 10221.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.071381 restraints weight = 7641.729| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21223 Z= 0.144 Angle : 0.693 10.238 28738 Z= 0.338 Chirality : 0.048 0.309 3200 Planarity : 0.005 0.053 3677 Dihedral : 20.896 179.761 3015 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.21 % Allowed : 7.87 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -1.90 (0.15), residues: 2599 helix: -0.85 (0.13), residues: 1141 sheet: -1.89 (0.26), residues: 358 loop : -1.30 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 373 TYR 0.020 0.002 TYR D 144 PHE 0.020 0.001 PHE F 476 TRP 0.014 0.002 TRP C 341 HIS 0.008 0.001 HIS F 288 Details of bonding type rmsd covalent geometry : bond 0.00315 (21214) covalent geometry : angle 0.69236 (28728) SS BOND : bond 0.00331 ( 5) SS BOND : angle 2.04603 ( 10) hydrogen bonds : bond 0.03928 ( 956) hydrogen bonds : angle 5.77026 ( 2568) Misc. bond : bond 0.00034 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 310 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS F 768 " (corrupted residue). Skipping it. REVERT: A 81 ASP cc_start: 0.7684 (t0) cc_final: 0.7476 (t0) REVERT: A 188 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: B 60 GLN cc_start: 0.8564 (tt0) cc_final: 0.7910 (tt0) REVERT: B 212 ASP cc_start: 0.8687 (t0) cc_final: 0.8172 (t0) REVERT: C 284 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8658 (mtpp) REVERT: C 306 MET cc_start: 0.8482 (mmm) cc_final: 0.8223 (mmt) REVERT: C 317 ASP cc_start: 0.7990 (m-30) cc_final: 0.7764 (m-30) REVERT: D 45 MET cc_start: 0.8181 (mmm) cc_final: 0.7905 (tpt) REVERT: D 133 MET cc_start: 0.8660 (tmm) cc_final: 0.8438 (ppp) REVERT: D 188 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: D 228 MET cc_start: 0.8307 (mmm) cc_final: 0.8081 (tpp) REVERT: D 271 GLU cc_start: 0.7071 (tt0) cc_final: 0.6695 (tm-30) REVERT: E 133 MET cc_start: 0.8713 (tmm) cc_final: 0.8486 (tmm) REVERT: F 216 MET cc_start: 0.1740 (OUTLIER) cc_final: 0.0175 (mmt) REVERT: F 386 MET cc_start: 0.6540 (mmm) cc_final: 0.6305 (tpp) REVERT: F 445 LEU cc_start: 0.8663 (mt) cc_final: 0.7940 (mm) REVERT: F 568 ASN cc_start: 0.7998 (p0) cc_final: 0.7478 (t0) REVERT: F 639 SER cc_start: 0.7351 (p) cc_final: 0.7072 (t) REVERT: F 694 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7083 (tp30) REVERT: F 699 ARG cc_start: 0.7162 (tpt170) cc_final: 0.6353 (ttm-80) outliers start: 50 outliers final: 24 residues processed: 342 average time/residue: 0.1517 time to fit residues: 80.7184 Evaluate side-chains 260 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 467 MET Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 663 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 175 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 204 optimal weight: 20.0000 chunk 155 optimal weight: 0.8980 chunk 243 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 233 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 242 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS C 93 ASN C 116 ASN C 122 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN F 70 GLN F 221 GLN F 242 ASN ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 ASN ** F 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.081591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.065418 restraints weight = 57660.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.067638 restraints weight = 26623.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.069057 restraints weight = 14932.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.070005 restraints weight = 9736.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.070572 restraints weight = 7135.655| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21223 Z= 0.123 Angle : 0.635 9.904 28738 Z= 0.306 Chirality : 0.047 0.338 3200 Planarity : 0.004 0.045 3677 Dihedral : 20.442 174.809 3013 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.34 % Allowed : 9.28 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.89 (0.16), residues: 2599 helix: 0.14 (0.15), residues: 1148 sheet: -1.32 (0.25), residues: 408 loop : -0.96 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 152 TYR 0.018 0.001 TYR F 207 PHE 0.027 0.001 PHE F 208 TRP 0.013 0.001 TRP D 341 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00278 (21214) covalent geometry : angle 0.63282 (28728) SS BOND : bond 0.00399 ( 5) SS BOND : angle 2.72403 ( 10) hydrogen bonds : bond 0.03426 ( 956) hydrogen bonds : angle 5.14565 ( 2568) Misc. bond : bond 0.00046 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS F 768 " (corrupted residue). Skipping it. REVERT: A 81 ASP cc_start: 0.7787 (t0) cc_final: 0.7554 (t0) REVERT: A 188 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: A 218 CYS cc_start: 0.5781 (m) cc_final: 0.5570 (m) REVERT: B 188 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: C 228 MET cc_start: 0.8308 (tpp) cc_final: 0.7951 (mpp) REVERT: D 45 MET cc_start: 0.8276 (mmm) cc_final: 0.8044 (tpt) REVERT: D 133 MET cc_start: 0.8595 (tmm) cc_final: 0.8210 (ppp) REVERT: D 188 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: D 271 GLU cc_start: 0.7116 (tt0) cc_final: 0.6572 (tm-30) REVERT: E 133 MET cc_start: 0.8788 (tmm) cc_final: 0.8444 (tmm) REVERT: F 234 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.6824 (t80) REVERT: F 386 MET cc_start: 0.6570 (mmm) cc_final: 0.6136 (tpp) REVERT: F 555 LYS cc_start: 0.7587 (mtpt) cc_final: 0.7329 (mttt) REVERT: F 568 ASN cc_start: 0.7964 (p0) cc_final: 0.7472 (t0) REVERT: F 599 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8658 (mt) REVERT: F 639 SER cc_start: 0.6969 (p) cc_final: 0.6713 (t) REVERT: F 694 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7123 (tp30) REVERT: F 699 ARG cc_start: 0.7301 (tpt170) cc_final: 0.6452 (ttm-80) outliers start: 53 outliers final: 29 residues processed: 304 average time/residue: 0.1482 time to fit residues: 70.4729 Evaluate side-chains 260 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 258 CYS Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 239 LYS Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 450 HIS Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 663 PHE Chi-restraints excluded: chain F residue 708 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 21 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 154 optimal weight: 0.0980 chunk 44 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 chunk 255 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 259 optimal weight: 0.7980 chunk 217 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN D 60 GLN D 116 ASN ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 ASN ** F 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.079876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.063775 restraints weight = 58059.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065962 restraints weight = 26997.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.067412 restraints weight = 15275.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.068308 restraints weight = 9992.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068939 restraints weight = 7389.239| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21223 Z= 0.146 Angle : 0.636 8.681 28738 Z= 0.308 Chirality : 0.047 0.306 3200 Planarity : 0.004 0.044 3677 Dihedral : 20.281 179.874 3013 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.21 % Allowed : 11.23 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.46 (0.16), residues: 2599 helix: 0.43 (0.15), residues: 1149 sheet: -1.11 (0.25), residues: 413 loop : -0.64 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 219 TYR 0.019 0.001 TYR F 207 PHE 0.034 0.001 PHE A 224 TRP 0.012 0.002 TRP D 341 HIS 0.005 0.001 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00332 (21214) covalent geometry : angle 0.63271 (28728) SS BOND : bond 0.00814 ( 5) SS BOND : angle 3.34629 ( 10) hydrogen bonds : bond 0.03359 ( 956) hydrogen bonds : angle 4.84828 ( 2568) Misc. bond : bond 0.00055 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS F 768 " (corrupted residue). Skipping it. REVERT: A 188 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: B 49 GLU cc_start: 0.7548 (mp0) cc_final: 0.6777 (mm-30) REVERT: B 188 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: B 271 GLU cc_start: 0.6814 (tt0) cc_final: 0.6542 (tm-30) REVERT: C 228 MET cc_start: 0.8337 (tpp) cc_final: 0.8126 (mpp) REVERT: D 45 MET cc_start: 0.8404 (mmm) cc_final: 0.8122 (tpt) REVERT: D 49 GLU cc_start: 0.7265 (mp0) cc_final: 0.6509 (mm-30) REVERT: D 133 MET cc_start: 0.8650 (tmm) cc_final: 0.8209 (ppp) REVERT: D 212 ASP cc_start: 0.8704 (t0) cc_final: 0.8458 (t0) REVERT: E 81 ASP cc_start: 0.7687 (t0) cc_final: 0.7435 (t0) REVERT: E 133 MET cc_start: 0.8776 (tmm) cc_final: 0.8468 (tmm) REVERT: E 188 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: E 212 ASP cc_start: 0.8634 (t0) cc_final: 0.8219 (t0) REVERT: E 228 MET cc_start: 0.8307 (tpp) cc_final: 0.8051 (mpp) REVERT: E 280 PHE cc_start: 0.8940 (t80) cc_final: 0.8202 (t80) REVERT: F 234 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6933 (t80) REVERT: F 386 MET cc_start: 0.6620 (mmm) cc_final: 0.6133 (tpp) REVERT: F 467 MET cc_start: 0.4403 (ptm) cc_final: 0.3694 (ptm) REVERT: F 568 ASN cc_start: 0.8027 (p0) cc_final: 0.7480 (t0) REVERT: F 599 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8601 (mt) REVERT: F 639 SER cc_start: 0.7186 (p) cc_final: 0.6975 (t) REVERT: F 694 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7166 (tp30) REVERT: F 699 ARG cc_start: 0.7158 (tpt170) cc_final: 0.6415 (ttm-80) outliers start: 50 outliers final: 31 residues processed: 282 average time/residue: 0.1439 time to fit residues: 64.7473 Evaluate side-chains 255 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 239 LYS Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 663 PHE Chi-restraints excluded: chain F residue 708 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 245 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 74 HIS B 122 GLN E 74 HIS F 59 GLN F 166 HIS F 341 ASN F 479 ASN F 487 ASN ** F 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.078992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063011 restraints weight = 57891.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065180 restraints weight = 27049.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.066550 restraints weight = 15297.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.067542 restraints weight = 10068.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068109 restraints weight = 7328.950| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21223 Z= 0.152 Angle : 0.625 9.349 28738 Z= 0.301 Chirality : 0.047 0.338 3200 Planarity : 0.004 0.042 3677 Dihedral : 20.137 178.969 3013 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.25 % Allowed : 12.91 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.21 (0.16), residues: 2599 helix: 0.62 (0.15), residues: 1143 sheet: -0.98 (0.25), residues: 413 loop : -0.46 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 316 TYR 0.018 0.001 TYR F 207 PHE 0.039 0.001 PHE F 208 TRP 0.012 0.001 TRP D 341 HIS 0.011 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00348 (21214) covalent geometry : angle 0.62188 (28728) SS BOND : bond 0.00569 ( 5) SS BOND : angle 3.24931 ( 10) hydrogen bonds : bond 0.03297 ( 956) hydrogen bonds : angle 4.70216 ( 2568) Misc. bond : bond 0.00043 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS F 768 " (corrupted residue). Skipping it. REVERT: A 188 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: A 271 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6632 (tm-30) REVERT: B 49 GLU cc_start: 0.7473 (mp0) cc_final: 0.6730 (mm-30) REVERT: B 188 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: B 271 GLU cc_start: 0.6873 (tt0) cc_final: 0.6584 (tm-30) REVERT: C 212 ASP cc_start: 0.8825 (t0) cc_final: 0.8511 (t0) REVERT: D 45 MET cc_start: 0.8474 (mmm) cc_final: 0.8211 (tpt) REVERT: D 49 GLU cc_start: 0.7167 (mp0) cc_final: 0.6299 (mm-30) REVERT: D 133 MET cc_start: 0.8627 (tmm) cc_final: 0.8216 (ppp) REVERT: D 212 ASP cc_start: 0.8703 (t0) cc_final: 0.8451 (t0) REVERT: D 271 GLU cc_start: 0.7533 (tt0) cc_final: 0.7090 (tm-30) REVERT: E 49 GLU cc_start: 0.5924 (mp0) cc_final: 0.5380 (mm-30) REVERT: E 81 ASP cc_start: 0.7774 (t0) cc_final: 0.7510 (t0) REVERT: E 133 MET cc_start: 0.8768 (tmm) cc_final: 0.8518 (tmm) REVERT: E 212 ASP cc_start: 0.8642 (t0) cc_final: 0.8243 (t0) REVERT: E 280 PHE cc_start: 0.8980 (t80) cc_final: 0.8253 (t80) REVERT: F 234 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.6859 (t80) REVERT: F 341 ASN cc_start: 0.8667 (m-40) cc_final: 0.8401 (t0) REVERT: F 386 MET cc_start: 0.6688 (mmm) cc_final: 0.6217 (tpp) REVERT: F 405 ARG cc_start: 0.7968 (mmp80) cc_final: 0.7737 (mmp80) REVERT: F 555 LYS cc_start: 0.7539 (mtpt) cc_final: 0.7271 (mttt) REVERT: F 568 ASN cc_start: 0.7972 (p0) cc_final: 0.7489 (t0) REVERT: F 599 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8669 (mt) REVERT: F 694 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7143 (tp30) REVERT: F 699 ARG cc_start: 0.7271 (tpt170) cc_final: 0.6355 (tpm170) outliers start: 51 outliers final: 34 residues processed: 270 average time/residue: 0.1424 time to fit residues: 61.2681 Evaluate side-chains 251 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 479 ASN Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 663 PHE Chi-restraints excluded: chain F residue 708 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 196 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 139 optimal weight: 0.0060 chunk 185 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 chunk 206 optimal weight: 9.9990 chunk 90 optimal weight: 0.0770 chunk 55 optimal weight: 0.6980 overall best weight: 1.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN C 74 HIS C 355 GLN D 60 GLN E 60 GLN F 253 GLN F 479 ASN F 487 ASN ** F 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.079163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.063099 restraints weight = 57933.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.065257 restraints weight = 27170.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066695 restraints weight = 15408.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.067576 restraints weight = 10030.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.068215 restraints weight = 7412.339| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21223 Z= 0.135 Angle : 0.616 8.779 28738 Z= 0.297 Chirality : 0.046 0.307 3200 Planarity : 0.004 0.042 3677 Dihedral : 20.023 179.899 3013 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.39 % Allowed : 13.17 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.02 (0.17), residues: 2599 helix: 0.75 (0.15), residues: 1142 sheet: -0.83 (0.25), residues: 414 loop : -0.29 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 316 TYR 0.017 0.001 TYR F 207 PHE 0.037 0.001 PHE F 208 TRP 0.012 0.001 TRP D 341 HIS 0.006 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00309 (21214) covalent geometry : angle 0.61114 (28728) SS BOND : bond 0.00432 ( 5) SS BOND : angle 4.01680 ( 10) hydrogen bonds : bond 0.03205 ( 956) hydrogen bonds : angle 4.59369 ( 2568) Misc. bond : bond 0.00050 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS F 768 " (corrupted residue). Skipping it. REVERT: A 49 GLU cc_start: 0.6904 (mp0) cc_final: 0.6414 (mm-30) REVERT: A 188 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: A 208 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7107 (mt-10) REVERT: A 271 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6676 (tm-30) REVERT: B 49 GLU cc_start: 0.7464 (mp0) cc_final: 0.6761 (mm-30) REVERT: B 188 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: B 212 ASP cc_start: 0.8784 (t0) cc_final: 0.8248 (t0) REVERT: B 271 GLU cc_start: 0.7051 (tt0) cc_final: 0.6717 (tm-30) REVERT: C 212 ASP cc_start: 0.8772 (t0) cc_final: 0.8453 (t0) REVERT: D 49 GLU cc_start: 0.7160 (mp0) cc_final: 0.6360 (mm-30) REVERT: D 212 ASP cc_start: 0.8692 (t0) cc_final: 0.8446 (t0) REVERT: D 271 GLU cc_start: 0.7521 (tt0) cc_final: 0.7129 (tm-30) REVERT: E 49 GLU cc_start: 0.5884 (mp0) cc_final: 0.5433 (mm-30) REVERT: E 81 ASP cc_start: 0.7782 (t0) cc_final: 0.7497 (t0) REVERT: E 133 MET cc_start: 0.8752 (tmm) cc_final: 0.8518 (tmm) REVERT: E 188 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: E 212 ASP cc_start: 0.8675 (t0) cc_final: 0.8279 (t0) REVERT: E 228 MET cc_start: 0.8386 (tpp) cc_final: 0.8113 (mpp) REVERT: E 280 PHE cc_start: 0.8974 (t80) cc_final: 0.8238 (t80) REVERT: F 114 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7972 (mm) REVERT: F 225 MET cc_start: 0.8376 (mmm) cc_final: 0.8122 (mmm) REVERT: F 234 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7076 (t80) REVERT: F 386 MET cc_start: 0.6651 (mmm) cc_final: 0.6293 (tpp) REVERT: F 405 ARG cc_start: 0.7936 (mmp80) cc_final: 0.7735 (mmp80) REVERT: F 516 THR cc_start: 0.6316 (OUTLIER) cc_final: 0.5984 (t) REVERT: F 568 ASN cc_start: 0.8017 (p0) cc_final: 0.7531 (t0) REVERT: F 599 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8664 (mt) REVERT: F 623 GLN cc_start: 0.9060 (mt0) cc_final: 0.8814 (mp10) REVERT: F 683 ILE cc_start: 0.8317 (mm) cc_final: 0.7931 (pt) REVERT: F 694 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7128 (tp30) REVERT: F 699 ARG cc_start: 0.7371 (tpt170) cc_final: 0.6484 (tpm170) outliers start: 54 outliers final: 32 residues processed: 265 average time/residue: 0.1380 time to fit residues: 58.7756 Evaluate side-chains 246 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 479 ASN Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 708 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 223 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 222 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN C 60 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN E 60 GLN F 479 ASN F 601 ASN ** F 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.079184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063112 restraints weight = 58198.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065267 restraints weight = 27348.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066694 restraints weight = 15516.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.067566 restraints weight = 10147.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.068155 restraints weight = 7507.427| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21223 Z= 0.141 Angle : 0.618 9.314 28738 Z= 0.300 Chirality : 0.047 0.300 3200 Planarity : 0.004 0.042 3677 Dihedral : 20.014 179.787 3013 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.39 % Allowed : 13.09 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.15 (0.17), residues: 2599 helix: 0.84 (0.16), residues: 1139 sheet: -0.73 (0.25), residues: 414 loop : -0.20 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 211 TYR 0.016 0.001 TYR F 207 PHE 0.019 0.001 PHE F 208 TRP 0.011 0.001 TRP D 341 HIS 0.006 0.001 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00323 (21214) covalent geometry : angle 0.61383 (28728) SS BOND : bond 0.00444 ( 5) SS BOND : angle 3.99429 ( 10) hydrogen bonds : bond 0.03210 ( 956) hydrogen bonds : angle 4.55282 ( 2568) Misc. bond : bond 0.00051 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 221 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS F 768 " (corrupted residue). Skipping it. REVERT: A 49 GLU cc_start: 0.6840 (mp0) cc_final: 0.6407 (mm-30) REVERT: A 60 GLN cc_start: 0.8882 (tp40) cc_final: 0.8555 (tp40) REVERT: A 188 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: A 208 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6767 (mt-10) REVERT: A 271 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6680 (tm-30) REVERT: B 49 GLU cc_start: 0.7436 (mp0) cc_final: 0.6794 (mm-30) REVERT: B 188 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: B 212 ASP cc_start: 0.8789 (t0) cc_final: 0.8270 (t0) REVERT: B 271 GLU cc_start: 0.7055 (tt0) cc_final: 0.6697 (tm-30) REVERT: C 212 ASP cc_start: 0.8814 (t0) cc_final: 0.8501 (t0) REVERT: C 228 MET cc_start: 0.8318 (tpp) cc_final: 0.8064 (mpp) REVERT: D 49 GLU cc_start: 0.7151 (mp0) cc_final: 0.6353 (mm-30) REVERT: D 212 ASP cc_start: 0.8734 (t0) cc_final: 0.8410 (t0) REVERT: D 228 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7903 (mpp) REVERT: D 271 GLU cc_start: 0.7529 (tt0) cc_final: 0.7123 (tm-30) REVERT: E 49 GLU cc_start: 0.5820 (mp0) cc_final: 0.5414 (mm-30) REVERT: E 81 ASP cc_start: 0.7779 (t0) cc_final: 0.7513 (t0) REVERT: E 133 MET cc_start: 0.8741 (tmm) cc_final: 0.8515 (tmm) REVERT: E 188 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: E 212 ASP cc_start: 0.8680 (t0) cc_final: 0.8308 (t0) REVERT: E 228 MET cc_start: 0.8411 (tpp) cc_final: 0.8169 (mpp) REVERT: E 280 PHE cc_start: 0.9022 (t80) cc_final: 0.8276 (t80) REVERT: F 52 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7829 (m-10) REVERT: F 114 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7969 (mm) REVERT: F 234 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7053 (t80) REVERT: F 386 MET cc_start: 0.6740 (mmm) cc_final: 0.6370 (tpp) REVERT: F 516 THR cc_start: 0.6333 (OUTLIER) cc_final: 0.5999 (t) REVERT: F 526 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7582 (mt-10) REVERT: F 568 ASN cc_start: 0.8018 (p0) cc_final: 0.7519 (t0) REVERT: F 599 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8641 (mt) REVERT: F 623 GLN cc_start: 0.9047 (mt0) cc_final: 0.8802 (mp10) REVERT: F 683 ILE cc_start: 0.8307 (mm) cc_final: 0.7919 (pt) REVERT: F 699 ARG cc_start: 0.7382 (tpt170) cc_final: 0.6609 (tpm170) outliers start: 54 outliers final: 36 residues processed: 259 average time/residue: 0.1340 time to fit residues: 56.2629 Evaluate side-chains 252 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 479 ASN Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 708 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 206 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN C 60 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN F 479 ASN F 490 ASN ** F 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.080550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.064379 restraints weight = 57335.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.066541 restraints weight = 27109.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.067955 restraints weight = 15423.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.068855 restraints weight = 10123.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.069492 restraints weight = 7474.371| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21223 Z= 0.107 Angle : 0.605 10.594 28738 Z= 0.290 Chirality : 0.045 0.236 3200 Planarity : 0.004 0.042 3677 Dihedral : 19.872 179.440 3013 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.12 % Allowed : 13.84 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.33 (0.17), residues: 2599 helix: 1.00 (0.16), residues: 1139 sheet: -0.67 (0.25), residues: 414 loop : -0.11 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 366 TYR 0.015 0.001 TYR F 207 PHE 0.020 0.001 PHE F 208 TRP 0.011 0.001 TRP D 341 HIS 0.006 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00240 (21214) covalent geometry : angle 0.60173 (28728) SS BOND : bond 0.00434 ( 5) SS BOND : angle 3.39963 ( 10) hydrogen bonds : bond 0.03042 ( 956) hydrogen bonds : angle 4.42886 ( 2568) Misc. bond : bond 0.00041 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 230 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS F 768 " (corrupted residue). Skipping it. REVERT: A 49 GLU cc_start: 0.6799 (mp0) cc_final: 0.6310 (mm-30) REVERT: A 60 GLN cc_start: 0.8801 (tp40) cc_final: 0.8554 (tp40) REVERT: A 188 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: A 208 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6822 (mt-10) REVERT: A 271 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6710 (tm-30) REVERT: B 49 GLU cc_start: 0.7403 (mp0) cc_final: 0.6808 (mm-30) REVERT: B 188 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: B 212 ASP cc_start: 0.8816 (t0) cc_final: 0.8295 (t0) REVERT: B 271 GLU cc_start: 0.7107 (tt0) cc_final: 0.6752 (tm-30) REVERT: C 212 ASP cc_start: 0.8796 (t0) cc_final: 0.8492 (t0) REVERT: D 49 GLU cc_start: 0.7106 (mp0) cc_final: 0.6343 (mm-30) REVERT: D 212 ASP cc_start: 0.8726 (t0) cc_final: 0.8474 (t0) REVERT: D 228 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7942 (mpp) REVERT: D 271 GLU cc_start: 0.7519 (tt0) cc_final: 0.7124 (tm-30) REVERT: E 49 GLU cc_start: 0.5852 (mp0) cc_final: 0.5411 (mm-30) REVERT: E 81 ASP cc_start: 0.7788 (t0) cc_final: 0.7581 (t0) REVERT: E 212 ASP cc_start: 0.8714 (t0) cc_final: 0.8345 (t0) REVERT: E 228 MET cc_start: 0.8394 (tpp) cc_final: 0.8067 (mpp) REVERT: E 280 PHE cc_start: 0.8917 (t80) cc_final: 0.8151 (t80) REVERT: E 347 LEU cc_start: 0.9087 (tp) cc_final: 0.8873 (tp) REVERT: F 52 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7850 (m-10) REVERT: F 114 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8062 (mp) REVERT: F 203 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7412 (mt0) REVERT: F 234 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7135 (t80) REVERT: F 386 MET cc_start: 0.6710 (mmm) cc_final: 0.6410 (tpp) REVERT: F 405 ARG cc_start: 0.7811 (mmp80) cc_final: 0.7174 (ttt90) REVERT: F 568 ASN cc_start: 0.8021 (p0) cc_final: 0.7528 (t0) REVERT: F 599 LEU cc_start: 0.8888 (tt) cc_final: 0.8638 (mt) REVERT: F 623 GLN cc_start: 0.9042 (mt0) cc_final: 0.8813 (mp10) REVERT: F 683 ILE cc_start: 0.8191 (mm) cc_final: 0.7829 (pt) REVERT: F 699 ARG cc_start: 0.7339 (tpt170) cc_final: 0.6815 (tpm170) outliers start: 48 outliers final: 29 residues processed: 264 average time/residue: 0.1400 time to fit residues: 59.5208 Evaluate side-chains 247 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 479 ASN Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 684 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 236 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 190 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 chunk 119 optimal weight: 0.3980 chunk 246 optimal weight: 0.4980 chunk 243 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS E 60 GLN F 124 ASN F 479 ASN F 487 ASN ** F 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.079315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.063259 restraints weight = 57521.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.065390 restraints weight = 27290.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066786 restraints weight = 15573.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.067729 restraints weight = 10211.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.068303 restraints weight = 7488.434| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21223 Z= 0.143 Angle : 0.638 14.992 28738 Z= 0.306 Chirality : 0.047 0.276 3200 Planarity : 0.004 0.041 3677 Dihedral : 19.951 179.429 3013 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.95 % Allowed : 14.50 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.34 (0.17), residues: 2599 helix: 1.00 (0.16), residues: 1140 sheet: -0.68 (0.25), residues: 414 loop : -0.08 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 316 TYR 0.016 0.001 TYR F 207 PHE 0.020 0.001 PHE F 208 TRP 0.010 0.001 TRP D 341 HIS 0.006 0.001 HIS D 162 Details of bonding type rmsd covalent geometry : bond 0.00326 (21214) covalent geometry : angle 0.63400 (28728) SS BOND : bond 0.00454 ( 5) SS BOND : angle 3.70509 ( 10) hydrogen bonds : bond 0.03170 ( 956) hydrogen bonds : angle 4.43913 ( 2568) Misc. bond : bond 0.00052 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS F 768 " (corrupted residue). Skipping it. REVERT: A 49 GLU cc_start: 0.6787 (mp0) cc_final: 0.6328 (mm-30) REVERT: A 60 GLN cc_start: 0.8802 (tp40) cc_final: 0.8516 (tp40) REVERT: A 188 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: A 271 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6748 (tm-30) REVERT: B 49 GLU cc_start: 0.7404 (mp0) cc_final: 0.6812 (mm-30) REVERT: B 188 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: B 212 ASP cc_start: 0.8819 (t0) cc_final: 0.8300 (t0) REVERT: B 271 GLU cc_start: 0.7151 (tt0) cc_final: 0.6768 (tm-30) REVERT: C 212 ASP cc_start: 0.8792 (t0) cc_final: 0.8523 (t0) REVERT: D 49 GLU cc_start: 0.7126 (mp0) cc_final: 0.6356 (mm-30) REVERT: D 212 ASP cc_start: 0.8732 (t0) cc_final: 0.8446 (t0) REVERT: D 228 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7978 (mpp) REVERT: D 271 GLU cc_start: 0.7555 (tt0) cc_final: 0.7133 (tm-30) REVERT: E 49 GLU cc_start: 0.5823 (mp0) cc_final: 0.5426 (mm-30) REVERT: E 212 ASP cc_start: 0.8688 (t0) cc_final: 0.8325 (t0) REVERT: E 228 MET cc_start: 0.8428 (tpp) cc_final: 0.8032 (mpp) REVERT: E 280 PHE cc_start: 0.9004 (t80) cc_final: 0.8270 (t80) REVERT: F 203 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7434 (mt0) REVERT: F 234 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7184 (t80) REVERT: F 386 MET cc_start: 0.6834 (mmm) cc_final: 0.6465 (tpp) REVERT: F 405 ARG cc_start: 0.7897 (mmp80) cc_final: 0.7455 (mmp80) REVERT: F 516 THR cc_start: 0.6368 (OUTLIER) cc_final: 0.6045 (t) REVERT: F 526 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7574 (mt-10) REVERT: F 568 ASN cc_start: 0.8013 (p0) cc_final: 0.7515 (t0) REVERT: F 599 LEU cc_start: 0.8904 (tt) cc_final: 0.8641 (mt) REVERT: F 623 GLN cc_start: 0.9094 (mt0) cc_final: 0.8836 (mp10) REVERT: F 683 ILE cc_start: 0.8234 (mm) cc_final: 0.7877 (pt) REVERT: F 699 ARG cc_start: 0.7218 (tpt170) cc_final: 0.6871 (tpm170) outliers start: 44 outliers final: 32 residues processed: 246 average time/residue: 0.1459 time to fit residues: 57.5069 Evaluate side-chains 247 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 479 ASN Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 684 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 218 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 255 optimal weight: 30.0000 chunk 198 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 479 ASN F 487 ASN ** F 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 760 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.077880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.061988 restraints weight = 57891.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.064084 restraints weight = 27301.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.065459 restraints weight = 15586.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.066398 restraints weight = 10221.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.066958 restraints weight = 7492.828| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21223 Z= 0.194 Angle : 0.680 13.963 28738 Z= 0.329 Chirality : 0.048 0.336 3200 Planarity : 0.004 0.043 3677 Dihedral : 20.160 179.401 3013 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.90 % Allowed : 14.77 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.25 (0.17), residues: 2599 helix: 0.89 (0.15), residues: 1140 sheet: -0.69 (0.26), residues: 414 loop : -0.10 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 366 TYR 0.018 0.001 TYR F 207 PHE 0.017 0.001 PHE A 280 TRP 0.012 0.002 TRP C 80 HIS 0.008 0.001 HIS D 162 Details of bonding type rmsd covalent geometry : bond 0.00444 (21214) covalent geometry : angle 0.67461 (28728) SS BOND : bond 0.00128 ( 5) SS BOND : angle 4.71594 ( 10) hydrogen bonds : bond 0.03426 ( 956) hydrogen bonds : angle 4.53301 ( 2568) Misc. bond : bond 0.00060 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.6828 (mp0) cc_final: 0.6338 (mm-30) REVERT: A 60 GLN cc_start: 0.8826 (tp40) cc_final: 0.8531 (tp40) REVERT: A 188 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: B 49 GLU cc_start: 0.7424 (mp0) cc_final: 0.6815 (mm-30) REVERT: B 133 MET cc_start: 0.8832 (tmm) cc_final: 0.8528 (ppp) REVERT: B 188 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: B 212 ASP cc_start: 0.8802 (t0) cc_final: 0.8294 (t0) REVERT: B 271 GLU cc_start: 0.7192 (tt0) cc_final: 0.6838 (tm-30) REVERT: C 212 ASP cc_start: 0.8814 (t0) cc_final: 0.8520 (t0) REVERT: D 212 ASP cc_start: 0.8767 (t0) cc_final: 0.8433 (t0) REVERT: D 228 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7991 (mpp) REVERT: D 271 GLU cc_start: 0.7600 (tt0) cc_final: 0.7184 (tm-30) REVERT: E 49 GLU cc_start: 0.5775 (mp0) cc_final: 0.5429 (mm-30) REVERT: E 212 ASP cc_start: 0.8700 (t0) cc_final: 0.8304 (t0) REVERT: E 228 MET cc_start: 0.8474 (tpp) cc_final: 0.8092 (mpp) REVERT: F 234 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7109 (t80) REVERT: F 386 MET cc_start: 0.6911 (mmm) cc_final: 0.6460 (tpp) REVERT: F 405 ARG cc_start: 0.7915 (mmp80) cc_final: 0.7445 (mmp80) REVERT: F 516 THR cc_start: 0.6311 (OUTLIER) cc_final: 0.5934 (t) REVERT: F 555 LYS cc_start: 0.7632 (tttt) cc_final: 0.7391 (tttm) REVERT: F 568 ASN cc_start: 0.7957 (p0) cc_final: 0.7535 (t0) REVERT: F 623 GLN cc_start: 0.9114 (mt0) cc_final: 0.8843 (mp10) REVERT: F 699 ARG cc_start: 0.7221 (tpt170) cc_final: 0.6848 (tpm170) outliers start: 43 outliers final: 30 residues processed: 249 average time/residue: 0.1403 time to fit residues: 56.2147 Evaluate side-chains 240 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 162 HIS Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain D residue 162 HIS Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 234 PHE Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 479 ASN Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 643 SER Chi-restraints excluded: chain F residue 684 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 64 optimal weight: 4.9990 chunk 233 optimal weight: 8.9990 chunk 84 optimal weight: 0.3980 chunk 193 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN E 60 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 479 ASN ** F 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.078317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.062383 restraints weight = 57869.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.064481 restraints weight = 27269.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065878 restraints weight = 15565.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.066756 restraints weight = 10206.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.067372 restraints weight = 7536.066| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21223 Z= 0.165 Angle : 0.677 14.391 28738 Z= 0.325 Chirality : 0.048 0.316 3200 Planarity : 0.004 0.046 3677 Dihedral : 20.148 179.812 3013 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.86 % Allowed : 15.16 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.26 (0.17), residues: 2599 helix: 0.90 (0.15), residues: 1140 sheet: -0.69 (0.26), residues: 414 loop : -0.11 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 366 TYR 0.017 0.001 TYR F 207 PHE 0.018 0.001 PHE F 208 TRP 0.011 0.002 TRP D 341 HIS 0.008 0.001 HIS D 162 Details of bonding type rmsd covalent geometry : bond 0.00378 (21214) covalent geometry : angle 0.67353 (28728) SS BOND : bond 0.00620 ( 5) SS BOND : angle 3.75934 ( 10) hydrogen bonds : bond 0.03349 ( 956) hydrogen bonds : angle 4.56415 ( 2568) Misc. bond : bond 0.00051 ( 4) =============================================================================== Job complete usr+sys time: 3500.58 seconds wall clock time: 61 minutes 32.98 seconds (3692.98 seconds total)