Starting phenix.real_space_refine on Fri Mar 6 20:25:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lz1_30021/03_2026/6lz1_30021.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lz1_30021/03_2026/6lz1_30021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lz1_30021/03_2026/6lz1_30021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lz1_30021/03_2026/6lz1_30021.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lz1_30021/03_2026/6lz1_30021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lz1_30021/03_2026/6lz1_30021.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 164 5.16 5 C 22020 2.51 5 N 5808 2.21 5 O 6496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 228 residue(s): 0.03s 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: 34492 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8622 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 1027} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 10.40, per 1000 atoms: 0.30 Number of scatterers: 34492 At special positions: 0 Unit cell: (138.32, 98.8, 169.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 164 16.00 O 6496 8.00 N 5808 7.00 C 22020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 615 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" NE2 HIS B 615 " pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 615 " pdb=" ZN D1201 " pdb="ZN ZN D1201 " - pdb=" NE2 HIS D 615 " 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8128 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 48 sheets defined 29.4% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 4.049A pdb=" N LEU A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.900A pdb=" N LYS A 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 Processing helix chain 'A' and resid 228 through 245 removed outlier: 3.802A pdb=" N TYR A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 removed outlier: 4.065A pdb=" N ASN A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.533A pdb=" N LYS A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.937A pdb=" N ARG A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 removed outlier: 3.806A pdb=" N TYR A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 465 through 475 removed outlier: 4.160A pdb=" N ILE A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 516 removed outlier: 3.683A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 539 removed outlier: 3.514A pdb=" N PHE A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 562 removed outlier: 3.574A pdb=" N TYR A 561 " --> pdb=" O ARG A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 592 Processing helix chain 'A' and resid 598 through 612 removed outlier: 3.847A pdb=" N CYS A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 653 Proline residue: A 632 - end of helix Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 780 through 785 removed outlier: 3.899A pdb=" N LEU A 784 " --> pdb=" O VAL A 781 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 785 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 957 through 969 removed outlier: 3.726A pdb=" N VAL A 961 " --> pdb=" O ASP A 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 24 removed outlier: 4.049A pdb=" N LEU B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.900A pdb=" N LYS B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 224 Processing helix chain 'B' and resid 228 through 245 removed outlier: 3.802A pdb=" N TYR B 232 " --> pdb=" O CYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 265 removed outlier: 4.065A pdb=" N ASN B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.533A pdb=" N LYS B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.937A pdb=" N ARG B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 removed outlier: 3.806A pdb=" N TYR B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 353 Processing helix chain 'B' and resid 372 through 391 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 465 through 475 removed outlier: 4.160A pdb=" N ILE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 516 removed outlier: 3.683A pdb=" N LEU B 503 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 539 removed outlier: 3.514A pdb=" N PHE B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.574A pdb=" N TYR B 561 " --> pdb=" O ARG B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 592 Processing helix chain 'B' and resid 598 through 612 removed outlier: 3.847A pdb=" N CYS B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 653 Proline residue: B 632 - end of helix Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 780 through 785 removed outlier: 3.899A pdb=" N LEU B 784 " --> pdb=" O VAL B 781 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 785 " --> pdb=" O PHE B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 887 Processing helix chain 'B' and resid 957 through 969 removed outlier: 3.726A pdb=" N VAL B 961 " --> pdb=" O ASP B 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 24 removed outlier: 4.049A pdb=" N LEU C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 113 through 118 removed outlier: 3.900A pdb=" N LYS C 118 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 224 Processing helix chain 'C' and resid 228 through 245 removed outlier: 3.802A pdb=" N TYR C 232 " --> pdb=" O CYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 265 removed outlier: 4.065A pdb=" N ASN C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.533A pdb=" N LYS C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.937A pdb=" N ARG C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL C 307 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 removed outlier: 3.806A pdb=" N TYR C 333 " --> pdb=" O GLN C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 353 Processing helix chain 'C' and resid 372 through 391 Processing helix chain 'C' and resid 409 through 417 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 465 through 475 removed outlier: 4.160A pdb=" N ILE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 516 removed outlier: 3.683A pdb=" N LEU C 503 " --> pdb=" O THR C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 539 removed outlier: 3.514A pdb=" N PHE C 531 " --> pdb=" O THR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 562 removed outlier: 3.574A pdb=" N TYR C 561 " --> pdb=" O ARG C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 592 Processing helix chain 'C' and resid 598 through 612 removed outlier: 3.847A pdb=" N CYS C 612 " --> pdb=" O ASP C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 653 Proline residue: C 632 - end of helix Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 780 through 785 removed outlier: 3.899A pdb=" N LEU C 784 " --> pdb=" O VAL C 781 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 785 " --> pdb=" O PHE C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 887 Processing helix chain 'C' and resid 957 through 969 removed outlier: 3.726A pdb=" N VAL C 961 " --> pdb=" O ASP C 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 4.049A pdb=" N LEU D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.900A pdb=" N LYS D 118 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 224 Processing helix chain 'D' and resid 228 through 245 removed outlier: 3.802A pdb=" N TYR D 232 " --> pdb=" O CYS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 265 removed outlier: 4.065A pdb=" N ASN D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D 262 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 removed outlier: 3.533A pdb=" N LYS D 276 " --> pdb=" O VAL D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.937A pdb=" N ARG D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL D 307 " --> pdb=" O ARG D 303 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR D 312 " --> pdb=" O ARG D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 340 removed outlier: 3.806A pdb=" N TYR D 333 " --> pdb=" O GLN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 353 Processing helix chain 'D' and resid 372 through 391 Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 465 through 475 removed outlier: 4.160A pdb=" N ILE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 516 removed outlier: 3.683A pdb=" N LEU D 503 " --> pdb=" O THR D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 539 removed outlier: 3.514A pdb=" N PHE D 531 " --> pdb=" O THR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 562 removed outlier: 3.574A pdb=" N TYR D 561 " --> pdb=" O ARG D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 592 Processing helix chain 'D' and resid 598 through 612 removed outlier: 3.847A pdb=" N CYS D 612 " --> pdb=" O ASP D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 653 Proline residue: D 632 - end of helix Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 780 through 785 removed outlier: 3.899A pdb=" N LEU D 784 " --> pdb=" O VAL D 781 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU D 785 " --> pdb=" O PHE D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 882 through 887 Processing helix chain 'D' and resid 957 through 969 removed outlier: 3.726A pdb=" N VAL D 961 " --> pdb=" O ASP D 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.824A pdb=" N GLU A 89 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 65 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 133 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 143 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.656A pdb=" N PHE A 193 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 152 through 154 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE A 325 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL A 326 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY A 287 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE A 284 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE A 489 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE A 286 " --> pdb=" O PHE A 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE A 325 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL A 326 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY A 287 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 283 " --> pdb=" O LYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 399 removed outlier: 6.482A pdb=" N PHE A 398 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TRP A 548 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN A 441 " --> pdb=" O TRP A 548 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 656 removed outlier: 3.859A pdb=" N ARG A 972 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU A 666 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 702 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 712 through 716 removed outlier: 3.617A pdb=" N ARG A 747 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.636A pdb=" N LYS A 850 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG A 929 " --> pdb=" O LYS A 850 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 852 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY A 915 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 795 through 799 removed outlier: 6.686A pdb=" N SER A 806 " --> pdb=" O LYS A 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 813 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER A 817 " --> pdb=" O ILE A 813 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE A 896 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER A 900 " --> pdb=" O PHE A 864 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE A 864 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 989 through 993 Processing sheet with id=AB3, first strand: chain 'A' and resid 997 through 1004 removed outlier: 6.563A pdb=" N ARG A1014 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE A1002 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE A1012 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A1072 " --> pdb=" O CYS A1040 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.824A pdb=" N GLU B 89 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU B 65 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 133 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 143 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.656A pdb=" N PHE B 193 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 152 through 154 Processing sheet with id=AB7, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE B 325 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL B 326 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 287 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE B 284 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE B 489 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 286 " --> pdb=" O PHE B 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE B 325 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL B 326 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 287 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL B 283 " --> pdb=" O LYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 397 through 399 removed outlier: 6.482A pdb=" N PHE B 398 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TRP B 548 " --> pdb=" O THR B 439 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN B 441 " --> pdb=" O TRP B 548 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 654 through 656 removed outlier: 3.859A pdb=" N ARG B 972 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU B 666 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 702 " --> pdb=" O LEU B 666 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 712 through 716 removed outlier: 3.617A pdb=" N ARG B 747 " --> pdb=" O ASP B 742 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 787 through 789 removed outlier: 6.636A pdb=" N LYS B 850 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG B 929 " --> pdb=" O LYS B 850 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 852 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY B 915 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 795 through 799 removed outlier: 6.686A pdb=" N SER B 806 " --> pdb=" O LYS B 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 813 " --> pdb=" O SER B 817 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER B 817 " --> pdb=" O ILE B 813 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE B 896 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER B 900 " --> pdb=" O PHE B 864 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE B 864 " --> pdb=" O SER B 900 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 989 through 993 Processing sheet with id=AC6, first strand: chain 'B' and resid 997 through 1004 removed outlier: 6.563A pdb=" N ARG B1014 " --> pdb=" O SER B1000 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE B1002 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B1012 " --> pdb=" O ILE B1002 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR B1072 " --> pdb=" O CYS B1040 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.824A pdb=" N GLU C 89 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 65 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 133 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN C 143 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.656A pdb=" N PHE C 193 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 152 through 154 Processing sheet with id=AD1, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE C 325 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL C 326 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY C 287 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE C 284 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE C 489 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 286 " --> pdb=" O PHE C 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE C 325 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL C 326 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY C 287 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL C 283 " --> pdb=" O LYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 397 through 399 removed outlier: 6.482A pdb=" N PHE C 398 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TRP C 548 " --> pdb=" O THR C 439 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN C 441 " --> pdb=" O TRP C 548 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 654 through 656 removed outlier: 3.859A pdb=" N ARG C 972 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU C 666 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 702 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 712 through 716 removed outlier: 3.617A pdb=" N ARG C 747 " --> pdb=" O ASP C 742 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 787 through 789 removed outlier: 6.636A pdb=" N LYS C 850 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG C 929 " --> pdb=" O LYS C 850 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C 852 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY C 915 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 795 through 799 removed outlier: 6.686A pdb=" N SER C 806 " --> pdb=" O LYS C 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 813 " --> pdb=" O SER C 817 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER C 817 " --> pdb=" O ILE C 813 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE C 896 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER C 900 " --> pdb=" O PHE C 864 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE C 864 " --> pdb=" O SER C 900 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 989 through 993 Processing sheet with id=AD9, first strand: chain 'C' and resid 997 through 1004 removed outlier: 6.563A pdb=" N ARG C1014 " --> pdb=" O SER C1000 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE C1002 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE C1012 " --> pdb=" O ILE C1002 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR C1072 " --> pdb=" O CYS C1040 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.824A pdb=" N GLU D 89 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU D 65 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU D 133 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN D 143 " --> pdb=" O VAL D 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 96 through 97 removed outlier: 3.656A pdb=" N PHE D 193 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 152 through 154 Processing sheet with id=AE4, first strand: chain 'D' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE D 325 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL D 326 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY D 287 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE D 284 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE D 489 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE D 286 " --> pdb=" O PHE D 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 357 through 358 removed outlier: 6.069A pdb=" N PHE D 325 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL D 326 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY D 287 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL D 283 " --> pdb=" O LYS D 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 397 through 399 removed outlier: 6.482A pdb=" N PHE D 398 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TRP D 548 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN D 441 " --> pdb=" O TRP D 548 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 656 removed outlier: 3.859A pdb=" N ARG D 972 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU D 666 " --> pdb=" O ALA D 702 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 702 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 712 through 716 removed outlier: 3.617A pdb=" N ARG D 747 " --> pdb=" O ASP D 742 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 787 through 789 removed outlier: 6.636A pdb=" N LYS D 850 " --> pdb=" O ARG D 929 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG D 929 " --> pdb=" O LYS D 850 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU D 852 " --> pdb=" O LEU D 927 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY D 915 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 795 through 799 removed outlier: 6.686A pdb=" N SER D 806 " --> pdb=" O LYS D 798 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 813 " --> pdb=" O SER D 817 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER D 817 " --> pdb=" O ILE D 813 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE D 896 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER D 900 " --> pdb=" O PHE D 864 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE D 864 " --> pdb=" O SER D 900 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 989 through 993 Processing sheet with id=AF3, first strand: chain 'D' and resid 997 through 1004 removed outlier: 6.563A pdb=" N ARG D1014 " --> pdb=" O SER D1000 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE D1002 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE D1012 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR D1072 " --> pdb=" O CYS D1040 " (cutoff:3.500A) 1428 hydrogen bonds defined for protein. 3996 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: 8.72 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11232 1.34 - 1.46: 7696 1.46 - 1.58: 16216 1.58 - 1.69: 0 1.69 - 1.81: 232 Bond restraints: 35376 Sorted by residual: bond pdb=" CA GLU C1017 " pdb=" C GLU C1017 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" CA GLU D1017 " pdb=" C GLU D1017 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" CA GLU A1017 " pdb=" C GLU A1017 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" CA GLU B1017 " pdb=" C GLU B1017 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" CG LEU D 264 " pdb=" CD2 LEU D 264 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 35371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 46152 1.40 - 2.80: 1520 2.80 - 4.20: 276 4.20 - 5.60: 56 5.60 - 7.00: 16 Bond angle restraints: 48020 Sorted by residual: angle pdb=" N GLN C 425 " pdb=" CA GLN C 425 " pdb=" CB GLN C 425 " ideal model delta sigma weight residual 110.90 104.21 6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" N GLN B 425 " pdb=" CA GLN B 425 " pdb=" CB GLN B 425 " ideal model delta sigma weight residual 110.90 104.21 6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" N GLN D 425 " pdb=" CA GLN D 425 " pdb=" CB GLN D 425 " ideal model delta sigma weight residual 110.90 104.21 6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" N GLN A 425 " pdb=" CA GLN A 425 " pdb=" CB GLN A 425 " ideal model delta sigma weight residual 110.90 104.21 6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" N GLU C1017 " pdb=" CA GLU C1017 " pdb=" C GLU C1017 " ideal model delta sigma weight residual 110.28 103.28 7.00 1.48e+00 4.57e-01 2.24e+01 ... (remaining 48015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 18284 17.05 - 34.09: 2112 34.09 - 51.14: 424 51.14 - 68.19: 112 68.19 - 85.23: 48 Dihedral angle restraints: 20980 sinusoidal: 8400 harmonic: 12580 Sorted by residual: dihedral pdb=" CA TYR B 42 " pdb=" C TYR B 42 " pdb=" N ASP B 43 " pdb=" CA ASP B 43 " ideal model delta harmonic sigma weight residual -180.00 -155.19 -24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA TYR D 42 " pdb=" C TYR D 42 " pdb=" N ASP D 43 " pdb=" CA ASP D 43 " ideal model delta harmonic sigma weight residual 180.00 -155.19 -24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA TYR C 42 " pdb=" C TYR C 42 " pdb=" N ASP C 43 " pdb=" CA ASP C 43 " ideal model delta harmonic sigma weight residual -180.00 -155.19 -24.81 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 20977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3664 0.045 - 0.090: 1176 0.090 - 0.135: 348 0.135 - 0.180: 16 0.180 - 0.225: 8 Chirality restraints: 5212 Sorted by residual: chirality pdb=" CA THR B 903 " pdb=" N THR B 903 " pdb=" C THR B 903 " pdb=" CB THR B 903 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA THR D 903 " pdb=" N THR D 903 " pdb=" C THR D 903 " pdb=" CB THR D 903 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA THR A 903 " pdb=" N THR A 903 " pdb=" C THR A 903 " pdb=" CB THR A 903 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 5209 not shown) Planarity restraints: 6216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 422 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C PHE D 422 " 0.039 2.00e-02 2.50e+03 pdb=" O PHE D 422 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 423 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 422 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C PHE C 422 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE C 422 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 423 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 422 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C PHE B 422 " 0.039 2.00e-02 2.50e+03 pdb=" O PHE B 422 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 423 " -0.013 2.00e-02 2.50e+03 ... (remaining 6213 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 724 2.66 - 3.22: 32592 3.22 - 3.78: 55422 3.78 - 4.34: 81682 4.34 - 4.90: 135842 Nonbonded interactions: 306262 Sorted by model distance: nonbonded pdb=" OD2 ASP A 402 " pdb="ZN ZN A1201 " model vdw 2.099 2.230 nonbonded pdb=" OD2 ASP D 402 " pdb="ZN ZN D1201 " model vdw 2.099 2.230 nonbonded pdb=" OD2 ASP B 402 " pdb="ZN ZN B1201 " model vdw 2.099 2.230 nonbonded pdb=" OD2 ASP C 402 " pdb="ZN ZN C1201 " model vdw 2.099 2.230 nonbonded pdb=" OD2 ASP C 292 " pdb="ZN ZN C1201 " model vdw 2.104 2.230 ... (remaining 306257 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.050 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 39.790 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.009 0.642 35380 Z= 0.320 Angle : 0.615 7.001 48020 Z= 0.360 Chirality : 0.047 0.225 5212 Planarity : 0.004 0.032 6216 Dihedral : 15.467 85.234 12852 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.52 % Allowed : 17.25 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.11), residues: 4296 helix: -1.18 (0.13), residues: 1172 sheet: -2.09 (0.15), residues: 944 loop : -3.00 (0.11), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 572 TYR 0.015 0.001 TYR D 627 PHE 0.013 0.001 PHE A 97 TRP 0.018 0.001 TRP B 159 HIS 0.004 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00512 (35376) covalent geometry : angle 0.61474 (48020) hydrogen bonds : bond 0.12427 ( 1428) hydrogen bonds : angle 6.61706 ( 3996) metal coordination : bond 0.64232 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 336 time to evaluate : 1.339 Fit side-chains REVERT: A 433 ASN cc_start: 0.7603 (m110) cc_final: 0.7312 (m-40) REVERT: A 1004 MET cc_start: 0.8341 (mmm) cc_final: 0.8113 (tpt) REVERT: B 433 ASN cc_start: 0.7603 (m110) cc_final: 0.7310 (m-40) REVERT: B 1004 MET cc_start: 0.8343 (mmm) cc_final: 0.8117 (tpt) REVERT: C 433 ASN cc_start: 0.7603 (m110) cc_final: 0.7311 (m-40) REVERT: C 1004 MET cc_start: 0.8346 (mmm) cc_final: 0.8117 (tpt) REVERT: D 433 ASN cc_start: 0.7604 (m110) cc_final: 0.7314 (m-40) REVERT: D 1004 MET cc_start: 0.8347 (mmm) cc_final: 0.8117 (tpt) outliers start: 96 outliers final: 72 residues processed: 408 average time/residue: 0.2051 time to fit residues: 139.0142 Evaluate side-chains 364 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 292 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 662 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 921 ASN Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 662 ASN Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 796 SER Chi-restraints excluded: chain C residue 806 SER Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 921 ASN Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 662 ASN Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 796 SER Chi-restraints excluded: chain D residue 806 SER Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 921 ASN Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 1046 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.0670 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 266 ASN A 288 HIS A 369 ASN A 412 GLN ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 HIS A 458 ASN A 475 GLN A 651 GLN A 758 HIS A 829 ASN A 919 HIS A 921 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 HIS A1076 ASN B 37 ASN B 266 ASN B 288 HIS B 369 ASN B 412 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 HIS B 458 ASN B 475 GLN B 651 GLN B 758 HIS B 829 ASN B 919 HIS B 921 ASN ** B 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1076 ASN C 37 ASN C 266 ASN C 288 HIS C 369 ASN C 412 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 HIS C 458 ASN C 475 GLN C 651 GLN C 758 HIS C 829 ASN C 919 HIS C 921 ASN ** C 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1001 HIS C1076 ASN D 37 ASN D 266 ASN D 288 HIS D 369 ASN D 412 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 HIS D 458 ASN D 475 GLN D 651 GLN D 758 HIS D 829 ASN D 919 HIS D 921 ASN ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1001 HIS D1076 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.113124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.096464 restraints weight = 50376.730| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.92 r_work: 0.3076 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35380 Z= 0.153 Angle : 0.554 5.738 48020 Z= 0.299 Chirality : 0.045 0.139 5212 Planarity : 0.004 0.032 6216 Dihedral : 6.712 51.405 4728 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.58 % Allowed : 16.51 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.12), residues: 4296 helix: -0.04 (0.14), residues: 1188 sheet: -1.86 (0.15), residues: 960 loop : -2.53 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 191 TYR 0.019 0.001 TYR D 627 PHE 0.012 0.001 PHE C 856 TRP 0.016 0.001 TRP C 159 HIS 0.006 0.001 HIS B 861 Details of bonding type rmsd covalent geometry : bond 0.00352 (35376) covalent geometry : angle 0.55409 (48020) hydrogen bonds : bond 0.03887 ( 1428) hydrogen bonds : angle 5.29963 ( 3996) metal coordination : bond 0.00947 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 332 time to evaluate : 1.186 Fit side-chains REVERT: A 308 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7893 (ptp90) REVERT: A 433 ASN cc_start: 0.8196 (m110) cc_final: 0.7523 (m-40) REVERT: A 634 MET cc_start: 0.8506 (mmm) cc_final: 0.8299 (mmt) REVERT: A 684 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6816 (pm20) REVERT: A 716 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7864 (mmtt) REVERT: A 718 ASP cc_start: 0.7360 (p0) cc_final: 0.7090 (t0) REVERT: B 308 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7897 (ptp90) REVERT: B 433 ASN cc_start: 0.8201 (m110) cc_final: 0.7529 (m-40) REVERT: B 634 MET cc_start: 0.8507 (mmm) cc_final: 0.8296 (mmt) REVERT: B 684 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: B 716 LYS cc_start: 0.8278 (ttpt) cc_final: 0.7858 (mmtt) REVERT: B 718 ASP cc_start: 0.7382 (p0) cc_final: 0.7112 (t0) REVERT: C 308 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7907 (ptp90) REVERT: C 433 ASN cc_start: 0.8204 (m110) cc_final: 0.7543 (m-40) REVERT: C 634 MET cc_start: 0.8509 (mmm) cc_final: 0.8297 (mmt) REVERT: C 684 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: C 716 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7858 (mmtt) REVERT: C 718 ASP cc_start: 0.7392 (p0) cc_final: 0.7112 (t0) REVERT: D 308 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7901 (ptp90) REVERT: D 433 ASN cc_start: 0.8199 (m110) cc_final: 0.7531 (m-40) REVERT: D 634 MET cc_start: 0.8515 (mmm) cc_final: 0.8307 (mmt) REVERT: D 684 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6826 (pm20) REVERT: D 716 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7864 (mmtt) REVERT: D 718 ASP cc_start: 0.7371 (p0) cc_final: 0.7100 (t0) outliers start: 136 outliers final: 88 residues processed: 436 average time/residue: 0.2049 time to fit residues: 148.2514 Evaluate side-chains 388 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 292 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 921 ASN Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 879 HIS Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 921 ASN Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 921 ASN Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 343 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 373 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 306 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 179 optimal weight: 0.6980 chunk 308 optimal weight: 1.9990 chunk 239 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 982 ASN ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 982 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 982 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.094722 restraints weight = 50828.546| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.78 r_work: 0.3041 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 35380 Z= 0.255 Angle : 0.606 5.879 48020 Z= 0.325 Chirality : 0.048 0.154 5212 Planarity : 0.004 0.042 6216 Dihedral : 6.649 58.449 4668 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.13 % Allowed : 16.96 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.12), residues: 4296 helix: 0.21 (0.15), residues: 1188 sheet: -1.78 (0.15), residues: 960 loop : -2.45 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 396 TYR 0.024 0.002 TYR D 627 PHE 0.015 0.002 PHE C 856 TRP 0.020 0.001 TRP C 159 HIS 0.005 0.001 HIS D 476 Details of bonding type rmsd covalent geometry : bond 0.00607 (35376) covalent geometry : angle 0.60618 (48020) hydrogen bonds : bond 0.04249 ( 1428) hydrogen bonds : angle 5.28168 ( 3996) metal coordination : bond 0.00347 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 304 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7951 (ptp90) REVERT: A 433 ASN cc_start: 0.8218 (m110) cc_final: 0.7446 (m-40) REVERT: A 634 MET cc_start: 0.8550 (mmm) cc_final: 0.8230 (mmp) REVERT: A 684 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6977 (pm20) REVERT: A 716 LYS cc_start: 0.8284 (ttpt) cc_final: 0.7873 (mmtt) REVERT: A 718 ASP cc_start: 0.7322 (p0) cc_final: 0.7102 (t0) REVERT: A 864 PHE cc_start: 0.9325 (p90) cc_final: 0.9115 (p90) REVERT: B 308 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7956 (ptp90) REVERT: B 433 ASN cc_start: 0.8227 (m110) cc_final: 0.7458 (m-40) REVERT: B 634 MET cc_start: 0.8551 (mmm) cc_final: 0.8227 (mmp) REVERT: B 684 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: B 716 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7860 (mmtt) REVERT: B 718 ASP cc_start: 0.7333 (p0) cc_final: 0.7117 (t0) REVERT: B 864 PHE cc_start: 0.9327 (p90) cc_final: 0.9116 (p90) REVERT: C 308 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7963 (ptp90) REVERT: C 433 ASN cc_start: 0.8232 (m110) cc_final: 0.7464 (m-40) REVERT: C 634 MET cc_start: 0.8562 (mmm) cc_final: 0.8245 (mmp) REVERT: C 684 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6980 (pm20) REVERT: C 716 LYS cc_start: 0.8279 (ttpt) cc_final: 0.7871 (mmtt) REVERT: C 718 ASP cc_start: 0.7336 (p0) cc_final: 0.7114 (t0) REVERT: C 864 PHE cc_start: 0.9324 (p90) cc_final: 0.9114 (p90) REVERT: D 308 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7957 (ptp90) REVERT: D 433 ASN cc_start: 0.8224 (m110) cc_final: 0.7451 (m-40) REVERT: D 634 MET cc_start: 0.8552 (mmm) cc_final: 0.8232 (mmp) REVERT: D 684 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: D 716 LYS cc_start: 0.8287 (ttpt) cc_final: 0.7867 (mmtt) REVERT: D 718 ASP cc_start: 0.7342 (p0) cc_final: 0.7121 (t0) REVERT: D 864 PHE cc_start: 0.9325 (p90) cc_final: 0.9113 (p90) outliers start: 157 outliers final: 125 residues processed: 436 average time/residue: 0.1994 time to fit residues: 146.2024 Evaluate side-chains 425 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 292 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 921 ASN Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 996 ASN Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 921 ASN Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 982 ASN Chi-restraints excluded: chain C residue 996 ASN Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 921 ASN Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 982 ASN Chi-restraints excluded: chain D residue 996 ASN Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 275 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 282 optimal weight: 0.7980 chunk 290 optimal weight: 5.9990 chunk 336 optimal weight: 0.0270 chunk 245 optimal weight: 2.9990 chunk 402 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 216 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 332 GLN A 385 HIS ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS B 137 GLN B 385 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 HIS ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 385 HIS ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS D 137 GLN D 385 HIS ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098081 restraints weight = 50200.072| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.92 r_work: 0.3095 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35380 Z= 0.118 Angle : 0.526 8.067 48020 Z= 0.281 Chirality : 0.044 0.132 5212 Planarity : 0.003 0.032 6216 Dihedral : 6.298 57.840 4668 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.26 % Allowed : 18.51 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.12), residues: 4296 helix: 0.57 (0.15), residues: 1188 sheet: -1.56 (0.15), residues: 936 loop : -2.31 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 396 TYR 0.017 0.001 TYR D 627 PHE 0.012 0.001 PHE A 856 TRP 0.014 0.001 TRP B 159 HIS 0.004 0.001 HIS D 861 Details of bonding type rmsd covalent geometry : bond 0.00270 (35376) covalent geometry : angle 0.52552 (48020) hydrogen bonds : bond 0.03438 ( 1428) hydrogen bonds : angle 5.00530 ( 3996) metal coordination : bond 0.00098 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 309 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7877 (ptp90) REVERT: A 433 ASN cc_start: 0.8211 (m110) cc_final: 0.7501 (m-40) REVERT: A 684 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7025 (pm20) REVERT: A 716 LYS cc_start: 0.8240 (ttpt) cc_final: 0.7844 (mmtt) REVERT: B 308 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7891 (ptp90) REVERT: B 433 ASN cc_start: 0.8202 (m110) cc_final: 0.7497 (m-40) REVERT: B 684 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7013 (pm20) REVERT: B 716 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7830 (mmtt) REVERT: C 308 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7894 (ptp90) REVERT: C 433 ASN cc_start: 0.8203 (m110) cc_final: 0.7500 (m-40) REVERT: C 684 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7086 (pm20) REVERT: C 716 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7833 (mmtt) REVERT: D 308 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7889 (ptp90) REVERT: D 433 ASN cc_start: 0.8206 (m110) cc_final: 0.7497 (m-40) REVERT: D 684 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: D 716 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7843 (mmtt) outliers start: 124 outliers final: 96 residues processed: 417 average time/residue: 0.2021 time to fit residues: 141.8365 Evaluate side-chains 395 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 291 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 824 SER Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 996 ASN Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 879 HIS Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 996 ASN Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 996 ASN Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 172 optimal weight: 0.0970 chunk 287 optimal weight: 1.9990 chunk 387 optimal weight: 7.9990 chunk 286 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 225 optimal weight: 0.3980 chunk 285 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 362 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS A 921 ASN A 982 ASN B 290 HIS B 332 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 HIS B 921 ASN B 982 ASN ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 HIS C 332 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 818 HIS C 921 ASN C 982 ASN D 332 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 818 HIS D 921 ASN D 982 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099175 restraints weight = 50189.222| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.93 r_work: 0.3114 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35380 Z= 0.116 Angle : 0.515 8.603 48020 Z= 0.274 Chirality : 0.043 0.132 5212 Planarity : 0.003 0.031 6216 Dihedral : 5.871 51.961 4652 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.47 % Allowed : 18.64 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.12), residues: 4296 helix: 0.84 (0.15), residues: 1188 sheet: -1.40 (0.15), residues: 936 loop : -2.22 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 396 TYR 0.009 0.001 TYR A 787 PHE 0.013 0.001 PHE B 856 TRP 0.013 0.001 TRP B 159 HIS 0.003 0.001 HIS A 861 Details of bonding type rmsd covalent geometry : bond 0.00266 (35376) covalent geometry : angle 0.51505 (48020) hydrogen bonds : bond 0.03289 ( 1428) hydrogen bonds : angle 4.86628 ( 3996) metal coordination : bond 0.00096 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 316 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8102 (mt-10) REVERT: A 308 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7861 (ptp90) REVERT: A 433 ASN cc_start: 0.8206 (m110) cc_final: 0.7510 (m-40) REVERT: A 716 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7826 (mmtt) REVERT: A 890 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: B 21 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8101 (mt-10) REVERT: B 308 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7872 (ptp90) REVERT: B 433 ASN cc_start: 0.8197 (m110) cc_final: 0.7511 (m-40) REVERT: B 716 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7814 (mmtt) REVERT: B 890 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: C 21 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8083 (mt-10) REVERT: C 308 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7877 (ptp90) REVERT: C 433 ASN cc_start: 0.8194 (m110) cc_final: 0.7509 (m-40) REVERT: C 716 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7819 (mmtt) REVERT: C 890 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: D 21 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8078 (mt-10) REVERT: D 308 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7865 (ptp90) REVERT: D 433 ASN cc_start: 0.8200 (m110) cc_final: 0.7508 (m-40) REVERT: D 716 LYS cc_start: 0.8230 (ttpt) cc_final: 0.7826 (mmtt) REVERT: D 890 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8114 (tt0) outliers start: 132 outliers final: 88 residues processed: 424 average time/residue: 0.1978 time to fit residues: 141.5341 Evaluate side-chains 388 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 292 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 890 GLU Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 996 ASN Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 879 HIS Chi-restraints excluded: chain C residue 890 GLU Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 996 ASN Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 996 ASN Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 348 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 398 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 182 optimal weight: 0.3980 chunk 334 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 982 ASN ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 982 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 982 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.096994 restraints weight = 50318.579| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.93 r_work: 0.3078 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35380 Z= 0.170 Angle : 0.549 9.753 48020 Z= 0.291 Chirality : 0.045 0.167 5212 Planarity : 0.004 0.034 6216 Dihedral : 5.982 52.913 4652 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.89 % Allowed : 18.93 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.12), residues: 4296 helix: 0.84 (0.15), residues: 1188 sheet: -1.35 (0.15), residues: 904 loop : -2.22 (0.12), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 396 TYR 0.010 0.001 TYR B1016 PHE 0.017 0.001 PHE B 380 TRP 0.015 0.001 TRP B 159 HIS 0.004 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00402 (35376) covalent geometry : angle 0.54854 (48020) hydrogen bonds : bond 0.03568 ( 1428) hydrogen bonds : angle 4.89376 ( 3996) metal coordination : bond 0.00195 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 284 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7927 (ptp90) REVERT: A 433 ASN cc_start: 0.8219 (m110) cc_final: 0.7494 (m-40) REVERT: A 716 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7818 (mmtt) REVERT: A 890 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: B 308 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7927 (ptp90) REVERT: B 433 ASN cc_start: 0.8215 (m110) cc_final: 0.7492 (m-40) REVERT: B 716 LYS cc_start: 0.8231 (ttpt) cc_final: 0.7804 (mmtt) REVERT: B 890 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: C 308 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7931 (ptp90) REVERT: C 433 ASN cc_start: 0.8210 (m110) cc_final: 0.7491 (m-40) REVERT: C 716 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7807 (mmtt) REVERT: C 890 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8638 (tt0) REVERT: D 308 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7923 (ptp90) REVERT: D 433 ASN cc_start: 0.8214 (m110) cc_final: 0.7487 (m-40) REVERT: D 716 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7809 (mmtt) REVERT: D 890 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8123 (tt0) outliers start: 148 outliers final: 112 residues processed: 412 average time/residue: 0.1942 time to fit residues: 136.3128 Evaluate side-chains 398 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 278 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 890 GLU Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 996 ASN Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 890 GLU Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 982 ASN Chi-restraints excluded: chain C residue 996 ASN Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 837 VAL Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 982 ASN Chi-restraints excluded: chain D residue 996 ASN Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 18 optimal weight: 0.8980 chunk 314 optimal weight: 1.9990 chunk 319 optimal weight: 9.9990 chunk 425 optimal weight: 1.9990 chunk 371 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 403 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 326 optimal weight: 20.0000 chunk 347 optimal weight: 3.9990 chunk 125 optimal weight: 0.3980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.114738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098187 restraints weight = 50223.668| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.93 r_work: 0.3099 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35380 Z= 0.131 Angle : 0.530 11.160 48020 Z= 0.281 Chirality : 0.044 0.179 5212 Planarity : 0.003 0.032 6216 Dihedral : 5.913 52.253 4652 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.36 % Allowed : 19.58 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.12), residues: 4296 helix: 0.95 (0.15), residues: 1188 sheet: -1.26 (0.16), residues: 904 loop : -2.15 (0.12), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 396 TYR 0.010 0.001 TYR B1016 PHE 0.013 0.001 PHE A 856 TRP 0.013 0.001 TRP D 159 HIS 0.003 0.001 HIS A 861 Details of bonding type rmsd covalent geometry : bond 0.00307 (35376) covalent geometry : angle 0.53039 (48020) hydrogen bonds : bond 0.03374 ( 1428) hydrogen bonds : angle 4.83220 ( 3996) metal coordination : bond 0.00117 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 300 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.6728 (ttm-80) REVERT: A 308 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7946 (ptp90) REVERT: A 433 ASN cc_start: 0.8210 (m110) cc_final: 0.7507 (m-40) REVERT: A 647 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: A 716 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7800 (mmtt) REVERT: A 890 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: B 46 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.6718 (ttm-80) REVERT: B 308 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7943 (ptp90) REVERT: B 433 ASN cc_start: 0.8197 (m110) cc_final: 0.7494 (m-40) REVERT: B 647 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: B 716 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7782 (mmtt) REVERT: B 890 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: C 46 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.6713 (ttm-80) REVERT: C 308 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7945 (ptp90) REVERT: C 433 ASN cc_start: 0.8197 (m110) cc_final: 0.7504 (m-40) REVERT: C 647 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: C 716 LYS cc_start: 0.8213 (ttpt) cc_final: 0.7789 (mmtt) REVERT: C 890 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: D 46 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.6718 (ttm-80) REVERT: D 308 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7942 (ptp90) REVERT: D 433 ASN cc_start: 0.8205 (m110) cc_final: 0.7502 (m-40) REVERT: D 647 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: D 716 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7794 (mmtt) REVERT: D 890 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8105 (tt0) outliers start: 128 outliers final: 105 residues processed: 412 average time/residue: 0.2043 time to fit residues: 141.3414 Evaluate side-chains 404 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 283 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 647 GLN Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 890 GLU Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 996 ASN Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 647 GLN Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 879 HIS Chi-restraints excluded: chain C residue 890 GLU Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 996 ASN Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 647 GLN Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 837 VAL Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 996 ASN Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 306 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 380 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 270 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 300 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 420 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN A 982 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 GLN B 982 ASN ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN C 982 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 894 GLN D 982 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.095784 restraints weight = 50548.777| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.75 r_work: 0.3063 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 35380 Z= 0.244 Angle : 0.604 11.945 48020 Z= 0.319 Chirality : 0.047 0.169 5212 Planarity : 0.004 0.040 6216 Dihedral : 6.189 54.421 4652 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.65 % Allowed : 19.72 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.12), residues: 4296 helix: 0.85 (0.15), residues: 1168 sheet: -1.49 (0.15), residues: 936 loop : -2.07 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 924 TYR 0.013 0.002 TYR A 406 PHE 0.021 0.002 PHE C 591 TRP 0.018 0.001 TRP B 159 HIS 0.004 0.001 HIS D 476 Details of bonding type rmsd covalent geometry : bond 0.00582 (35376) covalent geometry : angle 0.60418 (48020) hydrogen bonds : bond 0.03960 ( 1428) hydrogen bonds : angle 5.01556 ( 3996) metal coordination : bond 0.00305 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 270 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.6754 (ttm-80) REVERT: A 308 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7956 (ptp90) REVERT: A 433 ASN cc_start: 0.8215 (m110) cc_final: 0.7457 (m-40) REVERT: A 647 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: A 716 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7811 (mmtt) REVERT: B 46 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.6759 (ttm-80) REVERT: B 308 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7961 (ptp90) REVERT: B 433 ASN cc_start: 0.8210 (m110) cc_final: 0.7447 (m-40) REVERT: B 647 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: B 716 LYS cc_start: 0.8245 (ttpt) cc_final: 0.7799 (mmtt) REVERT: C 46 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.6745 (ttm-80) REVERT: C 308 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7963 (ptp90) REVERT: C 433 ASN cc_start: 0.8204 (m110) cc_final: 0.7454 (m-40) REVERT: C 647 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: C 716 LYS cc_start: 0.8232 (ttpt) cc_final: 0.7794 (mmtt) REVERT: D 46 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.6765 (ttm-80) REVERT: D 308 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7961 (ptp90) REVERT: D 433 ASN cc_start: 0.8208 (m110) cc_final: 0.7449 (m-40) REVERT: D 647 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: D 716 LYS cc_start: 0.8244 (ttpt) cc_final: 0.7800 (mmtt) outliers start: 139 outliers final: 119 residues processed: 387 average time/residue: 0.2055 time to fit residues: 132.8293 Evaluate side-chains 389 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 258 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 647 GLN Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 996 ASN Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 647 GLN Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 982 ASN Chi-restraints excluded: chain C residue 996 ASN Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 556 PHE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 647 GLN Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 837 VAL Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 982 ASN Chi-restraints excluded: chain D residue 996 ASN Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 194 optimal weight: 1.9990 chunk 411 optimal weight: 1.9990 chunk 414 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 324 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 323 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 982 ASN ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 982 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 982 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097309 restraints weight = 50174.510| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.92 r_work: 0.3095 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35380 Z= 0.148 Angle : 0.549 11.043 48020 Z= 0.290 Chirality : 0.045 0.166 5212 Planarity : 0.003 0.032 6216 Dihedral : 6.047 53.015 4652 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.68 % Allowed : 19.51 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.12), residues: 4296 helix: 0.87 (0.15), residues: 1188 sheet: -1.35 (0.16), residues: 904 loop : -2.13 (0.12), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 396 TYR 0.009 0.001 TYR C1016 PHE 0.020 0.001 PHE C 591 TRP 0.015 0.001 TRP B 159 HIS 0.003 0.001 HIS D 453 Details of bonding type rmsd covalent geometry : bond 0.00348 (35376) covalent geometry : angle 0.54853 (48020) hydrogen bonds : bond 0.03530 ( 1428) hydrogen bonds : angle 4.91241 ( 3996) metal coordination : bond 0.00134 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 277 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.6829 (ttm-80) REVERT: A 308 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7970 (ptp90) REVERT: A 433 ASN cc_start: 0.8218 (m110) cc_final: 0.7311 (m-40) REVERT: A 474 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8477 (p0) REVERT: A 647 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: A 716 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7821 (mmtt) REVERT: B 46 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.6817 (ttm-80) REVERT: B 308 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7972 (ptp90) REVERT: B 433 ASN cc_start: 0.8201 (m110) cc_final: 0.7306 (m-40) REVERT: B 647 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: B 716 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7804 (mmtt) REVERT: B 1004 MET cc_start: 0.9106 (mmm) cc_final: 0.8806 (tpt) REVERT: C 46 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.6809 (ttm-80) REVERT: C 308 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7974 (ptp90) REVERT: C 433 ASN cc_start: 0.8212 (m110) cc_final: 0.7319 (m-40) REVERT: C 474 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8454 (p0) REVERT: C 647 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: C 716 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7806 (mmtt) REVERT: D 46 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.6824 (ttm-80) REVERT: D 308 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7969 (ptp90) REVERT: D 433 ASN cc_start: 0.8215 (m110) cc_final: 0.7315 (m-40) REVERT: D 474 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8476 (p0) REVERT: D 647 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: D 716 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7815 (mmtt) outliers start: 140 outliers final: 121 residues processed: 392 average time/residue: 0.2029 time to fit residues: 133.4641 Evaluate side-chains 405 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 269 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 647 GLN Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 996 ASN Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 647 GLN Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 879 HIS Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 982 ASN Chi-restraints excluded: chain C residue 996 ASN Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 647 GLN Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 837 VAL Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 982 ASN Chi-restraints excluded: chain D residue 996 ASN Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 19 optimal weight: 9.9990 chunk 196 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 362 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 349 optimal weight: 9.9990 chunk 396 optimal weight: 6.9990 chunk 424 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 982 ASN ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 982 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 982 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.096020 restraints weight = 50582.320| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.93 r_work: 0.3073 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 35380 Z= 0.201 Angle : 0.574 10.617 48020 Z= 0.303 Chirality : 0.046 0.168 5212 Planarity : 0.004 0.038 6216 Dihedral : 6.117 54.176 4652 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.81 % Allowed : 19.82 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.12), residues: 4296 helix: 0.80 (0.15), residues: 1192 sheet: -1.39 (0.16), residues: 904 loop : -2.12 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 924 TYR 0.011 0.002 TYR B 406 PHE 0.022 0.002 PHE D 591 TRP 0.016 0.001 TRP D 159 HIS 0.004 0.001 HIS A 615 Details of bonding type rmsd covalent geometry : bond 0.00479 (35376) covalent geometry : angle 0.57398 (48020) hydrogen bonds : bond 0.03728 ( 1428) hydrogen bonds : angle 4.92969 ( 3996) metal coordination : bond 0.00232 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 274 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.6707 (ttm-80) REVERT: A 308 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7953 (ptp90) REVERT: A 433 ASN cc_start: 0.8227 (m110) cc_final: 0.7491 (m-40) REVERT: A 474 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8491 (p0) REVERT: A 647 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: A 716 LYS cc_start: 0.8232 (ttpt) cc_final: 0.7826 (mmtt) REVERT: B 46 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.6708 (ttm-80) REVERT: B 308 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7957 (ptp90) REVERT: B 433 ASN cc_start: 0.8214 (m110) cc_final: 0.7476 (m-40) REVERT: B 474 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8481 (p0) REVERT: B 647 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: B 716 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7821 (mmtt) REVERT: C 46 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.6686 (ttm-80) REVERT: C 149 GLU cc_start: 0.8614 (pm20) cc_final: 0.8343 (pm20) REVERT: C 308 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7955 (ptp90) REVERT: C 433 ASN cc_start: 0.8223 (m110) cc_final: 0.7493 (m-40) REVERT: C 474 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8468 (p0) REVERT: C 647 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: C 716 LYS cc_start: 0.8234 (ttpt) cc_final: 0.7818 (mmtt) REVERT: D 46 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.6713 (ttm-80) REVERT: D 308 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7950 (ptp90) REVERT: D 433 ASN cc_start: 0.8225 (m110) cc_final: 0.7484 (m-40) REVERT: D 474 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8487 (p0) REVERT: D 647 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: D 716 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7820 (mmtt) outliers start: 145 outliers final: 125 residues processed: 398 average time/residue: 0.2018 time to fit residues: 134.6619 Evaluate side-chains 415 residues out of total 3808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 274 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 694 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 935 ASP Chi-restraints excluded: chain A residue 982 ASN Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 647 GLN Chi-restraints excluded: chain B residue 694 CYS Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 907 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 935 ASP Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 996 ASN Chi-restraints excluded: chain B residue 1046 ASP Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 647 GLN Chi-restraints excluded: chain C residue 694 CYS Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 879 HIS Chi-restraints excluded: chain C residue 907 SER Chi-restraints excluded: chain C residue 909 LEU Chi-restraints excluded: chain C residue 935 ASP Chi-restraints excluded: chain C residue 982 ASN Chi-restraints excluded: chain C residue 996 ASN Chi-restraints excluded: chain C residue 1046 ASP Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 582 GLU Chi-restraints excluded: chain D residue 647 GLN Chi-restraints excluded: chain D residue 694 CYS Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 837 VAL Chi-restraints excluded: chain D residue 863 GLU Chi-restraints excluded: chain D residue 879 HIS Chi-restraints excluded: chain D residue 907 SER Chi-restraints excluded: chain D residue 909 LEU Chi-restraints excluded: chain D residue 935 ASP Chi-restraints excluded: chain D residue 982 ASN Chi-restraints excluded: chain D residue 996 ASN Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 28 optimal weight: 2.9990 chunk 403 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 295 optimal weight: 4.9990 chunk 350 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 982 ASN B 982 ASN ** B1001 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 982 ASN D 982 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098028 restraints weight = 49948.690| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.92 r_work: 0.3098 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35380 Z= 0.137 Angle : 0.544 10.226 48020 Z= 0.287 Chirality : 0.045 0.166 5212 Planarity : 0.003 0.033 6216 Dihedral : 5.996 52.946 4652 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.68 % Allowed : 19.90 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.12), residues: 4296 helix: 0.93 (0.15), residues: 1188 sheet: -1.31 (0.16), residues: 904 loop : -2.08 (0.12), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 396 TYR 0.009 0.001 TYR B1016 PHE 0.019 0.001 PHE C 591 TRP 0.014 0.001 TRP D 159 HIS 0.004 0.001 HIS D 453 Details of bonding type rmsd covalent geometry : bond 0.00321 (35376) covalent geometry : angle 0.54372 (48020) hydrogen bonds : bond 0.03434 ( 1428) hydrogen bonds : angle 4.84846 ( 3996) metal coordination : bond 0.00124 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6750.23 seconds wall clock time: 117 minutes 21.75 seconds (7041.75 seconds total)