Starting phenix.real_space_refine on Sat Jul 4 23:33:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rrf_54186/07_2026/9rrf_54186_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rrf_54186/07_2026/9rrf_54186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rrf_54186/07_2026/9rrf_54186_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rrf_54186/07_2026/9rrf_54186_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rrf_54186/07_2026/9rrf_54186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rrf_54186/07_2026/9rrf_54186.map" } resolution = 2.3 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= 0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 4 5.49 5 S 120 5.16 5 C 14844 2.51 5 N 3688 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22684 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5542 Classifications: {'peptide': 680} Link IDs: {'PTRANS': 25, 'TRANS': 654} Chain breaks: 3 Chain: "B" Number of atoms: 5542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5542 Classifications: {'peptide': 680} Link IDs: {'PTRANS': 25, 'TRANS': 654} Chain breaks: 3 Chain: "C" Number of atoms: 5542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5542 Classifications: {'peptide': 680} Link IDs: {'PTRANS': 25, 'TRANS': 654} Chain breaks: 3 Chain: "D" Number of atoms: 5542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5542 Classifications: {'peptide': 680} Link IDs: {'PTRANS': 25, 'TRANS': 654} Chain breaks: 3 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 128 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 128 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 128 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 128 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1166 SG CYS A 176 101.103 83.940 59.834 1.00132.19 S ATOM 1180 SG CYS A 178 102.903 85.998 56.976 1.00148.58 S ATOM 1202 SG CYS A 181 98.997 85.563 57.111 1.00138.25 S ATOM 6708 SG CYS B 176 23.216 40.376 59.841 1.00135.97 S ATOM 6722 SG CYS B 178 21.417 38.321 56.981 1.00151.98 S ATOM 6744 SG CYS B 181 25.322 38.755 57.118 1.00140.64 S ATOM 12250 SG CYS C 176 83.941 23.216 59.841 1.00126.19 S ATOM 12264 SG CYS C 178 85.998 21.416 56.982 1.00137.79 S ATOM 12286 SG CYS C 181 85.564 25.321 57.117 1.00129.63 S ATOM 17792 SG CYS D 176 40.378 101.101 59.837 1.00125.23 S ATOM 17806 SG CYS D 178 38.320 102.900 56.979 1.00136.89 S ATOM 17828 SG CYS D 181 38.755 98.996 57.115 1.00128.16 S Time building chain proxies: 4.81, per 1000 atoms: 0.21 Number of scatterers: 22684 At special positions: 0 Unit cell: (125.06, 125.06, 134.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 120 16.00 P 4 15.00 O 4020 8.00 N 3688 7.00 C 14844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 980.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 181 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 176 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 178 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 176 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 178 " pdb=" ZN C 801 " pdb="ZN ZN C 801 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 181 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 178 " pdb=" ZN D 801 " pdb="ZN ZN D 801 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 176 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 178 " Number of angles added : 12 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5240 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 4 sheets defined 80.0% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.875A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.862A pdb=" N MET A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 108 through 118 removed outlier: 3.746A pdb=" N TYR A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.780A pdb=" N LYS A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.617A pdb=" N GLN A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.645A pdb=" N LEU A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.601A pdb=" N ILE A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 386 removed outlier: 4.281A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 423 Proline residue: A 409 - end of helix removed outlier: 3.585A pdb=" N TRP A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 433 through 460 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 513 through 540 removed outlier: 3.559A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 545 through 553 Proline residue: A 550 - end of helix Processing helix chain 'A' and resid 567 through 579 removed outlier: 3.799A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.526A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 614 Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.549A pdb=" N LEU A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N HIS A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 649 Processing helix chain 'A' and resid 658 through 663 removed outlier: 4.039A pdb=" N ILE A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 733 removed outlier: 3.778A pdb=" N LYS A 733 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 754 removed outlier: 3.522A pdb=" N GLU A 740 " --> pdb=" O GLU A 736 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG A 754 " --> pdb=" O ILE A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.876A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.859A pdb=" N MET B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 108 through 118 removed outlier: 3.745A pdb=" N TYR B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 215 through 234 removed outlier: 3.779A pdb=" N LYS B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.616A pdb=" N GLN B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.643A pdb=" N LEU B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.602A pdb=" N ILE B 360 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 386 removed outlier: 4.282A pdb=" N SER B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 423 Proline residue: B 409 - end of helix removed outlier: 3.585A pdb=" N TRP B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 433 Processing helix chain 'B' and resid 433 through 460 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 500 Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 513 through 540 removed outlier: 3.558A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 545 through 553 Proline residue: B 550 - end of helix Processing helix chain 'B' and resid 567 through 579 removed outlier: 3.800A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.525A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 614 Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.554A pdb=" N LEU B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N HIS B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 649 Processing helix chain 'B' and resid 658 through 663 removed outlier: 4.038A pdb=" N ILE B 663 " --> pdb=" O PRO B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 733 removed outlier: 3.779A pdb=" N LYS B 733 " --> pdb=" O ILE B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 754 removed outlier: 3.523A pdb=" N GLU B 740 " --> pdb=" O GLU B 736 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG B 754 " --> pdb=" O ILE B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.880A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.863A pdb=" N MET C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 108 through 118 removed outlier: 3.746A pdb=" N TYR C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 215 through 234 removed outlier: 3.780A pdb=" N LYS C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.616A pdb=" N GLN C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 340 through 351 removed outlier: 3.643A pdb=" N LEU C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.603A pdb=" N ILE C 360 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 386 removed outlier: 4.283A pdb=" N SER C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 423 Proline residue: C 409 - end of helix removed outlier: 3.586A pdb=" N TRP C 423 " --> pdb=" O ILE C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 433 Processing helix chain 'C' and resid 433 through 460 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 Processing helix chain 'C' and resid 503 through 513 Processing helix chain 'C' and resid 513 through 540 removed outlier: 3.559A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 545 through 553 Proline residue: C 550 - end of helix Processing helix chain 'C' and resid 567 through 579 removed outlier: 3.799A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.525A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 614 Processing helix chain 'C' and resid 615 through 634 removed outlier: 3.555A pdb=" N LEU C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N HIS C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 649 Processing helix chain 'C' and resid 658 through 663 removed outlier: 4.038A pdb=" N ILE C 663 " --> pdb=" O PRO C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 733 removed outlier: 3.781A pdb=" N LYS C 733 " --> pdb=" O ILE C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 754 removed outlier: 3.523A pdb=" N GLU C 740 " --> pdb=" O GLU C 736 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG C 754 " --> pdb=" O ILE C 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.878A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.857A pdb=" N MET D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 108 through 118 removed outlier: 3.749A pdb=" N TYR D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.780A pdb=" N LYS D 232 " --> pdb=" O LYS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.617A pdb=" N GLN D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 340 through 351 removed outlier: 3.644A pdb=" N LEU D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.603A pdb=" N ILE D 360 " --> pdb=" O GLY D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 386 removed outlier: 4.283A pdb=" N SER D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN D 386 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 423 Proline residue: D 409 - end of helix removed outlier: 3.585A pdb=" N TRP D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 433 Processing helix chain 'D' and resid 433 through 460 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 Processing helix chain 'D' and resid 503 through 513 Processing helix chain 'D' and resid 513 through 540 removed outlier: 3.559A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 545 through 553 Proline residue: D 550 - end of helix Processing helix chain 'D' and resid 567 through 579 removed outlier: 3.800A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.524A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 614 Processing helix chain 'D' and resid 615 through 634 removed outlier: 3.554A pdb=" N LEU D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N HIS D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 649 Processing helix chain 'D' and resid 658 through 663 removed outlier: 4.046A pdb=" N ILE D 663 " --> pdb=" O PRO D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 733 removed outlier: 3.781A pdb=" N LYS D 733 " --> pdb=" O ILE D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 754 removed outlier: 3.523A pdb=" N GLU D 740 " --> pdb=" O GLU D 736 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG D 754 " --> pdb=" O ILE D 750 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AA4, first strand: chain 'B' and resid 167 through 168 1475 hydrogen bonds defined for protein. 4245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3608 1.32 - 1.44: 6253 1.44 - 1.57: 13147 1.57 - 1.69: 8 1.69 - 1.81: 196 Bond restraints: 23212 Sorted by residual: bond pdb=" CA GLU C 81 " pdb=" CB GLU C 81 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.80e-01 bond pdb=" CB PHE A 520 " pdb=" CG PHE A 520 " ideal model delta sigma weight residual 1.502 1.483 0.019 2.30e-02 1.89e+03 6.70e-01 bond pdb=" CA GLU D 81 " pdb=" CB GLU D 81 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.51e-01 bond pdb=" SD MET A 604 " pdb=" CE MET A 604 " ideal model delta sigma weight residual 1.791 1.771 0.020 2.50e-02 1.60e+03 6.32e-01 bond pdb=" CB PHE B 520 " pdb=" CG PHE B 520 " ideal model delta sigma weight residual 1.502 1.484 0.018 2.30e-02 1.89e+03 6.31e-01 ... (remaining 23207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 30125 0.94 - 1.88: 956 1.88 - 2.83: 188 2.83 - 3.77: 98 3.77 - 4.71: 29 Bond angle restraints: 31396 Sorted by residual: angle pdb=" CB GLU B 467 " pdb=" CG GLU B 467 " pdb=" CD GLU B 467 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.70e+00 3.46e-01 7.07e+00 angle pdb=" CB GLU C 467 " pdb=" CG GLU C 467 " pdb=" CD GLU C 467 " ideal model delta sigma weight residual 112.60 117.06 -4.46 1.70e+00 3.46e-01 6.90e+00 angle pdb=" CB GLU A 467 " pdb=" CG GLU A 467 " pdb=" CD GLU A 467 " ideal model delta sigma weight residual 112.60 117.05 -4.45 1.70e+00 3.46e-01 6.85e+00 angle pdb=" CB GLU D 467 " pdb=" CG GLU D 467 " pdb=" CD GLU D 467 " ideal model delta sigma weight residual 112.60 117.02 -4.42 1.70e+00 3.46e-01 6.77e+00 angle pdb=" CA GLU B 81 " pdb=" CB GLU B 81 " pdb=" CG GLU B 81 " ideal model delta sigma weight residual 114.10 118.81 -4.71 2.00e+00 2.50e-01 5.55e+00 ... (remaining 31391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 11901 17.36 - 34.73: 1577 34.73 - 52.09: 505 52.09 - 69.46: 125 69.46 - 86.82: 52 Dihedral angle restraints: 14160 sinusoidal: 6104 harmonic: 8056 Sorted by residual: dihedral pdb=" CA ASN A 625 " pdb=" CB ASN A 625 " pdb=" CG ASN A 625 " pdb=" OD1 ASN A 625 " ideal model delta sinusoidal sigma weight residual 120.00 -168.24 -71.76 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN B 625 " pdb=" CB ASN B 625 " pdb=" CG ASN B 625 " pdb=" OD1 ASN B 625 " ideal model delta sinusoidal sigma weight residual 120.00 -168.24 -71.76 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN D 625 " pdb=" CB ASN D 625 " pdb=" CG ASN D 625 " pdb=" OD1 ASN D 625 " ideal model delta sinusoidal sigma weight residual 120.00 -168.31 -71.69 2 2.00e+01 2.50e-03 1.08e+01 ... (remaining 14157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1826 0.027 - 0.054: 1183 0.054 - 0.081: 343 0.081 - 0.108: 109 0.108 - 0.135: 43 Chirality restraints: 3504 Sorted by residual: chirality pdb=" CA PRO C 145 " pdb=" N PRO C 145 " pdb=" C PRO C 145 " pdb=" CB PRO C 145 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE C 664 " pdb=" N ILE C 664 " pdb=" C ILE C 664 " pdb=" CB ILE C 664 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE B 664 " pdb=" N ILE B 664 " pdb=" C ILE B 664 " pdb=" CB ILE B 664 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 3501 not shown) Planarity restraints: 3880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 81 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" CD GLU D 81 " 0.040 2.00e-02 2.50e+03 pdb=" OE1 GLU D 81 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU D 81 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 81 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" CD GLU B 81 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 81 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 81 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 81 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" CD GLU C 81 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU C 81 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU C 81 " 0.013 2.00e-02 2.50e+03 ... (remaining 3877 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3740 2.75 - 3.29: 22388 3.29 - 3.83: 37233 3.83 - 4.36: 45388 4.36 - 4.90: 75372 Nonbonded interactions: 184121 Sorted by model distance: nonbonded pdb=" O GLU B 81 " pdb=" OE1 GLU B 81 " model vdw 2.218 3.040 nonbonded pdb=" O GLU C 81 " pdb=" OE1 GLU C 81 " model vdw 2.222 3.040 nonbonded pdb=" O GLU A 81 " pdb=" OE1 GLU A 81 " model vdw 2.222 3.040 nonbonded pdb=" O GLU D 81 " pdb=" OE1 GLU D 81 " model vdw 2.224 3.040 nonbonded pdb=" N GLU A 467 " pdb=" OE1 GLU A 467 " model vdw 2.335 3.120 ... (remaining 184116 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: 0.07 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: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.140 Find NCS groups from input model: 0.200 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:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 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 : 0.005 0.032 23232 Z= 0.211 Angle : 0.467 4.712 31416 Z= 0.236 Chirality : 0.039 0.135 3504 Planarity : 0.004 0.049 3880 Dihedral : 18.121 86.821 8908 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.99 % Allowed : 25.37 % Favored : 73.64 % 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: 1.48 (0.16), residues: 2688 helix: 1.44 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : -0.12 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 71 TYR 0.011 0.001 TYR A 524 PHE 0.018 0.002 PHE D 497 TRP 0.009 0.001 TRP A 315 HIS 0.003 0.000 HIS B 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (23212) covalent geometry : angle 0.46173 / 0.23 (31396) SS BOND : bond 0.00088 / 0.04 ( 4) SS BOND : angle 0.26267 / 0.17 ( 8) hydrogen bonds : bond 0.23726 / 15.97 ( 1475) hydrogen bonds : angle 6.20728 / 4.47 ( 4245) metal coordination : bond 0.00519 / 0.38 ( 16) metal coordination : angle 3.50797 / 2.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 478 time to evaluate : 0.834 Fit side-chains REVERT: A 71 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7548 (mtp-110) REVERT: B 71 ARG cc_start: 0.7978 (mtm110) cc_final: 0.7518 (mtp-110) REVERT: B 286 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: C 71 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7543 (mtp-110) REVERT: D 71 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7563 (mtp-110) outliers start: 24 outliers final: 0 residues processed: 491 average time/residue: 0.6398 time to fit residues: 357.3359 Evaluate side-chains 333 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 286 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 HIS B 394 HIS B 443 ASN ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 HIS C 443 ASN D 394 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.166824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096965 restraints weight = 23470.224| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.43 r_work: 0.2917 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23232 Z= 0.134 Angle : 0.512 6.424 31416 Z= 0.274 Chirality : 0.038 0.152 3504 Planarity : 0.004 0.048 3880 Dihedral : 8.696 64.261 3542 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.97 % Allowed : 21.83 % Favored : 75.21 % 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: 2.61 (0.16), residues: 2688 helix: 2.34 (0.11), residues: 1984 sheet: None (None), residues: 0 loop : -0.03 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 71 TYR 0.010 0.001 TYR C 524 PHE 0.014 0.002 PHE C 520 TRP 0.014 0.001 TRP B 315 HIS 0.002 0.001 HIS D 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (23212) covalent geometry : angle 0.50885 / 0.27 (31396) SS BOND : bond 0.00244 / 0.12 ( 4) SS BOND : angle 0.46691 / 0.33 ( 8) hydrogen bonds : bond 0.05625 / 3.69 ( 1475) hydrogen bonds : angle 3.91543 / 2.83 ( 4245) metal coordination : bond 0.00777 / 0.58 ( 16) metal coordination : angle 2.88436 / 2.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 388 time to evaluate : 0.922 Fit side-chains REVERT: A 34 LYS cc_start: 0.7492 (mtpp) cc_final: 0.7146 (mttm) REVERT: A 71 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7445 (mtp-110) REVERT: A 88 LEU cc_start: 0.7532 (tp) cc_final: 0.7305 (tt) REVERT: A 108 VAL cc_start: 0.8399 (p) cc_final: 0.8148 (m) REVERT: A 309 GLN cc_start: 0.8131 (tt0) cc_final: 0.7694 (tt0) REVERT: A 408 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6231 (tp) REVERT: A 439 ASP cc_start: 0.8026 (m-30) cc_final: 0.7735 (m-30) REVERT: A 715 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7331 (mm-30) REVERT: A 738 LEU cc_start: 0.8211 (tp) cc_final: 0.7933 (mt) REVERT: A 745 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7959 (tt0) REVERT: B 34 LYS cc_start: 0.7486 (mtpp) cc_final: 0.7143 (mttm) REVERT: B 71 ARG cc_start: 0.7764 (mtm110) cc_final: 0.7423 (mtp-110) REVERT: B 88 LEU cc_start: 0.7528 (tp) cc_final: 0.7302 (tt) REVERT: B 108 VAL cc_start: 0.8377 (p) cc_final: 0.8128 (m) REVERT: B 309 GLN cc_start: 0.8139 (tt0) cc_final: 0.7702 (tt0) REVERT: B 439 ASP cc_start: 0.7995 (m-30) cc_final: 0.7730 (m-30) REVERT: B 715 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7323 (mm-30) REVERT: B 738 LEU cc_start: 0.8208 (tp) cc_final: 0.7935 (mt) REVERT: B 745 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7957 (tt0) REVERT: C 34 LYS cc_start: 0.7479 (mtpp) cc_final: 0.7134 (mttm) REVERT: C 71 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7433 (mtp-110) REVERT: C 88 LEU cc_start: 0.7531 (tp) cc_final: 0.7306 (tt) REVERT: C 108 VAL cc_start: 0.8400 (p) cc_final: 0.8147 (m) REVERT: C 286 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.6551 (p0) REVERT: C 309 GLN cc_start: 0.8142 (tt0) cc_final: 0.7704 (tt0) REVERT: C 439 ASP cc_start: 0.7995 (m-30) cc_final: 0.7727 (m-30) REVERT: C 715 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7331 (mm-30) REVERT: C 738 LEU cc_start: 0.8211 (tp) cc_final: 0.7919 (mt) REVERT: C 745 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7961 (tt0) REVERT: D 34 LYS cc_start: 0.7485 (mtpp) cc_final: 0.7137 (mttm) REVERT: D 71 ARG cc_start: 0.7767 (mtm110) cc_final: 0.7442 (mtp-110) REVERT: D 88 LEU cc_start: 0.7523 (tp) cc_final: 0.7298 (tt) REVERT: D 108 VAL cc_start: 0.8401 (p) cc_final: 0.8164 (m) REVERT: D 309 GLN cc_start: 0.8138 (tt0) cc_final: 0.7703 (tt0) REVERT: D 439 ASP cc_start: 0.8016 (m-30) cc_final: 0.7753 (m-30) REVERT: D 715 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7325 (mm-30) REVERT: D 738 LEU cc_start: 0.8210 (tp) cc_final: 0.7938 (mt) REVERT: D 745 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7961 (tt0) outliers start: 72 outliers final: 0 residues processed: 429 average time/residue: 0.5474 time to fit residues: 270.4558 Evaluate side-chains 359 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain C residue 286 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 29 optimal weight: 3.9990 chunk 239 optimal weight: 9.9990 chunk 264 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 233 optimal weight: 0.4980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 536 ASN A 742 ASN B 80 ASN B 742 ASN C 80 ASN C 742 ASN D 80 ASN D 742 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.086805 restraints weight = 23208.027| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.38 r_work: 0.2745 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 23232 Z= 0.202 Angle : 0.541 6.627 31416 Z= 0.291 Chirality : 0.041 0.161 3504 Planarity : 0.004 0.048 3880 Dihedral : 9.070 79.934 3540 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.54 % Allowed : 21.87 % Favored : 74.59 % 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: 2.61 (0.16), residues: 2688 helix: 2.44 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : -0.29 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 71 TYR 0.015 0.001 TYR A 524 PHE 0.022 0.002 PHE D 341 TRP 0.016 0.002 TRP B 315 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (23212) covalent geometry : angle 0.53749 / 0.29 (31396) SS BOND : bond 0.00011 / 0.01 ( 4) SS BOND : angle 0.35779 / 0.21 ( 8) hydrogen bonds : bond 0.07888 / 5.23 ( 1475) hydrogen bonds : angle 3.90467 / 2.82 ( 4245) metal coordination : bond 0.00740 / 0.53 ( 16) metal coordination : angle 3.01817 / 2.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 386 time to evaluate : 0.906 Fit side-chains REVERT: A 21 GLN cc_start: 0.7796 (pt0) cc_final: 0.7528 (pt0) REVERT: A 34 LYS cc_start: 0.7666 (mtpp) cc_final: 0.7359 (mttm) REVERT: A 156 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7804 (tp30) REVERT: A 286 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.6469 (p0) REVERT: A 323 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6791 (ppt-90) REVERT: A 355 ASN cc_start: 0.6495 (OUTLIER) cc_final: 0.6057 (m-40) REVERT: A 522 PHE cc_start: 0.8427 (t80) cc_final: 0.7627 (m-80) REVERT: A 715 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7606 (tp30) REVERT: A 738 LEU cc_start: 0.8376 (tp) cc_final: 0.8132 (mt) REVERT: A 739 THR cc_start: 0.8615 (m) cc_final: 0.8285 (m) REVERT: A 745 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7974 (tt0) REVERT: B 21 GLN cc_start: 0.7805 (pt0) cc_final: 0.7581 (pt0) REVERT: B 34 LYS cc_start: 0.7669 (mtpp) cc_final: 0.7362 (mttm) REVERT: B 95 TYR cc_start: 0.8649 (t80) cc_final: 0.8445 (t80) REVERT: B 156 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7815 (tp30) REVERT: B 286 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.6477 (p0) REVERT: B 323 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6793 (ppt-90) REVERT: B 355 ASN cc_start: 0.6500 (OUTLIER) cc_final: 0.6063 (m-40) REVERT: B 459 LYS cc_start: 0.7367 (ttpp) cc_final: 0.7050 (ttmt) REVERT: B 522 PHE cc_start: 0.8416 (t80) cc_final: 0.7639 (m-80) REVERT: B 715 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7605 (tp30) REVERT: B 738 LEU cc_start: 0.8365 (tp) cc_final: 0.8124 (mt) REVERT: B 739 THR cc_start: 0.8574 (m) cc_final: 0.8262 (m) REVERT: B 745 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7983 (tt0) REVERT: C 21 GLN cc_start: 0.7786 (pt0) cc_final: 0.7555 (pt0) REVERT: C 34 LYS cc_start: 0.7657 (mtpp) cc_final: 0.7349 (mttm) REVERT: C 156 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7806 (tp30) REVERT: C 286 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.6468 (p0) REVERT: C 323 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6794 (ppt-90) REVERT: C 355 ASN cc_start: 0.6479 (OUTLIER) cc_final: 0.6051 (m-40) REVERT: C 459 LYS cc_start: 0.7308 (ttpp) cc_final: 0.7003 (ttmt) REVERT: C 522 PHE cc_start: 0.8430 (t80) cc_final: 0.7630 (m-80) REVERT: C 715 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7595 (tp30) REVERT: C 738 LEU cc_start: 0.8355 (tp) cc_final: 0.8115 (mt) REVERT: C 745 GLU cc_start: 0.8229 (tm-30) cc_final: 0.8006 (tt0) REVERT: D 21 GLN cc_start: 0.7801 (pt0) cc_final: 0.7540 (pt0) REVERT: D 34 LYS cc_start: 0.7672 (mtpp) cc_final: 0.7368 (mttm) REVERT: D 156 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7818 (tp30) REVERT: D 286 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.6471 (p0) REVERT: D 323 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6791 (ppt-90) REVERT: D 355 ASN cc_start: 0.6488 (OUTLIER) cc_final: 0.6046 (m-40) REVERT: D 459 LYS cc_start: 0.7327 (ttpp) cc_final: 0.7015 (ttmt) REVERT: D 522 PHE cc_start: 0.8413 (t80) cc_final: 0.7633 (m-80) REVERT: D 715 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7584 (tp30) REVERT: D 738 LEU cc_start: 0.8381 (tp) cc_final: 0.8136 (mt) REVERT: D 739 THR cc_start: 0.8606 (m) cc_final: 0.8277 (m) REVERT: D 745 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7967 (tt0) outliers start: 86 outliers final: 13 residues processed: 436 average time/residue: 0.5422 time to fit residues: 273.5397 Evaluate side-chains 386 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 361 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 411 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 74 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 92 HIS B 80 ASN B 92 HIS C 80 ASN C 92 HIS D 92 HIS D 629 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.157195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.086793 restraints weight = 23448.155| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.40 r_work: 0.2758 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 23232 Z= 0.193 Angle : 0.526 8.016 31416 Z= 0.278 Chirality : 0.040 0.161 3504 Planarity : 0.004 0.050 3880 Dihedral : 8.945 76.544 3540 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.04 % Allowed : 21.29 % Favored : 74.67 % 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: 2.69 (0.16), residues: 2688 helix: 2.49 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.26 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 71 TYR 0.015 0.001 TYR A 524 PHE 0.022 0.002 PHE C 341 TRP 0.018 0.001 TRP B 315 HIS 0.003 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (23212) covalent geometry : angle 0.51951 / 0.28 (31396) SS BOND : bond 0.00051 / 0.03 ( 4) SS BOND : angle 0.29676 / 0.17 ( 8) hydrogen bonds : bond 0.07146 / 4.71 ( 1475) hydrogen bonds : angle 3.76526 / 2.71 ( 4245) metal coordination : bond 0.01149 / 0.81 ( 16) metal coordination : angle 4.26781 / 3.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 371 time to evaluate : 0.893 Fit side-chains REVERT: A 21 GLN cc_start: 0.7952 (pt0) cc_final: 0.7656 (pt0) REVERT: A 34 LYS cc_start: 0.7662 (mtpp) cc_final: 0.7357 (mttm) REVERT: A 156 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7722 (tp30) REVERT: A 286 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.6869 (m-30) REVERT: A 323 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6876 (ppt-90) REVERT: A 355 ASN cc_start: 0.6555 (OUTLIER) cc_final: 0.6260 (m-40) REVERT: A 360 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 521 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7815 (mp) REVERT: A 522 PHE cc_start: 0.8362 (t80) cc_final: 0.7591 (m-80) REVERT: A 715 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7576 (tp30) REVERT: A 739 THR cc_start: 0.8580 (m) cc_final: 0.8281 (m) REVERT: A 745 GLU cc_start: 0.8251 (tm-30) cc_final: 0.8007 (tt0) REVERT: B 21 GLN cc_start: 0.7970 (pt0) cc_final: 0.7680 (pt0) REVERT: B 34 LYS cc_start: 0.7657 (mtpp) cc_final: 0.7343 (mttm) REVERT: B 156 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7744 (tp30) REVERT: B 286 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.6541 (p0) REVERT: B 323 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6878 (ppt-90) REVERT: B 355 ASN cc_start: 0.6559 (OUTLIER) cc_final: 0.6258 (m-40) REVERT: B 360 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7823 (tt) REVERT: B 521 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7818 (mp) REVERT: B 522 PHE cc_start: 0.8377 (t80) cc_final: 0.7609 (m-80) REVERT: B 715 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7585 (tp30) REVERT: B 739 THR cc_start: 0.8553 (m) cc_final: 0.8274 (m) REVERT: B 745 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7979 (tt0) REVERT: C 21 GLN cc_start: 0.7957 (pt0) cc_final: 0.7663 (pt0) REVERT: C 34 LYS cc_start: 0.7654 (mtpp) cc_final: 0.7340 (mttm) REVERT: C 135 GLN cc_start: 0.8172 (mt0) cc_final: 0.7924 (mt0) REVERT: C 286 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.6926 (m-30) REVERT: C 323 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6873 (ppt-90) REVERT: C 355 ASN cc_start: 0.6551 (OUTLIER) cc_final: 0.6255 (m-40) REVERT: C 360 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7839 (tt) REVERT: C 361 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8049 (mtmt) REVERT: C 382 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7433 (mp) REVERT: C 521 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7817 (mp) REVERT: C 522 PHE cc_start: 0.8375 (t80) cc_final: 0.7598 (m-80) REVERT: C 715 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7559 (tp30) REVERT: C 738 LEU cc_start: 0.8371 (tp) cc_final: 0.8105 (mt) REVERT: C 745 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8009 (tt0) REVERT: D 21 GLN cc_start: 0.7966 (pt0) cc_final: 0.7673 (pt0) REVERT: D 34 LYS cc_start: 0.7676 (mtpp) cc_final: 0.7371 (mttm) REVERT: D 156 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7735 (tp30) REVERT: D 286 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.6860 (m-30) REVERT: D 323 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6873 (ppt-90) REVERT: D 355 ASN cc_start: 0.6552 (OUTLIER) cc_final: 0.6246 (m-40) REVERT: D 360 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7829 (tt) REVERT: D 361 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8048 (mtmt) REVERT: D 521 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7822 (mp) REVERT: D 522 PHE cc_start: 0.8373 (t80) cc_final: 0.7606 (m-80) REVERT: D 715 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7571 (tp30) REVERT: D 738 LEU cc_start: 0.8359 (tp) cc_final: 0.8113 (mt) REVERT: D 739 THR cc_start: 0.8578 (m) cc_final: 0.8278 (m) REVERT: D 745 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7972 (tt0) outliers start: 98 outliers final: 20 residues processed: 426 average time/residue: 0.6438 time to fit residues: 313.2703 Evaluate side-chains 397 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 354 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 521 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 234 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 171 optimal weight: 0.0570 chunk 38 optimal weight: 8.9990 chunk 265 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 92 HIS A 443 ASN B 80 ASN B 92 HIS C 80 ASN C 92 HIS C 443 ASN D 92 HIS D 443 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.158858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.089260 restraints weight = 22824.403| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.34 r_work: 0.2795 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23232 Z= 0.146 Angle : 0.505 14.446 31416 Z= 0.259 Chirality : 0.038 0.156 3504 Planarity : 0.004 0.047 3880 Dihedral : 8.637 78.107 3540 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.71 % Allowed : 21.42 % Favored : 74.88 % 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: 2.87 (0.16), residues: 2688 helix: 2.65 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.28 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 71 TYR 0.013 0.001 TYR B 524 PHE 0.020 0.001 PHE C 341 TRP 0.016 0.001 TRP B 315 HIS 0.002 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (23212) covalent geometry : angle 0.49901 / 0.26 (31396) SS BOND : bond 0.00066 / 0.03 ( 4) SS BOND : angle 0.29551 / 0.17 ( 8) hydrogen bonds : bond 0.06150 / 4.06 ( 1475) hydrogen bonds : angle 3.66256 / 2.65 ( 4245) metal coordination : bond 0.01198 / 0.88 ( 16) metal coordination : angle 3.97451 / 3.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 371 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7950 (pt0) cc_final: 0.7611 (pt0) REVERT: A 34 LYS cc_start: 0.7609 (mtpp) cc_final: 0.7314 (mttm) REVERT: A 156 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7624 (tp30) REVERT: A 286 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6760 (m-30) REVERT: A 323 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6887 (ppt-90) REVERT: A 355 ASN cc_start: 0.6608 (OUTLIER) cc_final: 0.6392 (m-40) REVERT: A 360 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7790 (tt) REVERT: A 522 PHE cc_start: 0.8229 (t80) cc_final: 0.7444 (m-80) REVERT: A 715 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7431 (tp30) REVERT: A 745 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7964 (tt0) REVERT: B 21 GLN cc_start: 0.7965 (pt0) cc_final: 0.7633 (pt0) REVERT: B 34 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7312 (mttm) REVERT: B 156 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7639 (tp30) REVERT: B 286 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.6761 (m-30) REVERT: B 323 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6891 (ppt-90) REVERT: B 355 ASN cc_start: 0.6592 (OUTLIER) cc_final: 0.6391 (m-40) REVERT: B 360 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7801 (tt) REVERT: B 522 PHE cc_start: 0.8223 (t80) cc_final: 0.7451 (m-80) REVERT: B 715 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7432 (tp30) REVERT: B 745 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7959 (tt0) REVERT: C 21 GLN cc_start: 0.7956 (pt0) cc_final: 0.7624 (pt0) REVERT: C 34 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7318 (mttm) REVERT: C 156 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7627 (tp30) REVERT: C 286 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.6858 (m-30) REVERT: C 323 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6907 (ppt-90) REVERT: C 355 ASN cc_start: 0.6614 (OUTLIER) cc_final: 0.6398 (m-40) REVERT: C 360 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7807 (tt) REVERT: C 382 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7256 (mp) REVERT: C 459 LYS cc_start: 0.7203 (ttpp) cc_final: 0.6824 (ttmt) REVERT: C 522 PHE cc_start: 0.8224 (t80) cc_final: 0.7441 (m-80) REVERT: C 715 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7420 (tp30) REVERT: C 745 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7956 (tt0) REVERT: D 21 GLN cc_start: 0.7953 (pt0) cc_final: 0.7618 (pt0) REVERT: D 34 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7316 (mttm) REVERT: D 156 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7632 (tp30) REVERT: D 286 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6748 (m-30) REVERT: D 323 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6886 (ppt-90) REVERT: D 355 ASN cc_start: 0.6619 (OUTLIER) cc_final: 0.6413 (m-40) REVERT: D 360 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7802 (tt) REVERT: D 459 LYS cc_start: 0.7212 (ttpp) cc_final: 0.6829 (ttmt) REVERT: D 522 PHE cc_start: 0.8229 (t80) cc_final: 0.7458 (m-80) REVERT: D 715 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7439 (tp30) REVERT: D 739 THR cc_start: 0.8502 (m) cc_final: 0.8219 (m) REVERT: D 745 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7957 (tt0) outliers start: 90 outliers final: 25 residues processed: 426 average time/residue: 0.5887 time to fit residues: 290.1231 Evaluate side-chains 403 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 361 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 623 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 179 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 260 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 92 HIS A 443 ASN B 80 ASN B 92 HIS B 443 ASN C 80 ASN C 92 HIS C 436 ASN C 443 ASN C 731 ASN D 92 HIS D 443 ASN D 731 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.157450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.087513 restraints weight = 23107.952| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.36 r_work: 0.2768 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23232 Z= 0.173 Angle : 0.525 11.399 31416 Z= 0.271 Chirality : 0.039 0.159 3504 Planarity : 0.004 0.049 3880 Dihedral : 8.837 75.834 3540 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.87 % Allowed : 21.42 % Favored : 74.71 % 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: 2.74 (0.16), residues: 2688 helix: 2.55 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.34 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 545 TYR 0.016 0.001 TYR B 524 PHE 0.021 0.002 PHE D 341 TRP 0.017 0.001 TRP B 315 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (23212) covalent geometry : angle 0.51967 / 0.27 (31396) SS BOND : bond 0.00044 / 0.02 ( 4) SS BOND : angle 0.27620 / 0.16 ( 8) hydrogen bonds : bond 0.06801 / 4.49 ( 1475) hydrogen bonds : angle 3.72272 / 2.69 ( 4245) metal coordination : bond 0.01189 / 0.88 ( 16) metal coordination : angle 3.76875 / 2.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 354 time to evaluate : 0.890 Fit side-chains REVERT: A 21 GLN cc_start: 0.8006 (pt0) cc_final: 0.7669 (pt0) REVERT: A 34 LYS cc_start: 0.7645 (mtpp) cc_final: 0.7387 (mttm) REVERT: A 156 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7650 (tp30) REVERT: A 272 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.8003 (ttm-80) REVERT: A 286 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.6766 (m-30) REVERT: A 323 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6876 (ppt-90) REVERT: A 360 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 522 PHE cc_start: 0.8298 (t80) cc_final: 0.7538 (m-80) REVERT: A 526 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8566 (tt) REVERT: A 715 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7493 (tp30) REVERT: B 21 GLN cc_start: 0.8006 (pt0) cc_final: 0.7673 (pt0) REVERT: B 34 LYS cc_start: 0.7655 (mtpp) cc_final: 0.7397 (mttm) REVERT: B 156 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7662 (tp30) REVERT: B 272 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.8001 (ttm-80) REVERT: B 286 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.6746 (m-30) REVERT: B 323 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6882 (ppt-90) REVERT: B 360 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7839 (tt) REVERT: B 522 PHE cc_start: 0.8294 (t80) cc_final: 0.7536 (m-80) REVERT: B 526 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8564 (tt) REVERT: B 715 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7494 (tp30) REVERT: C 21 GLN cc_start: 0.7997 (pt0) cc_final: 0.7662 (pt0) REVERT: C 34 LYS cc_start: 0.7641 (mtpp) cc_final: 0.7386 (mttm) REVERT: C 156 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7647 (tp30) REVERT: C 272 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7990 (ttm-80) REVERT: C 286 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.6873 (m-30) REVERT: C 323 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6883 (ppt-90) REVERT: C 360 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7832 (tt) REVERT: C 361 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8048 (mtmt) REVERT: C 382 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7366 (mp) REVERT: C 410 TRP cc_start: 0.7920 (OUTLIER) cc_final: 0.7682 (m-90) REVERT: C 522 PHE cc_start: 0.8293 (t80) cc_final: 0.7533 (m-80) REVERT: C 526 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8561 (tt) REVERT: C 715 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7482 (tp30) REVERT: C 745 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7979 (tt0) REVERT: D 21 GLN cc_start: 0.8009 (pt0) cc_final: 0.7671 (pt0) REVERT: D 34 LYS cc_start: 0.7654 (mtpp) cc_final: 0.7395 (mttm) REVERT: D 156 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7662 (tp30) REVERT: D 272 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.8000 (ttm-80) REVERT: D 286 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.6782 (m-30) REVERT: D 323 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6881 (ppt-90) REVERT: D 360 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7827 (tt) REVERT: D 361 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8048 (mtmt) REVERT: D 522 PHE cc_start: 0.8301 (t80) cc_final: 0.7553 (m-80) REVERT: D 526 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8568 (tt) REVERT: D 715 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7496 (tp30) outliers start: 94 outliers final: 33 residues processed: 408 average time/residue: 0.6017 time to fit residues: 281.2197 Evaluate side-chains 408 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 355 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 707 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 269 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 92 HIS B 80 ASN B 92 HIS B 625 ASN C 80 ASN C 92 HIS C 742 ASN D 92 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.158688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089314 restraints weight = 22967.837| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.36 r_work: 0.2795 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23232 Z= 0.144 Angle : 0.511 13.993 31416 Z= 0.260 Chirality : 0.038 0.156 3504 Planarity : 0.004 0.047 3880 Dihedral : 8.668 76.115 3540 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.67 % Allowed : 21.83 % Favored : 74.51 % 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: 2.82 (0.16), residues: 2688 helix: 2.62 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.32 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 71 TYR 0.014 0.001 TYR B 524 PHE 0.020 0.001 PHE D 341 TRP 0.016 0.001 TRP B 315 HIS 0.002 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (23212) covalent geometry : angle 0.50683 / 0.26 (31396) SS BOND : bond 0.00055 / 0.03 ( 4) SS BOND : angle 0.27667 / 0.16 ( 8) hydrogen bonds : bond 0.06022 / 3.97 ( 1475) hydrogen bonds : angle 3.66024 / 2.65 ( 4245) metal coordination : bond 0.01084 / 0.80 ( 16) metal coordination : angle 3.52585 / 2.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 342 time to evaluate : 0.860 Fit side-chains REVERT: A 21 GLN cc_start: 0.8003 (pt0) cc_final: 0.7677 (pt0) REVERT: A 34 LYS cc_start: 0.7613 (mtpp) cc_final: 0.7359 (mttm) REVERT: A 156 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7637 (tp30) REVERT: A 286 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: A 323 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6894 (ppt-90) REVERT: A 360 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7826 (tt) REVERT: A 522 PHE cc_start: 0.8267 (t80) cc_final: 0.7497 (m-80) REVERT: A 526 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8583 (tt) REVERT: A 715 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7464 (tp30) REVERT: B 21 GLN cc_start: 0.8017 (pt0) cc_final: 0.7650 (pt0) REVERT: B 34 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7369 (mttm) REVERT: B 156 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7654 (tp30) REVERT: B 286 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6790 (m-30) REVERT: B 323 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6897 (ppt-90) REVERT: B 360 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7834 (tt) REVERT: B 522 PHE cc_start: 0.8263 (t80) cc_final: 0.7508 (m-80) REVERT: B 526 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8580 (tt) REVERT: B 715 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7464 (tp30) REVERT: C 21 GLN cc_start: 0.8004 (pt0) cc_final: 0.7679 (pt0) REVERT: C 34 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7358 (mttm) REVERT: C 156 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7647 (tp30) REVERT: C 286 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.6858 (m-30) REVERT: C 323 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6900 (ppt-90) REVERT: C 360 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7811 (tt) REVERT: C 382 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7317 (mp) REVERT: C 522 PHE cc_start: 0.8259 (t80) cc_final: 0.7491 (m-80) REVERT: C 526 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8578 (tt) REVERT: C 715 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7450 (tp30) REVERT: C 745 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7971 (tt0) REVERT: D 21 GLN cc_start: 0.8010 (pt0) cc_final: 0.7684 (pt0) REVERT: D 34 LYS cc_start: 0.7623 (mtpp) cc_final: 0.7365 (mttm) REVERT: D 66 MET cc_start: 0.8311 (mtm) cc_final: 0.8096 (mtt) REVERT: D 156 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7649 (tp30) REVERT: D 286 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: D 323 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6897 (ppt-90) REVERT: D 360 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7807 (tt) REVERT: D 522 PHE cc_start: 0.8270 (t80) cc_final: 0.7510 (m-80) REVERT: D 526 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8584 (tt) REVERT: D 715 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7465 (tp30) outliers start: 89 outliers final: 41 residues processed: 390 average time/residue: 0.5780 time to fit residues: 259.8622 Evaluate side-chains 400 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 342 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 623 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 0 optimal weight: 6.9990 chunk 213 optimal weight: 5.9990 chunk 161 optimal weight: 0.5980 chunk 184 optimal weight: 0.9980 chunk 263 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 266 optimal weight: 0.4980 chunk 216 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 254 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 625 ASN B 92 HIS B 436 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.160387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091045 restraints weight = 22940.239| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.36 r_work: 0.2832 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23232 Z= 0.122 Angle : 0.494 13.206 31416 Z= 0.248 Chirality : 0.037 0.154 3504 Planarity : 0.004 0.047 3880 Dihedral : 8.414 71.221 3540 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.58 % Allowed : 22.08 % Favored : 74.34 % 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: 2.96 (0.16), residues: 2688 helix: 2.72 (0.12), residues: 1976 sheet: None (None), residues: 0 loop : -0.29 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 71 TYR 0.012 0.001 TYR D 524 PHE 0.019 0.001 PHE D 341 TRP 0.015 0.001 TRP C 315 HIS 0.002 0.000 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (23212) covalent geometry : angle 0.48967 / 0.25 (31396) SS BOND : bond 0.00056 / 0.03 ( 4) SS BOND : angle 0.27254 / 0.17 ( 8) hydrogen bonds : bond 0.05318 / 3.50 ( 1475) hydrogen bonds : angle 3.58178 / 2.60 ( 4245) metal coordination : bond 0.01011 / 0.74 ( 16) metal coordination : angle 3.40447 / 2.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 351 time to evaluate : 0.917 Fit side-chains REVERT: A 21 GLN cc_start: 0.8009 (pt0) cc_final: 0.7635 (pt0) REVERT: A 34 LYS cc_start: 0.7642 (mtpp) cc_final: 0.7389 (mttm) REVERT: A 156 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7624 (tp30) REVERT: A 286 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.6820 (m-30) REVERT: A 360 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7835 (tt) REVERT: A 393 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7685 (mt) REVERT: A 526 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8545 (tt) REVERT: A 715 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7399 (tp30) REVERT: B 21 GLN cc_start: 0.8014 (pt0) cc_final: 0.7652 (pt0) REVERT: B 34 LYS cc_start: 0.7649 (mtpp) cc_final: 0.7396 (mttm) REVERT: B 286 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: B 360 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7841 (tt) REVERT: B 526 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8550 (tt) REVERT: B 715 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7401 (tp30) REVERT: C 21 GLN cc_start: 0.8003 (pt0) cc_final: 0.7633 (pt0) REVERT: C 34 LYS cc_start: 0.7640 (mtpp) cc_final: 0.7386 (mttm) REVERT: C 286 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.6917 (m-30) REVERT: C 360 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7830 (tt) REVERT: C 393 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7651 (mt) REVERT: C 410 TRP cc_start: 0.7915 (OUTLIER) cc_final: 0.7697 (m-90) REVERT: C 526 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8541 (tt) REVERT: C 715 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7388 (tp30) REVERT: C 745 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7981 (tt0) REVERT: D 21 GLN cc_start: 0.8011 (pt0) cc_final: 0.7639 (pt0) REVERT: D 34 LYS cc_start: 0.7649 (mtpp) cc_final: 0.7395 (mttm) REVERT: D 66 MET cc_start: 0.8335 (mtm) cc_final: 0.8122 (mtt) REVERT: D 71 ARG cc_start: 0.7600 (mtm110) cc_final: 0.7348 (mtp-110) REVERT: D 286 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.6827 (m-30) REVERT: D 360 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7822 (tt) REVERT: D 526 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8553 (tt) REVERT: D 715 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7387 (tp30) outliers start: 87 outliers final: 36 residues processed: 402 average time/residue: 0.5826 time to fit residues: 270.7515 Evaluate side-chains 399 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 348 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 707 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 52 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 218 optimal weight: 20.0000 chunk 206 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN C 92 HIS C 536 ASN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN C 742 ASN D 92 HIS D 731 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.157359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.087877 restraints weight = 23156.695| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.36 r_work: 0.2772 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23232 Z= 0.180 Angle : 0.554 15.532 31416 Z= 0.280 Chirality : 0.040 0.178 3504 Planarity : 0.004 0.048 3880 Dihedral : 8.844 58.712 3540 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.72 % Allowed : 22.61 % Favored : 74.67 % 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: 2.76 (0.16), residues: 2688 helix: 2.56 (0.11), residues: 1976 sheet: None (None), residues: 0 loop : -0.32 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 545 TYR 0.017 0.001 TYR D 524 PHE 0.022 0.002 PHE A 520 TRP 0.015 0.001 TRP B 315 HIS 0.003 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (23212) covalent geometry : angle 0.54988 / 0.28 (31396) SS BOND : bond 0.00044 / 0.02 ( 4) SS BOND : angle 0.25013 / 0.14 ( 8) hydrogen bonds : bond 0.06713 / 4.44 ( 1475) hydrogen bonds : angle 3.73952 / 2.71 ( 4245) metal coordination : bond 0.01083 / 0.80 ( 16) metal coordination : angle 3.57623 / 2.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 348 time to evaluate : 0.860 Fit side-chains REVERT: A 21 GLN cc_start: 0.7997 (pt0) cc_final: 0.7628 (pt0) REVERT: A 34 LYS cc_start: 0.7626 (mtpp) cc_final: 0.7374 (mttm) REVERT: A 66 MET cc_start: 0.8245 (mtm) cc_final: 0.8010 (mtt) REVERT: A 156 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7637 (tp30) REVERT: A 272 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.8000 (ttm-80) REVERT: A 286 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.6735 (m-30) REVERT: A 360 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7869 (tt) REVERT: A 522 PHE cc_start: 0.8296 (t80) cc_final: 0.7547 (m-80) REVERT: A 526 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8577 (tt) REVERT: A 715 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7465 (tp30) REVERT: B 21 GLN cc_start: 0.8015 (pt0) cc_final: 0.7652 (pt0) REVERT: B 34 LYS cc_start: 0.7624 (mtpp) cc_final: 0.7372 (mttm) REVERT: B 156 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7650 (tp30) REVERT: B 272 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.8003 (ttm-80) REVERT: B 286 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6772 (m-30) REVERT: B 360 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7901 (tt) REVERT: B 471 MET cc_start: 0.8928 (ttt) cc_final: 0.8723 (ttm) REVERT: B 522 PHE cc_start: 0.8288 (t80) cc_final: 0.7543 (m-80) REVERT: B 526 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8571 (tt) REVERT: B 715 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7468 (tp30) REVERT: C 21 GLN cc_start: 0.7996 (pt0) cc_final: 0.7626 (pt0) REVERT: C 34 LYS cc_start: 0.7600 (mtpp) cc_final: 0.7348 (mttm) REVERT: C 156 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7643 (tp30) REVERT: C 272 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.8000 (ttm-80) REVERT: C 286 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.6777 (m-30) REVERT: C 360 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7838 (tt) REVERT: C 410 TRP cc_start: 0.7948 (OUTLIER) cc_final: 0.7732 (m-90) REVERT: C 471 MET cc_start: 0.8936 (ttt) cc_final: 0.8721 (ttm) REVERT: C 522 PHE cc_start: 0.8284 (t80) cc_final: 0.7535 (m-80) REVERT: C 526 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8563 (tt) REVERT: C 715 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7460 (tp30) REVERT: C 745 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7920 (tt0) REVERT: D 21 GLN cc_start: 0.8002 (pt0) cc_final: 0.7630 (pt0) REVERT: D 34 LYS cc_start: 0.7610 (mtpp) cc_final: 0.7354 (mttm) REVERT: D 71 ARG cc_start: 0.7528 (mtm110) cc_final: 0.7265 (mtp-110) REVERT: D 156 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7652 (tp30) REVERT: D 272 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7995 (ttm-80) REVERT: D 286 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6740 (m-30) REVERT: D 360 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7838 (tt) REVERT: D 471 MET cc_start: 0.8941 (ttt) cc_final: 0.8726 (ttm) REVERT: D 522 PHE cc_start: 0.8294 (t80) cc_final: 0.7546 (m-80) REVERT: D 526 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8579 (tt) REVERT: D 715 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7470 (tp30) outliers start: 66 outliers final: 37 residues processed: 388 average time/residue: 0.5916 time to fit residues: 264.3175 Evaluate side-chains 392 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 342 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 252 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 254 optimal weight: 0.1980 chunk 264 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 230 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 533 ASN A 731 ASN B 92 HIS B 533 ASN B 731 ASN C 92 HIS C 533 ASN D 92 HIS D 533 ASN D 731 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.159391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.090070 restraints weight = 23128.191| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.37 r_work: 0.2818 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23232 Z= 0.131 Angle : 0.512 14.369 31416 Z= 0.257 Chirality : 0.038 0.154 3504 Planarity : 0.004 0.048 3880 Dihedral : 8.326 57.260 3540 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.35 % Allowed : 23.27 % Favored : 74.38 % 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: 2.90 (0.16), residues: 2688 helix: 2.68 (0.11), residues: 1976 sheet: None (None), residues: 0 loop : -0.31 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 222 TYR 0.013 0.001 TYR D 524 PHE 0.020 0.001 PHE C 341 TRP 0.016 0.001 TRP B 315 HIS 0.002 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (23212) covalent geometry : angle 0.50764 / 0.26 (31396) SS BOND : bond 0.00059 / 0.03 ( 4) SS BOND : angle 0.25297 / 0.15 ( 8) hydrogen bonds : bond 0.05601 / 3.69 ( 1475) hydrogen bonds : angle 3.63533 / 2.64 ( 4245) metal coordination : bond 0.00969 / 0.70 ( 16) metal coordination : angle 3.31840 / 2.54 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 343 time to evaluate : 0.884 Fit side-chains REVERT: A 21 GLN cc_start: 0.7991 (pt0) cc_final: 0.7617 (pt0) REVERT: A 34 LYS cc_start: 0.7650 (mtpp) cc_final: 0.7396 (mttm) REVERT: A 66 MET cc_start: 0.8232 (mtm) cc_final: 0.7987 (mtt) REVERT: A 71 ARG cc_start: 0.7627 (mtm110) cc_final: 0.7336 (mtp-110) REVERT: A 156 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7609 (tp30) REVERT: A 272 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7972 (ttm-80) REVERT: A 286 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.6806 (m-30) REVERT: A 360 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7866 (tt) REVERT: A 526 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8544 (tt) REVERT: A 715 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7458 (tp30) REVERT: B 21 GLN cc_start: 0.8011 (pt0) cc_final: 0.7642 (pt0) REVERT: B 34 LYS cc_start: 0.7651 (mtpp) cc_final: 0.7399 (mttm) REVERT: B 71 ARG cc_start: 0.7650 (mtm110) cc_final: 0.7376 (mtp-110) REVERT: B 156 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7616 (tp30) REVERT: B 272 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7984 (ttm-80) REVERT: B 286 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6799 (m-30) REVERT: B 360 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7887 (tt) REVERT: B 526 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8557 (tt) REVERT: B 715 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7454 (tp30) REVERT: C 21 GLN cc_start: 0.7991 (pt0) cc_final: 0.7618 (pt0) REVERT: C 34 LYS cc_start: 0.7648 (mtpp) cc_final: 0.7393 (mttm) REVERT: C 66 MET cc_start: 0.7970 (mtp) cc_final: 0.7555 (mtm) REVERT: C 71 ARG cc_start: 0.7551 (mtm110) cc_final: 0.7279 (mtp-110) REVERT: C 156 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7622 (tp30) REVERT: C 272 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7975 (ttm-80) REVERT: C 286 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6850 (m-30) REVERT: C 323 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6883 (ppt-90) REVERT: C 360 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7865 (tt) REVERT: C 410 TRP cc_start: 0.7908 (OUTLIER) cc_final: 0.7670 (m-90) REVERT: C 520 PHE cc_start: 0.8383 (t80) cc_final: 0.8128 (m-80) REVERT: C 526 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8538 (tt) REVERT: C 715 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7442 (tp30) REVERT: D 21 GLN cc_start: 0.7994 (pt0) cc_final: 0.7620 (pt0) REVERT: D 34 LYS cc_start: 0.7652 (mtpp) cc_final: 0.7400 (mttm) REVERT: D 66 MET cc_start: 0.7997 (mtt) cc_final: 0.7763 (mtm) REVERT: D 67 ASP cc_start: 0.7047 (m-30) cc_final: 0.6788 (m-30) REVERT: D 71 ARG cc_start: 0.7635 (mtm110) cc_final: 0.7191 (mtp-110) REVERT: D 156 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7601 (tp30) REVERT: D 272 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7973 (ttm-80) REVERT: D 286 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.6810 (m-30) REVERT: D 360 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7847 (tt) REVERT: D 520 PHE cc_start: 0.8357 (t80) cc_final: 0.8143 (m-80) REVERT: D 526 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8549 (tt) REVERT: D 715 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7447 (tp30) outliers start: 57 outliers final: 33 residues processed: 378 average time/residue: 0.6168 time to fit residues: 267.7983 Evaluate side-chains 389 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 342 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 323 ARG Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 203 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 236 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 731 ASN B 92 HIS B 731 ASN C 92 HIS C 731 ASN D 92 HIS D 731 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.158766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.089321 restraints weight = 23251.249| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.38 r_work: 0.2799 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23232 Z= 0.141 Angle : 0.525 14.634 31416 Z= 0.264 Chirality : 0.038 0.156 3504 Planarity : 0.004 0.047 3880 Dihedral : 8.199 57.414 3540 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.51 % Allowed : 23.39 % Favored : 74.09 % 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: 2.91 (0.16), residues: 2688 helix: 2.68 (0.11), residues: 1976 sheet: None (None), residues: 0 loop : -0.31 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 71 TYR 0.015 0.001 TYR D 524 PHE 0.020 0.001 PHE D 341 TRP 0.015 0.001 TRP B 315 HIS 0.002 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (23212) covalent geometry : angle 0.52042 / 0.26 (31396) SS BOND : bond 0.00053 / 0.03 ( 4) SS BOND : angle 0.26361 / 0.16 ( 8) hydrogen bonds : bond 0.05893 / 3.89 ( 1475) hydrogen bonds : angle 3.67102 / 2.67 ( 4245) metal coordination : bond 0.01010 / 0.74 ( 16) metal coordination : angle 3.43533 / 2.62 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12149.43 seconds wall clock time: 206 minutes 36.61 seconds (12396.61 seconds total)