Starting phenix.real_space_refine on Fri Jun 5 22:28:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rrf_54186/06_2026/9rrf_54186_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rrf_54186/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9rrf_54186/06_2026/9rrf_54186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rrf_54186/06_2026/9rrf_54186.map" model { file = "/net/cci-nas-00/data/ceres_data/9rrf_54186/06_2026/9rrf_54186_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rrf_54186/06_2026/9rrf_54186_trim.cif" } 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-6079/lib/python3.9/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, 129 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 129 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 129 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 129 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 5.26, per 1000 atoms: 0.23 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: 1.99 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.70 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: 4.17 Time building geometry restraints manager: 2.58 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: 0.06 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: 5.400 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.770 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.974 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: 0.7023 time to fit residues: 389.5563 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 : 0.760 ------------------------------------------------------------------------------- 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: 1.9990 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... Flipped N/Q/H residues before XYZ refinement: A 394 HIS B 394 HIS B 443 ASN 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 = 0.3934 r_free = 0.3934 target = 0.166610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.096833 restraints weight = 23516.923| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.43 r_work: 0.2915 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23232 Z= 0.139 Angle : 0.507 6.640 31416 Z= 0.272 Chirality : 0.038 0.154 3504 Planarity : 0.004 0.047 3880 Dihedral : 8.680 62.900 3542 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.25 % Allowed : 21.58 % Favored : 75.16 % 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: 2.68 (0.16), residues: 2688 helix: 2.40 (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 C 71 TYR 0.010 0.001 TYR A 524 PHE 0.013 0.002 PHE B 341 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 0.00283 / 0.14 (23212) covalent geometry : angle 0.50409 / 0.27 (31396) SS BOND : bond 0.00236 / 0.12 ( 4) SS BOND : angle 0.48270 / 0.34 ( 8) hydrogen bonds : bond 0.05937 / 3.90 ( 1475) hydrogen bonds : angle 3.95573 / 2.86 ( 4245) metal coordination : bond 0.00761 / 0.56 ( 16) metal coordination : angle 2.86833 / 2.19 ( 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 469 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 390 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7479 (mtpp) cc_final: 0.7141 (mttm) REVERT: A 71 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7451 (mtp-110) REVERT: A 88 LEU cc_start: 0.7559 (tp) cc_final: 0.7335 (tt) REVERT: A 108 VAL cc_start: 0.8433 (p) cc_final: 0.8174 (m) REVERT: A 309 GLN cc_start: 0.8126 (tt0) cc_final: 0.7693 (tt0) REVERT: A 408 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6153 (tp) REVERT: A 439 ASP cc_start: 0.8004 (m-30) cc_final: 0.7710 (m-30) REVERT: A 459 LYS cc_start: 0.6214 (OUTLIER) cc_final: 0.5956 (tmmt) REVERT: A 715 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7299 (mm-30) REVERT: A 738 LEU cc_start: 0.8200 (tp) cc_final: 0.7922 (mt) REVERT: A 745 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7957 (tt0) REVERT: B 34 LYS cc_start: 0.7489 (mtpp) cc_final: 0.7150 (mttm) REVERT: B 71 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7448 (mtp-110) REVERT: B 88 LEU cc_start: 0.7525 (tp) cc_final: 0.7302 (tt) REVERT: B 108 VAL cc_start: 0.8445 (p) cc_final: 0.8182 (m) REVERT: B 309 GLN cc_start: 0.8137 (tt0) cc_final: 0.7702 (tt0) REVERT: B 439 ASP cc_start: 0.8005 (m-30) cc_final: 0.7705 (m-30) REVERT: B 715 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7323 (mm-30) REVERT: B 738 LEU cc_start: 0.8206 (tp) cc_final: 0.7929 (mt) REVERT: B 745 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7968 (tt0) REVERT: C 34 LYS cc_start: 0.7490 (mtpp) cc_final: 0.7153 (mttm) REVERT: C 71 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7458 (mtp-110) REVERT: C 88 LEU cc_start: 0.7540 (tp) cc_final: 0.7317 (tt) REVERT: C 108 VAL cc_start: 0.8434 (p) cc_final: 0.8169 (m) REVERT: C 309 GLN cc_start: 0.8143 (tt0) cc_final: 0.7711 (tt0) REVERT: C 439 ASP cc_start: 0.8013 (m-30) cc_final: 0.7721 (m-30) REVERT: C 715 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7329 (mm-30) REVERT: C 738 LEU cc_start: 0.8214 (tp) cc_final: 0.7933 (mt) REVERT: C 745 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7974 (tt0) REVERT: D 34 LYS cc_start: 0.7494 (mtpp) cc_final: 0.7156 (mttm) REVERT: D 71 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7434 (mtp-110) REVERT: D 88 LEU cc_start: 0.7551 (tp) cc_final: 0.7327 (tt) REVERT: D 108 VAL cc_start: 0.8459 (p) cc_final: 0.8210 (m) REVERT: D 309 GLN cc_start: 0.8138 (tt0) cc_final: 0.7708 (tt0) REVERT: D 439 ASP cc_start: 0.8002 (m-30) cc_final: 0.7708 (m-30) REVERT: D 715 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7299 (mm-30) REVERT: D 738 LEU cc_start: 0.8213 (tp) cc_final: 0.7934 (mt) outliers start: 79 outliers final: 3 residues processed: 430 average time/residue: 0.6436 time to fit residues: 316.9416 Evaluate side-chains 357 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 352 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain D residue 459 LYS 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: 10.0000 chunk 264 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 625 ASN D 742 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.157227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.086901 restraints weight = 23209.260| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.38 r_work: 0.2755 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 23232 Z= 0.211 Angle : 0.547 6.523 31416 Z= 0.293 Chirality : 0.041 0.161 3504 Planarity : 0.004 0.048 3880 Dihedral : 9.001 81.045 3540 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.46 % Allowed : 22.32 % Favored : 74.22 % 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: 2.45 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : -0.32 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 71 TYR 0.013 0.001 TYR C 524 PHE 0.022 0.002 PHE D 341 TRP 0.018 0.002 TRP B 315 HIS 0.003 0.001 HIS D 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (23212) covalent geometry : angle 0.54375 / 0.29 (31396) SS BOND : bond 0.00021 / 0.01 ( 4) SS BOND : angle 0.39136 / 0.22 ( 8) hydrogen bonds : bond 0.07774 / 5.14 ( 1475) hydrogen bonds : angle 3.90692 / 2.82 ( 4245) metal coordination : bond 0.00773 / 0.55 ( 16) metal coordination : angle 2.98053 / 2.20 ( 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 478 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 394 time to evaluate : 0.873 Fit side-chains REVERT: A 21 GLN cc_start: 0.7785 (pt0) cc_final: 0.7550 (pt0) REVERT: A 34 LYS cc_start: 0.7624 (mtpp) cc_final: 0.7322 (mttm) REVERT: A 286 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.6468 (p0) REVERT: A 323 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6808 (ppt-90) REVERT: A 355 ASN cc_start: 0.6459 (OUTLIER) cc_final: 0.6078 (m-40) REVERT: A 516 ASP cc_start: 0.8435 (m-30) cc_final: 0.8231 (m-30) REVERT: A 522 PHE cc_start: 0.8420 (t80) cc_final: 0.7642 (m-80) REVERT: A 715 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7577 (tp30) REVERT: A 738 LEU cc_start: 0.8305 (tp) cc_final: 0.8089 (mt) REVERT: A 745 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7987 (tt0) REVERT: B 21 GLN cc_start: 0.7799 (pt0) cc_final: 0.7570 (pt0) REVERT: B 34 LYS cc_start: 0.7628 (mtpp) cc_final: 0.7325 (mttm) REVERT: B 286 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.6476 (p0) REVERT: B 323 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6809 (ppt-90) REVERT: B 355 ASN cc_start: 0.6459 (OUTLIER) cc_final: 0.6022 (m-40) REVERT: B 516 ASP cc_start: 0.8434 (m-30) cc_final: 0.8233 (m-30) REVERT: B 522 PHE cc_start: 0.8424 (t80) cc_final: 0.7670 (m-80) REVERT: B 715 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7590 (tp30) REVERT: B 738 LEU cc_start: 0.8306 (tp) cc_final: 0.8079 (mt) REVERT: B 745 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7959 (tt0) REVERT: C 21 GLN cc_start: 0.7784 (pt0) cc_final: 0.7551 (pt0) REVERT: C 34 LYS cc_start: 0.7631 (mtpp) cc_final: 0.7330 (mttm) REVERT: C 286 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.6466 (p0) REVERT: C 323 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6808 (ppt-90) REVERT: C 355 ASN cc_start: 0.6453 (OUTLIER) cc_final: 0.6074 (m-40) REVERT: C 516 ASP cc_start: 0.8426 (m-30) cc_final: 0.8223 (m-30) REVERT: C 522 PHE cc_start: 0.8423 (t80) cc_final: 0.7649 (m-80) REVERT: C 715 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7585 (tp30) REVERT: C 738 LEU cc_start: 0.8316 (tp) cc_final: 0.8077 (mt) REVERT: C 745 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7985 (tt0) REVERT: D 21 GLN cc_start: 0.7790 (pt0) cc_final: 0.7560 (pt0) REVERT: D 34 LYS cc_start: 0.7630 (mtpp) cc_final: 0.7327 (mttm) REVERT: D 286 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.6465 (p0) REVERT: D 323 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6804 (ppt-90) REVERT: D 355 ASN cc_start: 0.6467 (OUTLIER) cc_final: 0.6079 (m-40) REVERT: D 516 ASP cc_start: 0.8425 (m-30) cc_final: 0.8221 (m-30) REVERT: D 522 PHE cc_start: 0.8421 (t80) cc_final: 0.7667 (m-80) REVERT: D 715 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7581 (tp30) REVERT: D 738 LEU cc_start: 0.8316 (tp) cc_final: 0.8087 (mt) outliers start: 84 outliers final: 15 residues processed: 441 average time/residue: 0.5953 time to fit residues: 302.0803 Evaluate side-chains 401 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 374 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 117 SER 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 B residue 623 MET Chi-restraints excluded: chain C residue 189 SER 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 117 SER 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: 0.9980 chunk 171 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 92 HIS A 625 ASN B 80 ASN B 92 HIS C 80 ASN C 92 HIS D 92 HIS D 625 ASN D 629 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.089578 restraints weight = 23372.767| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.39 r_work: 0.2800 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 23232 Z= 0.136 Angle : 0.480 8.553 31416 Z= 0.251 Chirality : 0.037 0.156 3504 Planarity : 0.004 0.048 3880 Dihedral : 8.539 79.092 3540 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.83 % Allowed : 22.90 % Favored : 73.27 % 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: 2.93 (0.16), residues: 2688 helix: 2.70 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.24 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.012 0.001 TYR B 524 PHE 0.020 0.001 PHE B 341 TRP 0.015 0.001 TRP B 315 HIS 0.002 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (23212) covalent geometry : angle 0.47335 / 0.25 (31396) SS BOND : bond 0.00045 / 0.02 ( 4) SS BOND : angle 0.27014 / 0.17 ( 8) hydrogen bonds : bond 0.05947 / 3.92 ( 1475) hydrogen bonds : angle 3.64665 / 2.63 ( 4245) metal coordination : bond 0.01230 / 0.86 ( 16) metal coordination : angle 4.25246 / 3.26 ( 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 482 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 389 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7847 (pt0) cc_final: 0.7590 (pt0) REVERT: A 34 LYS cc_start: 0.7591 (mtpp) cc_final: 0.7295 (mttm) REVERT: A 66 MET cc_start: 0.8094 (mtm) cc_final: 0.7861 (mtt) REVERT: A 272 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7999 (ttm-80) REVERT: A 286 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.6878 (m-30) REVERT: A 355 ASN cc_start: 0.6448 (OUTLIER) cc_final: 0.6053 (m-40) REVERT: A 459 LYS cc_start: 0.7183 (ttpp) cc_final: 0.6844 (ttmt) REVERT: A 522 PHE cc_start: 0.8300 (t80) cc_final: 0.7518 (m-80) REVERT: A 715 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7548 (tp30) REVERT: A 738 LEU cc_start: 0.8365 (tp) cc_final: 0.8157 (mt) REVERT: A 745 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7926 (tt0) REVERT: B 21 GLN cc_start: 0.7873 (pt0) cc_final: 0.7620 (pt0) REVERT: B 34 LYS cc_start: 0.7591 (mtpp) cc_final: 0.7288 (mttm) REVERT: B 135 GLN cc_start: 0.8216 (mt0) cc_final: 0.7966 (mt0) REVERT: B 272 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.7993 (ttm-80) REVERT: B 286 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.6879 (m-30) REVERT: B 355 ASN cc_start: 0.6462 (OUTLIER) cc_final: 0.6055 (m-40) REVERT: B 459 LYS cc_start: 0.7184 (ttpp) cc_final: 0.6845 (ttmt) REVERT: B 522 PHE cc_start: 0.8304 (t80) cc_final: 0.7520 (m-80) REVERT: B 715 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7551 (tp30) REVERT: B 738 LEU cc_start: 0.8358 (tp) cc_final: 0.8146 (mt) REVERT: B 745 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7959 (tt0) REVERT: C 21 GLN cc_start: 0.7844 (pt0) cc_final: 0.7591 (pt0) REVERT: C 34 LYS cc_start: 0.7593 (mtpp) cc_final: 0.7296 (mttm) REVERT: C 135 GLN cc_start: 0.8213 (mt0) cc_final: 0.7960 (mt0) REVERT: C 272 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.7995 (ttm-80) REVERT: C 286 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.6872 (m-30) REVERT: C 355 ASN cc_start: 0.6449 (OUTLIER) cc_final: 0.6139 (m-40) REVERT: C 459 LYS cc_start: 0.7189 (ttpp) cc_final: 0.6850 (ttmt) REVERT: C 522 PHE cc_start: 0.8304 (t80) cc_final: 0.7517 (m-80) REVERT: C 715 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7542 (tp30) REVERT: C 738 LEU cc_start: 0.8362 (tp) cc_final: 0.8151 (mt) REVERT: C 745 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7963 (tt0) REVERT: D 21 GLN cc_start: 0.7848 (pt0) cc_final: 0.7596 (pt0) REVERT: D 34 LYS cc_start: 0.7594 (mtpp) cc_final: 0.7299 (mttm) REVERT: D 135 GLN cc_start: 0.8214 (mt0) cc_final: 0.7953 (mt0) REVERT: D 272 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7987 (ttm-80) REVERT: D 286 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.6870 (m-30) REVERT: D 355 ASN cc_start: 0.6456 (OUTLIER) cc_final: 0.6039 (m-40) REVERT: D 459 LYS cc_start: 0.7185 (ttpp) cc_final: 0.6847 (ttmt) REVERT: D 522 PHE cc_start: 0.8304 (t80) cc_final: 0.7521 (m-80) REVERT: D 715 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7557 (tp30) REVERT: D 738 LEU cc_start: 0.8373 (tp) cc_final: 0.8149 (mt) outliers start: 93 outliers final: 23 residues processed: 442 average time/residue: 0.6752 time to fit residues: 340.4980 Evaluate side-chains 411 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 380 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 341 PHE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain A residue 666 SER 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 341 PHE Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 666 SER 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 341 PHE Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 666 SER 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 341 PHE Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 623 MET Chi-restraints excluded: chain D residue 666 SER 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: 2.9990 chunk 171 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 265 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 443 ASN B 92 HIS C 92 HIS D 92 HIS D 443 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.087480 restraints weight = 23043.206| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.37 r_work: 0.2765 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23232 Z= 0.167 Angle : 0.502 6.679 31416 Z= 0.265 Chirality : 0.039 0.158 3504 Planarity : 0.004 0.047 3880 Dihedral : 8.586 75.478 3540 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.50 % Allowed : 21.38 % Favored : 75.12 % 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: 2.85 (0.16), residues: 2688 helix: 2.62 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.23 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 545 TYR 0.014 0.001 TYR D 524 PHE 0.021 0.002 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 0.00388 / 0.17 (23212) covalent geometry : angle 0.49633 / 0.26 (31396) SS BOND : bond 0.00045 / 0.02 ( 4) SS BOND : angle 0.26676 / 0.15 ( 8) hydrogen bonds : bond 0.06809 / 4.50 ( 1475) hydrogen bonds : angle 3.69540 / 2.67 ( 4245) metal coordination : bond 0.01255 / 0.92 ( 16) metal coordination : angle 4.04302 / 3.06 ( 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 463 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 378 time to evaluate : 0.910 Fit side-chains REVERT: A 21 GLN cc_start: 0.7933 (pt0) cc_final: 0.7639 (pt0) REVERT: A 34 LYS cc_start: 0.7630 (mtpp) cc_final: 0.7322 (mttm) REVERT: A 135 GLN cc_start: 0.8176 (mt0) cc_final: 0.7927 (mt0) REVERT: A 272 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.8035 (ttm-80) REVERT: A 286 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: A 323 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6880 (ppt-90) REVERT: A 355 ASN cc_start: 0.6603 (OUTLIER) cc_final: 0.6389 (m-40) REVERT: A 393 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7498 (mt) REVERT: A 410 TRP cc_start: 0.7908 (OUTLIER) cc_final: 0.7563 (m-90) REVERT: A 522 PHE cc_start: 0.8370 (t80) cc_final: 0.7589 (m-80) REVERT: A 715 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7559 (tp30) REVERT: A 745 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7962 (tt0) REVERT: B 21 GLN cc_start: 0.7952 (pt0) cc_final: 0.7667 (pt0) REVERT: B 34 LYS cc_start: 0.7637 (mtpp) cc_final: 0.7328 (mttm) REVERT: B 135 GLN cc_start: 0.8145 (mt0) cc_final: 0.7923 (mt0) REVERT: B 272 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.8036 (ttm-80) REVERT: B 286 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.6850 (m-30) REVERT: B 323 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6881 (ppt-90) REVERT: B 355 ASN cc_start: 0.6605 (OUTLIER) cc_final: 0.6391 (m-40) REVERT: B 393 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7500 (mt) REVERT: B 410 TRP cc_start: 0.7903 (OUTLIER) cc_final: 0.7558 (m-90) REVERT: B 522 PHE cc_start: 0.8373 (t80) cc_final: 0.7592 (m-80) REVERT: B 715 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7581 (tp30) REVERT: B 745 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7962 (tt0) REVERT: C 21 GLN cc_start: 0.7935 (pt0) cc_final: 0.7647 (pt0) REVERT: C 34 LYS cc_start: 0.7632 (mtpp) cc_final: 0.7325 (mttm) REVERT: C 135 GLN cc_start: 0.8139 (mt0) cc_final: 0.7915 (mt0) REVERT: C 272 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.8036 (ttm-80) REVERT: C 286 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: C 323 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6879 (ppt-90) REVERT: C 355 ASN cc_start: 0.6629 (OUTLIER) cc_final: 0.6422 (m-40) REVERT: C 393 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7509 (mt) REVERT: C 410 TRP cc_start: 0.7918 (OUTLIER) cc_final: 0.7573 (m-90) REVERT: C 522 PHE cc_start: 0.8392 (t80) cc_final: 0.7608 (m-80) REVERT: C 715 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7572 (tp30) REVERT: C 745 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7961 (tt0) REVERT: D 21 GLN cc_start: 0.7939 (pt0) cc_final: 0.7652 (pt0) REVERT: D 34 LYS cc_start: 0.7640 (mtpp) cc_final: 0.7332 (mttm) REVERT: D 135 GLN cc_start: 0.8143 (mt0) cc_final: 0.7916 (mt0) REVERT: D 272 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.8035 (ttm-80) REVERT: D 286 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.6833 (m-30) REVERT: D 323 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6879 (ppt-90) REVERT: D 355 ASN cc_start: 0.6602 (OUTLIER) cc_final: 0.6385 (m-40) REVERT: D 393 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7495 (mt) REVERT: D 410 TRP cc_start: 0.7918 (OUTLIER) cc_final: 0.7563 (m-90) REVERT: D 522 PHE cc_start: 0.8386 (t80) cc_final: 0.7608 (m-80) REVERT: D 715 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7562 (tp30) REVERT: D 738 LEU cc_start: 0.8349 (tp) cc_final: 0.8082 (mt) outliers start: 85 outliers final: 29 residues processed: 424 average time/residue: 0.6889 time to fit residues: 331.0958 Evaluate side-chains 421 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 372 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 223 LEU 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 350 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 LEU 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 350 ILE Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 223 LEU 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 350 ILE Chi-restraints excluded: chain C residue 355 ASN 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 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 350 ILE Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 410 TRP 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: 0.6980 chunk 170 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS B 92 HIS B 443 ASN C 92 HIS C 443 ASN D 92 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.089680 restraints weight = 23059.839| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.36 r_work: 0.2811 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23232 Z= 0.138 Angle : 0.502 14.650 31416 Z= 0.254 Chirality : 0.037 0.154 3504 Planarity : 0.004 0.048 3880 Dihedral : 8.417 74.554 3540 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.17 % Allowed : 21.87 % Favored : 74.96 % 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: 2.71 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.21 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 71 TYR 0.013 0.001 TYR B 524 PHE 0.020 0.001 PHE D 341 TRP 0.015 0.001 TRP B 315 HIS 0.002 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (23212) covalent geometry : angle 0.49733 / 0.25 (31396) SS BOND : bond 0.00045 / 0.02 ( 4) SS BOND : angle 0.26653 / 0.16 ( 8) hydrogen bonds : bond 0.05891 / 3.88 ( 1475) hydrogen bonds : angle 3.61057 / 2.62 ( 4245) metal coordination : bond 0.01068 / 0.77 ( 16) metal coordination : angle 3.69566 / 2.82 ( 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 465 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 388 time to evaluate : 0.865 Fit side-chains REVERT: A 21 GLN cc_start: 0.7944 (pt0) cc_final: 0.7608 (pt0) REVERT: A 34 LYS cc_start: 0.7635 (mtpp) cc_final: 0.7336 (mttm) REVERT: A 272 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.8013 (ttm-80) REVERT: A 286 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6785 (m-30) REVERT: A 323 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6926 (ppt-90) REVERT: A 410 TRP cc_start: 0.7815 (OUTLIER) cc_final: 0.7502 (m-90) REVERT: A 522 PHE cc_start: 0.8250 (t80) cc_final: 0.7498 (m-80) REVERT: A 715 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7485 (tp30) REVERT: A 745 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7965 (tt0) REVERT: B 21 GLN cc_start: 0.7955 (pt0) cc_final: 0.7623 (pt0) REVERT: B 34 LYS cc_start: 0.7647 (mtpp) cc_final: 0.7350 (mttm) REVERT: B 135 GLN cc_start: 0.8085 (mt0) cc_final: 0.7870 (mt0) REVERT: B 272 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7999 (ttm-80) REVERT: B 286 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.6782 (m-30) REVERT: B 323 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6929 (ppt-90) REVERT: B 410 TRP cc_start: 0.7814 (OUTLIER) cc_final: 0.7435 (m-90) REVERT: B 522 PHE cc_start: 0.8232 (t80) cc_final: 0.7478 (m-80) REVERT: B 715 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7474 (tp30) REVERT: B 738 LEU cc_start: 0.8390 (mt) cc_final: 0.8154 (mt) REVERT: B 745 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7941 (tt0) REVERT: C 21 GLN cc_start: 0.7947 (pt0) cc_final: 0.7612 (pt0) REVERT: C 34 LYS cc_start: 0.7634 (mtpp) cc_final: 0.7337 (mttm) REVERT: C 135 GLN cc_start: 0.8082 (mt0) cc_final: 0.7862 (mt0) REVERT: C 286 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: C 323 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6927 (ppt-90) REVERT: C 410 TRP cc_start: 0.7831 (OUTLIER) cc_final: 0.7448 (m-90) REVERT: C 522 PHE cc_start: 0.8236 (t80) cc_final: 0.7478 (m-80) REVERT: C 715 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7465 (tp30) REVERT: C 745 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7987 (tt0) REVERT: D 21 GLN cc_start: 0.7949 (pt0) cc_final: 0.7615 (pt0) REVERT: D 34 LYS cc_start: 0.7642 (mtpp) cc_final: 0.7345 (mttm) REVERT: D 272 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.8002 (ttm-80) REVERT: D 286 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.6799 (m-30) REVERT: D 323 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6927 (ppt-90) REVERT: D 361 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7974 (mtmt) REVERT: D 410 TRP cc_start: 0.7822 (OUTLIER) cc_final: 0.7490 (m-90) REVERT: D 522 PHE cc_start: 0.8239 (t80) cc_final: 0.7485 (m-80) REVERT: D 715 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7495 (tp30) outliers start: 77 outliers final: 34 residues processed: 428 average time/residue: 0.6671 time to fit residues: 324.9638 Evaluate side-chains 423 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 376 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 223 LEU 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 410 TRP 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 552 ASN Chi-restraints excluded: chain A residue 623 MET 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 410 TRP 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 552 ASN Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 223 LEU 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 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 552 ASN 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 361 LYS Chi-restraints excluded: chain D residue 410 TRP 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 552 ASN Chi-restraints excluded: chain D residue 623 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 269 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 86 optimal weight: 0.1980 chunk 181 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.159018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.089524 restraints weight = 22972.771| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.36 r_work: 0.2810 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4863 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= 0.139 Angle : 0.502 12.481 31416 Z= 0.256 Chirality : 0.038 0.155 3504 Planarity : 0.004 0.047 3880 Dihedral : 8.495 59.395 3540 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.91 % Allowed : 21.50 % 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: 2.94 (0.16), residues: 2688 helix: 2.68 (0.11), residues: 1976 sheet: None (None), residues: 0 loop : -0.20 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 71 TYR 0.014 0.001 TYR D 524 PHE 0.020 0.001 PHE B 341 TRP 0.015 0.001 TRP B 315 HIS 0.002 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (23212) covalent geometry : angle 0.49690 / 0.26 (31396) SS BOND : bond 0.00039 / 0.02 ( 4) SS BOND : angle 0.26835 / 0.16 ( 8) hydrogen bonds : bond 0.05945 / 3.92 ( 1475) hydrogen bonds : angle 3.60279 / 2.61 ( 4245) metal coordination : bond 0.01070 / 0.78 ( 16) metal coordination : angle 3.58710 / 2.73 ( 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 457 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 362 time to evaluate : 0.861 Fit side-chains REVERT: A 21 GLN cc_start: 0.7976 (pt0) cc_final: 0.7642 (pt0) REVERT: A 34 LYS cc_start: 0.7629 (mtpp) cc_final: 0.7334 (mttm) REVERT: A 286 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.6786 (m-30) REVERT: A 323 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6899 (ppt-90) REVERT: A 410 TRP cc_start: 0.7875 (OUTLIER) cc_final: 0.7645 (m-90) REVERT: A 522 PHE cc_start: 0.8239 (t80) cc_final: 0.7503 (m-80) REVERT: A 715 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7477 (tp30) REVERT: A 745 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7971 (tt0) REVERT: B 21 GLN cc_start: 0.7992 (pt0) cc_final: 0.7664 (pt0) REVERT: B 34 LYS cc_start: 0.7687 (mtpp) cc_final: 0.7392 (mttm) REVERT: B 286 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.6790 (m-30) REVERT: B 323 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6900 (ppt-90) REVERT: B 406 MET cc_start: 0.7721 (mtm) cc_final: 0.7476 (mtm) REVERT: B 410 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.7553 (m-90) REVERT: B 522 PHE cc_start: 0.8224 (t80) cc_final: 0.7486 (m-80) REVERT: B 715 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7478 (tp30) REVERT: B 738 LEU cc_start: 0.8482 (mt) cc_final: 0.8226 (mt) REVERT: B 745 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7965 (tt0) REVERT: C 21 GLN cc_start: 0.7977 (pt0) cc_final: 0.7646 (pt0) REVERT: C 34 LYS cc_start: 0.7675 (mtpp) cc_final: 0.7379 (mttm) REVERT: C 286 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.6797 (m-30) REVERT: C 323 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6903 (ppt-90) REVERT: C 410 TRP cc_start: 0.7873 (OUTLIER) cc_final: 0.7566 (m-90) REVERT: C 522 PHE cc_start: 0.8224 (t80) cc_final: 0.7481 (m-80) REVERT: C 715 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7464 (tp30) REVERT: C 745 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7986 (tt0) REVERT: D 21 GLN cc_start: 0.7974 (pt0) cc_final: 0.7643 (pt0) REVERT: D 34 LYS cc_start: 0.7680 (mtpp) cc_final: 0.7388 (mttm) REVERT: D 286 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: D 323 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6897 (ppt-90) REVERT: D 410 TRP cc_start: 0.7883 (OUTLIER) cc_final: 0.7628 (m-90) REVERT: D 522 PHE cc_start: 0.8233 (t80) cc_final: 0.7500 (m-80) REVERT: D 715 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7488 (tp30) outliers start: 95 outliers final: 41 residues processed: 421 average time/residue: 0.6388 time to fit residues: 307.0998 Evaluate side-chains 417 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 364 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 88 LEU 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 410 TRP 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 552 ASN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 LEU 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 410 TRP 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 552 ASN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 88 LEU 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 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 552 ASN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 223 LEU 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 410 TRP 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 552 ASN 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: 0.6980 chunk 161 optimal weight: 0.9980 chunk 184 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 266 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 254 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 533 ASN B 92 HIS C 92 HIS D 92 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.161482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.092359 restraints weight = 23023.258| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.38 r_work: 0.2857 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23232 Z= 0.112 Angle : 0.484 14.040 31416 Z= 0.241 Chirality : 0.037 0.151 3504 Planarity : 0.004 0.047 3880 Dihedral : 7.911 56.669 3540 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.55 % Allowed : 22.78 % 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: 3.05 (0.16), residues: 2688 helix: 2.74 (0.11), residues: 2000 sheet: None (None), residues: 0 loop : -0.22 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 71 TYR 0.011 0.001 TYR C 524 PHE 0.019 0.001 PHE D 341 TRP 0.014 0.001 TRP B 315 HIS 0.002 0.000 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (23212) covalent geometry : angle 0.47925 / 0.24 (31396) SS BOND : bond 0.00048 / 0.02 ( 4) SS BOND : angle 0.27604 / 0.17 ( 8) hydrogen bonds : bond 0.04905 / 3.22 ( 1475) hydrogen bonds : angle 3.50429 / 2.55 ( 4245) metal coordination : bond 0.00936 / 0.67 ( 16) metal coordination : angle 3.40571 / 2.61 ( 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: 62 poor density : 376 time to evaluate : 0.923 Fit side-chains REVERT: A 21 GLN cc_start: 0.7994 (pt0) cc_final: 0.7616 (pt0) REVERT: A 34 LYS cc_start: 0.7663 (mtpp) cc_final: 0.7379 (mttm) REVERT: A 66 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7392 (mtm) REVERT: A 225 TRP cc_start: 0.8588 (t60) cc_final: 0.8324 (t-100) REVERT: A 272 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7961 (ttm-80) REVERT: A 286 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.6822 (m-30) REVERT: A 323 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6946 (ppt-90) REVERT: A 410 TRP cc_start: 0.7832 (OUTLIER) cc_final: 0.7533 (m-90) REVERT: A 715 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7421 (tp30) REVERT: A 745 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7947 (tt0) REVERT: B 21 GLN cc_start: 0.8010 (pt0) cc_final: 0.7643 (pt0) REVERT: B 34 LYS cc_start: 0.7635 (mtpp) cc_final: 0.7345 (mttm) REVERT: B 225 TRP cc_start: 0.8597 (t60) cc_final: 0.8325 (t-100) REVERT: B 272 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7957 (ttm-80) REVERT: B 286 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: B 323 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6944 (ppt-90) REVERT: B 410 TRP cc_start: 0.7829 (OUTLIER) cc_final: 0.7541 (m-90) REVERT: B 522 PHE cc_start: 0.8201 (t80) cc_final: 0.7432 (m-80) REVERT: B 715 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7409 (tp30) REVERT: B 738 LEU cc_start: 0.8497 (mt) cc_final: 0.8203 (mt) REVERT: B 745 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7978 (tt0) REVERT: C 21 GLN cc_start: 0.7982 (pt0) cc_final: 0.7608 (pt0) REVERT: C 34 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7336 (mttm) REVERT: C 225 TRP cc_start: 0.8577 (t60) cc_final: 0.8317 (t-100) REVERT: C 272 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7969 (ttm-80) REVERT: C 286 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.6836 (m-30) REVERT: C 323 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6950 (ppt-90) REVERT: C 410 TRP cc_start: 0.7833 (OUTLIER) cc_final: 0.7544 (m-90) REVERT: C 715 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7405 (tp30) REVERT: C 745 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7997 (tt0) REVERT: D 21 GLN cc_start: 0.7986 (pt0) cc_final: 0.7615 (pt0) REVERT: D 34 LYS cc_start: 0.7646 (mtpp) cc_final: 0.7363 (mttm) REVERT: D 66 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7374 (mtm) REVERT: D 225 TRP cc_start: 0.8587 (t60) cc_final: 0.8325 (t-100) REVERT: D 272 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7953 (ttm-80) REVERT: D 286 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.6836 (m-30) REVERT: D 323 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6944 (ppt-90) REVERT: D 410 TRP cc_start: 0.7837 (OUTLIER) cc_final: 0.7527 (m-90) REVERT: D 653 GLU cc_start: 0.7760 (tt0) cc_final: 0.7442 (tt0) REVERT: D 715 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7427 (tp30) outliers start: 62 outliers final: 31 residues processed: 418 average time/residue: 0.6392 time to fit residues: 305.1977 Evaluate side-chains 410 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 365 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 235 ASN 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 410 TRP Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 518 LEU 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 286 ASP Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 518 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 410 TRP 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 552 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN 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 410 TRP Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 518 LEU 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: 1.9990 chunk 185 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 268 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 252 optimal weight: 0.9990 chunk 229 optimal weight: 0.0980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 731 ASN B 92 HIS B 731 ASN B 742 ASN C 92 HIS C 731 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 = 0.3866 r_free = 0.3866 target = 0.159064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.090708 restraints weight = 23025.683| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.35 r_work: 0.2823 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4982 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= 0.136 Angle : 0.515 14.812 31416 Z= 0.258 Chirality : 0.038 0.155 3504 Planarity : 0.004 0.047 3880 Dihedral : 8.004 57.796 3540 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.97 % Allowed : 22.08 % Favored : 74.96 % 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: 2.97 (0.16), residues: 2688 helix: 2.68 (0.11), residues: 2000 sheet: None (None), residues: 0 loop : -0.25 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 545 TYR 0.015 0.001 TYR C 524 PHE 0.020 0.001 PHE D 341 TRP 0.014 0.001 TRP B 315 HIS 0.002 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (23212) covalent geometry : angle 0.51037 / 0.26 (31396) SS BOND : bond 0.00029 / 0.01 ( 4) SS BOND : angle 0.22591 / 0.13 ( 8) hydrogen bonds : bond 0.05737 / 3.79 ( 1475) hydrogen bonds : angle 3.59176 / 2.61 ( 4245) metal coordination : bond 0.00975 / 0.70 ( 16) metal coordination : angle 3.50494 / 2.68 ( 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 442 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 370 time to evaluate : 0.708 Fit side-chains REVERT: A 21 GLN cc_start: 0.7981 (pt0) cc_final: 0.7616 (pt0) REVERT: A 34 LYS cc_start: 0.7624 (mtpp) cc_final: 0.7378 (mttm) REVERT: A 66 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7423 (mtm) REVERT: A 272 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7929 (ttm-80) REVERT: A 286 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6694 (m-30) REVERT: A 323 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6919 (ppt-90) REVERT: A 410 TRP cc_start: 0.7832 (OUTLIER) cc_final: 0.7602 (m-90) REVERT: A 522 PHE cc_start: 0.8185 (t80) cc_final: 0.7412 (m-80) REVERT: A 715 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7416 (tp30) REVERT: A 745 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7916 (tt0) REVERT: B 21 GLN cc_start: 0.8002 (pt0) cc_final: 0.7650 (pt0) REVERT: B 34 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7363 (mttm) REVERT: B 67 ASP cc_start: 0.7262 (m-30) cc_final: 0.6961 (m-30) REVERT: B 71 ARG cc_start: 0.7601 (mtm110) cc_final: 0.7204 (mtp-110) REVERT: B 272 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7928 (ttm-80) REVERT: B 286 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6686 (m-30) REVERT: B 323 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6917 (ppt-90) REVERT: B 393 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7612 (mt) REVERT: B 410 TRP cc_start: 0.7832 (OUTLIER) cc_final: 0.7614 (m-90) REVERT: B 522 PHE cc_start: 0.8186 (t80) cc_final: 0.7408 (m-80) REVERT: B 715 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7433 (tp30) REVERT: B 738 LEU cc_start: 0.8420 (mt) cc_final: 0.8184 (mt) REVERT: C 21 GLN cc_start: 0.7975 (pt0) cc_final: 0.7612 (pt0) REVERT: C 34 LYS cc_start: 0.7613 (mtpp) cc_final: 0.7360 (mttm) REVERT: C 272 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7915 (ttm-80) REVERT: C 286 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.6693 (m-30) REVERT: C 323 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6921 (ppt-90) REVERT: C 393 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7600 (mt) REVERT: C 410 TRP cc_start: 0.7830 (OUTLIER) cc_final: 0.7610 (m-90) REVERT: C 522 PHE cc_start: 0.8179 (t80) cc_final: 0.7410 (m-80) REVERT: C 715 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7433 (tp30) REVERT: D 21 GLN cc_start: 0.7985 (pt0) cc_final: 0.7622 (pt0) REVERT: D 34 LYS cc_start: 0.7620 (mtpp) cc_final: 0.7372 (mttm) REVERT: D 66 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7358 (mtm) REVERT: D 71 ARG cc_start: 0.7649 (mtm110) cc_final: 0.7306 (mtp-110) REVERT: D 272 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7927 (ttm-80) REVERT: D 286 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6698 (m-30) REVERT: D 323 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6919 (ppt-90) REVERT: D 393 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7610 (mt) REVERT: D 410 TRP cc_start: 0.7825 (OUTLIER) cc_final: 0.7593 (m-90) REVERT: D 522 PHE cc_start: 0.8190 (t80) cc_final: 0.7415 (m-80) REVERT: D 715 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7417 (tp30) outliers start: 72 outliers final: 29 residues processed: 406 average time/residue: 0.6645 time to fit residues: 305.9025 Evaluate side-chains 415 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 369 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 235 ASN 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 410 TRP 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 552 ASN Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 235 ASN 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 393 LEU Chi-restraints excluded: chain B residue 410 TRP 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 552 ASN 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 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 552 ASN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN 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 393 LEU Chi-restraints excluded: chain D residue 410 TRP 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 552 ASN Chi-restraints excluded: chain D residue 738 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 252 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 254 optimal weight: 0.5980 chunk 264 optimal weight: 0.9990 chunk 186 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 263 optimal weight: 0.8980 chunk 268 optimal weight: 3.9990 chunk 230 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 533 ASN A 731 ASN B 92 HIS B 731 ASN C 92 HIS C 533 ASN C 731 ASN D 92 HIS D 731 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.160102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092302 restraints weight = 23041.030| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.34 r_work: 0.2844 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5080 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= 0.120 Angle : 0.509 15.576 31416 Z= 0.252 Chirality : 0.037 0.198 3504 Planarity : 0.004 0.047 3880 Dihedral : 7.832 56.682 3540 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.10 % Allowed : 23.19 % 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: 3.05 (0.16), residues: 2688 helix: 2.74 (0.11), residues: 2000 sheet: None (None), residues: 0 loop : -0.22 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 71 TYR 0.013 0.001 TYR C 524 PHE 0.022 0.001 PHE A 520 TRP 0.014 0.001 TRP B 315 HIS 0.002 0.000 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (23212) covalent geometry : angle 0.50440 / 0.25 (31396) SS BOND : bond 0.00060 / 0.03 ( 4) SS BOND : angle 0.23965 / 0.15 ( 8) hydrogen bonds : bond 0.05184 / 3.42 ( 1475) hydrogen bonds : angle 3.56430 / 2.59 ( 4245) metal coordination : bond 0.00909 / 0.65 ( 16) metal coordination : angle 3.37091 / 2.59 ( 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 418 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 367 time to evaluate : 0.939 Fit side-chains REVERT: A 21 GLN cc_start: 0.7972 (pt0) cc_final: 0.7609 (pt0) REVERT: A 34 LYS cc_start: 0.7622 (mtpp) cc_final: 0.7374 (mttm) REVERT: A 71 ARG cc_start: 0.7711 (mtm110) cc_final: 0.7414 (mtp-110) REVERT: A 272 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7917 (ttm-80) REVERT: A 286 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.6724 (m-30) REVERT: A 323 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6927 (ppt-90) REVERT: A 410 TRP cc_start: 0.7813 (OUTLIER) cc_final: 0.7559 (m-90) REVERT: A 715 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7401 (tp30) REVERT: A 745 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7906 (tt0) REVERT: B 21 GLN cc_start: 0.7978 (pt0) cc_final: 0.7623 (pt0) REVERT: B 34 LYS cc_start: 0.7608 (mtpp) cc_final: 0.7355 (mttm) REVERT: B 67 ASP cc_start: 0.6939 (m-30) cc_final: 0.6646 (m-30) REVERT: B 71 ARG cc_start: 0.7601 (mtm110) cc_final: 0.7203 (mtp-110) REVERT: B 272 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7918 (ttm-80) REVERT: B 286 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6692 (m-30) REVERT: B 323 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6919 (ppt-90) REVERT: B 410 TRP cc_start: 0.7806 (OUTLIER) cc_final: 0.7563 (m-90) REVERT: B 715 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7413 (tp30) REVERT: B 738 LEU cc_start: 0.8427 (mt) cc_final: 0.8194 (mt) REVERT: C 21 GLN cc_start: 0.7965 (pt0) cc_final: 0.7601 (pt0) REVERT: C 34 LYS cc_start: 0.7611 (mtpp) cc_final: 0.7362 (mttm) REVERT: C 272 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7914 (ttm-80) REVERT: C 286 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: C 323 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6929 (ppt-90) REVERT: C 410 TRP cc_start: 0.7805 (OUTLIER) cc_final: 0.7562 (m-90) REVERT: C 520 PHE cc_start: 0.8340 (t80) cc_final: 0.8137 (m-80) REVERT: C 715 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7403 (tp30) REVERT: D 21 GLN cc_start: 0.7972 (pt0) cc_final: 0.7610 (pt0) REVERT: D 34 LYS cc_start: 0.7617 (mtpp) cc_final: 0.7368 (mttm) REVERT: D 66 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7373 (mtm) REVERT: D 71 ARG cc_start: 0.7685 (mtm110) cc_final: 0.7307 (mtp-110) REVERT: D 272 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7935 (ttm-80) REVERT: D 286 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6698 (m-30) REVERT: D 323 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6927 (ppt-90) REVERT: D 410 TRP cc_start: 0.7798 (OUTLIER) cc_final: 0.7497 (m-90) REVERT: D 715 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7405 (tp30) outliers start: 51 outliers final: 26 residues processed: 398 average time/residue: 0.6820 time to fit residues: 307.6430 Evaluate side-chains 401 residues out of total 2428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 362 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 286 ASP Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 235 ASN 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 410 TRP Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 552 ASN 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 410 TRP Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN 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 410 TRP Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 203 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 731 ASN B 92 HIS C 92 HIS D 92 HIS D 731 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.088192 restraints weight = 23394.152| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.35 r_work: 0.2775 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 23232 Z= 0.243 Angle : 0.608 16.212 31416 Z= 0.310 Chirality : 0.043 0.163 3504 Planarity : 0.004 0.049 3880 Dihedral : 8.686 59.201 3540 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.43 % Allowed : 22.53 % Favored : 75.04 % 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: 2.70 (0.16), residues: 2688 helix: 2.51 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.28 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 545 TYR 0.025 0.001 TYR D 524 PHE 0.023 0.002 PHE D 341 TRP 0.014 0.002 TRP B 315 HIS 0.004 0.001 HIS D 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.24 (23212) covalent geometry : angle 0.60425 / 0.31 (31396) SS BOND : bond 0.00018 / 0.01 ( 4) SS BOND : angle 0.25649 / 0.17 ( 8) hydrogen bonds : bond 0.07702 / 5.11 ( 1475) hydrogen bonds : angle 3.86040 / 2.80 ( 4245) metal coordination : bond 0.01198 / 0.90 ( 16) metal coordination : angle 3.72887 / 2.81 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13296.66 seconds wall clock time: 225 minutes 39.91 seconds (13539.91 seconds total)