Starting phenix.real_space_refine on Sun Aug 9 10:47:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wwc_66308/08_2026/9wwc_66308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wwc_66308/08_2026/9wwc_66308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wwc_66308/08_2026/9wwc_66308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wwc_66308/08_2026/9wwc_66308.map" model { file = "/net/cci-nas-00/data/ceres_data/9wwc_66308/08_2026/9wwc_66308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wwc_66308/08_2026/9wwc_66308.cif" } resolution = 4.5 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 21444 2.51 5 N 5385 2.21 5 O 6342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33297 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 6681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6681 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 42, 'TRANS': 790} Chain: "S" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2219 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 12, 'TRANS': 258} Chain: "A" Number of atoms: 2199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2199 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 12, 'TRANS': 255} Chain: "C" Number of atoms: 6681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6681 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 42, 'TRANS': 790} Chain: "D" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2219 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 12, 'TRANS': 258} Chain: "E" Number of atoms: 2199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2199 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 12, 'TRANS': 255} Chain: "F" Number of atoms: 6681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6681 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 42, 'TRANS': 790} Chain: "G" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2219 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 12, 'TRANS': 258} Chain: "H" Number of atoms: 2199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2199 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 12, 'TRANS': 255} Time building chain proxies: 7.01, per 1000 atoms: 0.21 Number of scatterers: 33297 At special positions: 0 Unit cell: (144.346, 149.501, 164.966, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 6342 8.00 N 5385 7.00 C 21444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7710 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 102 sheets defined 12.8% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'B' and resid 97 through 103 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 216 through 224 removed outlier: 4.361A pdb=" N VAL B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 Processing helix chain 'B' and resid 276 through 283 removed outlier: 3.636A pdb=" N LEU B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 483 through 487 Processing helix chain 'B' and resid 502 through 507 removed outlier: 3.913A pdb=" N LYS B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 531 Processing helix chain 'B' and resid 565 through 570 removed outlier: 3.506A pdb=" N ASN B 570 " --> pdb=" O THR B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 595 removed outlier: 3.959A pdb=" N PHE B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 669 through 674 Processing helix chain 'B' and resid 700 through 706 removed outlier: 4.308A pdb=" N LEU B 706 " --> pdb=" O ASP B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 751 No H-bonds generated for 'chain 'B' and resid 749 through 751' Processing helix chain 'B' and resid 752 through 758 removed outlier: 4.188A pdb=" N SER B 758 " --> pdb=" O ILE B 754 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 23 removed outlier: 3.601A pdb=" N LYS S 23 " --> pdb=" O ASN S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 76 Processing helix chain 'S' and resid 182 through 186 removed outlier: 3.571A pdb=" N GLY S 185 " --> pdb=" O ASN S 182 " (cutoff:3.500A) Processing helix chain 'S' and resid 205 through 212 Processing helix chain 'S' and resid 213 through 218 removed outlier: 3.955A pdb=" N ARG S 216 " --> pdb=" O ARG S 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'C' and resid 97 through 103 Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 216 through 224 removed outlier: 4.361A pdb=" N VAL C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 234 Processing helix chain 'C' and resid 276 through 283 removed outlier: 3.636A pdb=" N LEU C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 483 through 487 Processing helix chain 'C' and resid 502 through 507 removed outlier: 3.912A pdb=" N LYS C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 531 Processing helix chain 'C' and resid 565 through 570 removed outlier: 3.506A pdb=" N ASN C 570 " --> pdb=" O THR C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 595 removed outlier: 3.959A pdb=" N PHE C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 616 Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 700 through 706 removed outlier: 4.309A pdb=" N LEU C 706 " --> pdb=" O ASP C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 751 No H-bonds generated for 'chain 'C' and resid 749 through 751' Processing helix chain 'C' and resid 752 through 758 removed outlier: 4.188A pdb=" N SER C 758 " --> pdb=" O ILE C 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.601A pdb=" N LYS D 23 " --> pdb=" O ASN D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.571A pdb=" N GLY D 185 " --> pdb=" O ASN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 213 through 218 removed outlier: 3.955A pdb=" N ARG D 216 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 23 Processing helix chain 'E' and resid 71 through 76 Processing helix chain 'E' and resid 205 through 212 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'F' and resid 97 through 103 Processing helix chain 'F' and resid 156 through 164 Processing helix chain 'F' and resid 194 through 198 Processing helix chain 'F' and resid 216 through 224 removed outlier: 4.361A pdb=" N VAL F 220 " --> pdb=" O GLU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 234 Processing helix chain 'F' and resid 276 through 283 removed outlier: 3.636A pdb=" N LEU F 280 " --> pdb=" O ASP F 276 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 Processing helix chain 'F' and resid 483 through 487 Processing helix chain 'F' and resid 502 through 507 removed outlier: 3.913A pdb=" N LYS F 506 " --> pdb=" O LEU F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 531 Processing helix chain 'F' and resid 565 through 570 removed outlier: 3.506A pdb=" N ASN F 570 " --> pdb=" O THR F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 595 removed outlier: 3.959A pdb=" N PHE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 616 Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 669 through 674 Processing helix chain 'F' and resid 700 through 706 removed outlier: 4.309A pdb=" N LEU F 706 " --> pdb=" O ASP F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 751 No H-bonds generated for 'chain 'F' and resid 749 through 751' Processing helix chain 'F' and resid 752 through 758 removed outlier: 4.188A pdb=" N SER F 758 " --> pdb=" O ILE F 754 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 23 removed outlier: 3.601A pdb=" N LYS G 23 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 Processing helix chain 'G' and resid 182 through 186 removed outlier: 3.571A pdb=" N GLY G 185 " --> pdb=" O ASN G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 212 Processing helix chain 'G' and resid 213 through 218 removed outlier: 3.955A pdb=" N ARG G 216 " --> pdb=" O ARG G 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 23 Processing helix chain 'H' and resid 71 through 76 Processing helix chain 'H' and resid 205 through 212 Processing helix chain 'H' and resid 213 through 215 No H-bonds generated for 'chain 'H' and resid 213 through 215' Processing sheet with id=1, first strand: chain 'B' and resid 121 through 123 removed outlier: 4.645A pdb=" N PHE B 7 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 172 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE B 171 " --> pdb=" O GLN B 192 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN B 192 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 173 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER B 190 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE B 175 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 186 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 14 through 17 removed outlier: 7.009A pdb=" N TYR B 31 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL B 93 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 14 through 17 removed outlier: 7.009A pdb=" N TYR B 31 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL B 93 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 92 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 59 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER B 69 " --> pdb=" O TRP B 60 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=5, first strand: chain 'B' and resid 144 through 149 removed outlier: 3.501A pdb=" N LEU B 816 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 137 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N ASP B 814 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 804 " --> pdb=" O GLY B 811 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LYS B 805 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASP B 629 " --> pdb=" O LYS B 805 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 144 through 149 removed outlier: 3.501A pdb=" N LEU B 816 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 137 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N ASP B 814 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N GLY B 811 " --> pdb=" O ASP B 832 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ASP B 832 " --> pdb=" O GLY B 811 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL B 813 " --> pdb=" O LYS B 830 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS B 830 " --> pdb=" O VAL B 813 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER B 824 " --> pdb=" O ASN B 819 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS B 787 " --> pdb=" O SER B 650 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 152 through 155 Processing sheet with id=8, first strand: chain 'B' and resid 228 through 229 Processing sheet with id=9, first strand: chain 'B' and resid 511 through 513 Processing sheet with id=10, first strand: chain 'B' and resid 266 through 270 removed outlier: 3.521A pdb=" N VAL B 258 " --> pdb=" O GLN B 269 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN B 290 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 406 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU B 288 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 17.994A pdb=" N ALA B 287 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 15.488A pdb=" N ALA B 318 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 11.746A pdb=" N CYS B 289 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR B 316 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 312 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 308 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 313 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 326 " --> pdb=" O ARG B 313 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ALA B 322 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE B 323 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 337 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N TYR B 335 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 353 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 352 " --> pdb=" O GLN B 369 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN B 369 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 354 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG B 367 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE B 356 " --> pdb=" O MET B 365 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 266 through 270 removed outlier: 3.521A pdb=" N VAL B 258 " --> pdb=" O GLN B 269 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 381 through 382 Processing sheet with id=13, first strand: chain 'B' and resid 446 through 449 removed outlier: 3.519A pdb=" N SER B 449 " --> pdb=" O SER B 491 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'B' and resid 451 through 453 removed outlier: 3.815A pdb=" N ASN B 451 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 517 through 518 removed outlier: 3.596A pdb=" N ARG B 559 " --> pdb=" O ALA B 721 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 721 " --> pdb=" O ARG B 559 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 597 through 602 removed outlier: 3.627A pdb=" N GLU B 602 " --> pdb=" O LYS B 605 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'B' and resid 659 through 662 removed outlier: 6.177A pdb=" N ARG B 659 " --> pdb=" O GLU B 690 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE B 692 " --> pdb=" O ARG B 659 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLN B 661 " --> pdb=" O ILE B 692 " (cutoff:3.500A) No H-bonds generated for sheet with id=17 Processing sheet with id=18, first strand: chain 'B' and resid 678 through 679 removed outlier: 3.579A pdb=" N VAL B 770 " --> pdb=" O VAL B 777 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'B' and resid 734 through 739 removed outlier: 3.535A pdb=" N VAL B 742 " --> pdb=" O ILE B 739 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'S' and resid 12 through 13 removed outlier: 5.807A pdb=" N ALA S 111 " --> pdb=" O SER S 122 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE S 59 " --> pdb=" O PHE S 67 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'S' and resid 12 through 13 removed outlier: 5.807A pdb=" N ALA S 111 " --> pdb=" O SER S 122 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY S 107 " --> pdb=" O ILE S 127 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'S' and resid 43 through 48 removed outlier: 3.785A pdb=" N PHE S 43 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR S 89 " --> pdb=" O PHE S 84 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE S 84 " --> pdb=" O TYR S 89 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'S' and resid 161 through 165 removed outlier: 3.808A pdb=" N TYR S 140 " --> pdb=" O TYR S 220 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR S 220 " --> pdb=" O TYR S 140 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE S 221 " --> pdb=" O CYS S 233 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'S' and resid 146 through 147 Processing sheet with id=25, first strand: chain 'S' and resid 174 through 179 removed outlier: 3.707A pdb=" N GLU S 177 " --> pdb=" O ILE S 193 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE S 193 " --> pdb=" O GLU S 177 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP S 179 " --> pdb=" O LYS S 191 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS S 191 " --> pdb=" O ASP S 179 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR S 198 " --> pdb=" O PHE S 255 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE S 255 " --> pdb=" O TYR S 198 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'S' and resid 235 through 237 removed outlier: 4.018A pdb=" N THR S 235 " --> pdb=" O GLU S 256 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE S 255 " --> pdb=" O TYR S 198 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR S 198 " --> pdb=" O PHE S 255 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER S 194 " --> pdb=" O VAL S 261 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL S 261 " --> pdb=" O SER S 194 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'A' and resid 12 through 13 removed outlier: 5.385A pdb=" N ALA A 111 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY A 107 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR A 35 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'A' and resid 12 through 13 removed outlier: 5.385A pdb=" N ALA A 111 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 56 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE A 59 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'A' and resid 43 through 48 removed outlier: 4.010A pdb=" N PHE A 43 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'A' and resid 161 through 165 removed outlier: 3.521A pdb=" N TYR A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.566A pdb=" N ALA A 145 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'A' and resid 174 through 179 removed outlier: 3.601A pdb=" N LYS A 191 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 255 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 202 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'A' and resid 235 through 238 removed outlier: 3.798A pdb=" N PHE A 202 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 255 " --> pdb=" O TYR A 198 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=35, first strand: chain 'C' and resid 121 through 123 removed outlier: 4.646A pdb=" N PHE C 7 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C 172 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE C 171 " --> pdb=" O GLN C 192 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN C 192 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU C 173 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER C 190 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE C 175 " --> pdb=" O TYR C 188 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 186 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'C' and resid 14 through 17 removed outlier: 7.009A pdb=" N TYR C 31 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL C 93 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'C' and resid 14 through 17 removed outlier: 7.009A pdb=" N TYR C 31 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL C 93 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 92 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 59 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER C 69 " --> pdb=" O TRP C 60 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=39, first strand: chain 'C' and resid 144 through 149 removed outlier: 3.500A pdb=" N LEU C 816 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU C 137 " --> pdb=" O ASP C 814 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N ASP C 814 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 804 " --> pdb=" O GLY C 811 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LYS C 805 " --> pdb=" O SER C 627 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASP C 629 " --> pdb=" O LYS C 805 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'C' and resid 144 through 149 removed outlier: 3.500A pdb=" N LEU C 816 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU C 137 " --> pdb=" O ASP C 814 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N ASP C 814 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N GLY C 811 " --> pdb=" O ASP C 832 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ASP C 832 " --> pdb=" O GLY C 811 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL C 813 " --> pdb=" O LYS C 830 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS C 830 " --> pdb=" O VAL C 813 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER C 824 " --> pdb=" O ASN C 819 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS C 787 " --> pdb=" O SER C 650 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'C' and resid 152 through 155 Processing sheet with id=42, first strand: chain 'C' and resid 228 through 229 Processing sheet with id=43, first strand: chain 'C' and resid 511 through 513 Processing sheet with id=44, first strand: chain 'C' and resid 266 through 270 removed outlier: 3.521A pdb=" N VAL C 258 " --> pdb=" O GLN C 269 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN C 290 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA C 406 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU C 288 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 17.994A pdb=" N ALA C 287 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 15.488A pdb=" N ALA C 318 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 11.746A pdb=" N CYS C 289 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR C 316 " --> pdb=" O CYS C 289 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY C 312 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY C 308 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 313 " --> pdb=" O LYS C 326 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 326 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ALA C 322 " --> pdb=" O GLY C 317 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE C 323 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE C 337 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N TYR C 335 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 353 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA C 352 " --> pdb=" O GLN C 369 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN C 369 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C 354 " --> pdb=" O ARG C 367 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG C 367 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE C 356 " --> pdb=" O MET C 365 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'C' and resid 266 through 270 removed outlier: 3.521A pdb=" N VAL C 258 " --> pdb=" O GLN C 269 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'C' and resid 381 through 382 Processing sheet with id=47, first strand: chain 'C' and resid 446 through 449 removed outlier: 3.519A pdb=" N SER C 449 " --> pdb=" O SER C 491 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'C' and resid 451 through 453 removed outlier: 3.815A pdb=" N ASN C 451 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'C' and resid 517 through 518 removed outlier: 3.596A pdb=" N ARG C 559 " --> pdb=" O ALA C 721 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 721 " --> pdb=" O ARG C 559 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'C' and resid 597 through 602 removed outlier: 3.627A pdb=" N GLU C 602 " --> pdb=" O LYS C 605 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'C' and resid 659 through 662 removed outlier: 6.177A pdb=" N ARG C 659 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE C 692 " --> pdb=" O ARG C 659 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN C 661 " --> pdb=" O ILE C 692 " (cutoff:3.500A) No H-bonds generated for sheet with id=51 Processing sheet with id=52, first strand: chain 'C' and resid 678 through 679 removed outlier: 3.579A pdb=" N VAL C 770 " --> pdb=" O VAL C 777 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'C' and resid 734 through 739 removed outlier: 3.535A pdb=" N VAL C 742 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'D' and resid 12 through 13 removed outlier: 5.808A pdb=" N ALA D 111 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE D 59 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'D' and resid 12 through 13 removed outlier: 5.808A pdb=" N ALA D 111 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY D 107 " --> pdb=" O ILE D 127 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'D' and resid 43 through 48 removed outlier: 3.785A pdb=" N PHE D 43 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR D 89 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE D 84 " --> pdb=" O TYR D 89 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'D' and resid 161 through 165 removed outlier: 3.808A pdb=" N TYR D 140 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR D 220 " --> pdb=" O TYR D 140 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE D 221 " --> pdb=" O CYS D 233 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'D' and resid 146 through 147 Processing sheet with id=59, first strand: chain 'D' and resid 174 through 179 removed outlier: 3.707A pdb=" N GLU D 177 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D 193 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP D 179 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS D 191 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR D 198 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE D 255 " --> pdb=" O TYR D 198 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'D' and resid 235 through 237 removed outlier: 4.018A pdb=" N THR D 235 " --> pdb=" O GLU D 256 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE D 255 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR D 198 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER D 194 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 261 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'E' and resid 12 through 13 removed outlier: 5.385A pdb=" N ALA E 111 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY E 107 " --> pdb=" O ILE E 127 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR E 35 " --> pdb=" O VAL E 128 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'E' and resid 12 through 13 removed outlier: 5.385A pdb=" N ALA E 111 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER E 56 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE E 59 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'E' and resid 43 through 48 removed outlier: 4.011A pdb=" N PHE E 43 " --> pdb=" O TYR E 94 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'E' and resid 161 through 165 removed outlier: 3.521A pdb=" N TYR E 140 " --> pdb=" O TYR E 220 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'E' and resid 145 through 147 removed outlier: 3.566A pdb=" N ALA E 145 " --> pdb=" O ILE E 152 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'E' and resid 174 through 179 removed outlier: 3.600A pdb=" N LYS E 191 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 255 " --> pdb=" O TYR E 198 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE E 202 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'E' and resid 235 through 238 removed outlier: 3.798A pdb=" N PHE E 202 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 255 " --> pdb=" O TYR E 198 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=69, first strand: chain 'F' and resid 121 through 123 removed outlier: 4.645A pdb=" N PHE F 7 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU F 172 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE F 171 " --> pdb=" O GLN F 192 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN F 192 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU F 173 " --> pdb=" O SER F 190 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER F 190 " --> pdb=" O LEU F 173 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE F 175 " --> pdb=" O TYR F 188 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR F 186 " --> pdb=" O LYS F 177 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'F' and resid 14 through 17 removed outlier: 7.010A pdb=" N TYR F 31 " --> pdb=" O GLY F 17 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL F 93 " --> pdb=" O THR F 34 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'F' and resid 14 through 17 removed outlier: 7.010A pdb=" N TYR F 31 " --> pdb=" O GLY F 17 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL F 93 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG F 92 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL F 59 " --> pdb=" O ARG F 92 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER F 69 " --> pdb=" O TRP F 60 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain 'F' and resid 82 through 83 Processing sheet with id=73, first strand: chain 'F' and resid 144 through 149 removed outlier: 3.501A pdb=" N LEU F 816 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU F 137 " --> pdb=" O ASP F 814 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N ASP F 814 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE F 804 " --> pdb=" O GLY F 811 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LYS F 805 " --> pdb=" O SER F 627 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASP F 629 " --> pdb=" O LYS F 805 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'F' and resid 144 through 149 removed outlier: 3.501A pdb=" N LEU F 816 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU F 137 " --> pdb=" O ASP F 814 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N ASP F 814 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N GLY F 811 " --> pdb=" O ASP F 832 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ASP F 832 " --> pdb=" O GLY F 811 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL F 813 " --> pdb=" O LYS F 830 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS F 830 " --> pdb=" O VAL F 813 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER F 824 " --> pdb=" O ASN F 819 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS F 787 " --> pdb=" O SER F 650 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'F' and resid 152 through 155 Processing sheet with id=76, first strand: chain 'F' and resid 228 through 229 Processing sheet with id=77, first strand: chain 'F' and resid 511 through 513 Processing sheet with id=78, first strand: chain 'F' and resid 266 through 270 removed outlier: 3.521A pdb=" N VAL F 258 " --> pdb=" O GLN F 269 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN F 290 " --> pdb=" O ILE F 404 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA F 406 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU F 288 " --> pdb=" O ALA F 406 " (cutoff:3.500A) removed outlier: 17.994A pdb=" N ALA F 287 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 15.488A pdb=" N ALA F 318 " --> pdb=" O ALA F 287 " (cutoff:3.500A) removed outlier: 11.746A pdb=" N CYS F 289 " --> pdb=" O THR F 316 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR F 316 " --> pdb=" O CYS F 289 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY F 312 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY F 308 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG F 313 " --> pdb=" O LYS F 326 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS F 326 " --> pdb=" O ARG F 313 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA F 322 " --> pdb=" O GLY F 317 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE F 323 " --> pdb=" O GLN F 341 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE F 337 " --> pdb=" O LEU F 327 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N TYR F 335 " --> pdb=" O PRO F 329 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU F 353 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA F 352 " --> pdb=" O GLN F 369 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN F 369 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL F 354 " --> pdb=" O ARG F 367 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG F 367 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE F 356 " --> pdb=" O MET F 365 " (cutoff:3.500A) Processing sheet with id=79, first strand: chain 'F' and resid 266 through 270 removed outlier: 3.521A pdb=" N VAL F 258 " --> pdb=" O GLN F 269 " (cutoff:3.500A) Processing sheet with id=80, first strand: chain 'F' and resid 381 through 382 Processing sheet with id=81, first strand: chain 'F' and resid 446 through 449 removed outlier: 3.519A pdb=" N SER F 449 " --> pdb=" O SER F 491 " (cutoff:3.500A) Processing sheet with id=82, first strand: chain 'F' and resid 451 through 453 removed outlier: 3.815A pdb=" N ASN F 451 " --> pdb=" O ALA F 469 " (cutoff:3.500A) Processing sheet with id=83, first strand: chain 'F' and resid 517 through 518 removed outlier: 3.596A pdb=" N ARG F 559 " --> pdb=" O ALA F 721 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA F 721 " --> pdb=" O ARG F 559 " (cutoff:3.500A) Processing sheet with id=84, first strand: chain 'F' and resid 597 through 602 removed outlier: 3.627A pdb=" N GLU F 602 " --> pdb=" O LYS F 605 " (cutoff:3.500A) Processing sheet with id=85, first strand: chain 'F' and resid 659 through 662 removed outlier: 6.177A pdb=" N ARG F 659 " --> pdb=" O GLU F 690 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE F 692 " --> pdb=" O ARG F 659 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN F 661 " --> pdb=" O ILE F 692 " (cutoff:3.500A) No H-bonds generated for sheet with id=85 Processing sheet with id=86, first strand: chain 'F' and resid 678 through 679 removed outlier: 3.580A pdb=" N VAL F 770 " --> pdb=" O VAL F 777 " (cutoff:3.500A) Processing sheet with id=87, first strand: chain 'F' and resid 734 through 739 removed outlier: 3.535A pdb=" N VAL F 742 " --> pdb=" O ILE F 739 " (cutoff:3.500A) Processing sheet with id=88, first strand: chain 'G' and resid 12 through 13 removed outlier: 5.807A pdb=" N ALA G 111 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE G 59 " --> pdb=" O PHE G 67 " (cutoff:3.500A) Processing sheet with id=89, first strand: chain 'G' and resid 12 through 13 removed outlier: 5.807A pdb=" N ALA G 111 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY G 107 " --> pdb=" O ILE G 127 " (cutoff:3.500A) Processing sheet with id=90, first strand: chain 'G' and resid 43 through 48 removed outlier: 3.786A pdb=" N PHE G 43 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR G 89 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE G 84 " --> pdb=" O TYR G 89 " (cutoff:3.500A) Processing sheet with id=91, first strand: chain 'G' and resid 161 through 165 removed outlier: 3.809A pdb=" N TYR G 140 " --> pdb=" O TYR G 220 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR G 220 " --> pdb=" O TYR G 140 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE G 221 " --> pdb=" O CYS G 233 " (cutoff:3.500A) Processing sheet with id=92, first strand: chain 'G' and resid 146 through 147 Processing sheet with id=93, first strand: chain 'G' and resid 174 through 179 removed outlier: 3.708A pdb=" N GLU G 177 " --> pdb=" O ILE G 193 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE G 193 " --> pdb=" O GLU G 177 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP G 179 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS G 191 " --> pdb=" O ASP G 179 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR G 198 " --> pdb=" O PHE G 255 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE G 255 " --> pdb=" O TYR G 198 " (cutoff:3.500A) Processing sheet with id=94, first strand: chain 'G' and resid 235 through 237 removed outlier: 4.018A pdb=" N THR G 235 " --> pdb=" O GLU G 256 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE G 255 " --> pdb=" O TYR G 198 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR G 198 " --> pdb=" O PHE G 255 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER G 194 " --> pdb=" O VAL G 261 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL G 261 " --> pdb=" O SER G 194 " (cutoff:3.500A) Processing sheet with id=95, first strand: chain 'H' and resid 12 through 13 removed outlier: 5.385A pdb=" N ALA H 111 " --> pdb=" O SER H 122 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY H 107 " --> pdb=" O ILE H 127 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR H 35 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing sheet with id=96, first strand: chain 'H' and resid 12 through 13 removed outlier: 5.385A pdb=" N ALA H 111 " --> pdb=" O SER H 122 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER H 56 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE H 59 " --> pdb=" O PHE H 67 " (cutoff:3.500A) Processing sheet with id=97, first strand: chain 'H' and resid 43 through 48 removed outlier: 4.010A pdb=" N PHE H 43 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=98, first strand: chain 'H' and resid 161 through 165 removed outlier: 3.521A pdb=" N TYR H 140 " --> pdb=" O TYR H 220 " (cutoff:3.500A) Processing sheet with id=99, first strand: chain 'H' and resid 145 through 147 removed outlier: 3.566A pdb=" N ALA H 145 " --> pdb=" O ILE H 152 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'H' and resid 174 through 179 removed outlier: 3.600A pdb=" N LYS H 191 " --> pdb=" O ASP H 179 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE H 255 " --> pdb=" O TYR H 198 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE H 202 " --> pdb=" O VAL H 251 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'H' and resid 235 through 238 removed outlier: 3.799A pdb=" N PHE H 202 " --> pdb=" O VAL H 251 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE H 255 " --> pdb=" O TYR H 198 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'H' and resid 182 through 183 1131 hydrogen bonds defined for protein. 2844 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: 10.50 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10587 1.34 - 1.46: 8534 1.46 - 1.58: 14878 1.58 - 1.70: 0 1.70 - 1.81: 207 Bond restraints: 34206 Sorted by residual: bond pdb=" N SER C 73 " pdb=" CA SER C 73 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.45e+00 bond pdb=" CA ILE F 825 " pdb=" CB ILE F 825 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.30e+00 bond pdb=" N SER B 73 " pdb=" CA SER B 73 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.30e+00 bond pdb=" CA ILE C 825 " pdb=" CB ILE C 825 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.26e+00 bond pdb=" N SER F 73 " pdb=" CA SER F 73 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.25e+00 ... (remaining 34201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 45607 1.73 - 3.46: 806 3.46 - 5.19: 87 5.19 - 6.91: 15 6.91 - 8.64: 15 Bond angle restraints: 46530 Sorted by residual: angle pdb=" N ILE A 142 " pdb=" CA ILE A 142 " pdb=" C ILE A 142 " ideal model delta sigma weight residual 113.42 108.53 4.89 1.17e+00 7.31e-01 1.75e+01 angle pdb=" N ILE H 142 " pdb=" CA ILE H 142 " pdb=" C ILE H 142 " ideal model delta sigma weight residual 113.42 108.55 4.87 1.17e+00 7.31e-01 1.73e+01 angle pdb=" N ILE E 142 " pdb=" CA ILE E 142 " pdb=" C ILE E 142 " ideal model delta sigma weight residual 113.42 108.55 4.87 1.17e+00 7.31e-01 1.73e+01 angle pdb=" N ILE D 142 " pdb=" CA ILE D 142 " pdb=" C ILE D 142 " ideal model delta sigma weight residual 113.43 109.02 4.41 1.09e+00 8.42e-01 1.64e+01 angle pdb=" N ILE G 142 " pdb=" CA ILE G 142 " pdb=" C ILE G 142 " ideal model delta sigma weight residual 113.43 109.03 4.40 1.09e+00 8.42e-01 1.63e+01 ... (remaining 46525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 18366 17.97 - 35.93: 1374 35.93 - 53.90: 210 53.90 - 71.87: 69 71.87 - 89.84: 45 Dihedral angle restraints: 20064 sinusoidal: 7935 harmonic: 12129 Sorted by residual: dihedral pdb=" CA PRO S 189 " pdb=" C PRO S 189 " pdb=" N GLU S 190 " pdb=" CA GLU S 190 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA PRO G 189 " pdb=" C PRO G 189 " pdb=" N GLU G 190 " pdb=" CA GLU G 190 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA PRO D 189 " pdb=" C PRO D 189 " pdb=" N GLU D 190 " pdb=" CA GLU D 190 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 20061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3254 0.035 - 0.069: 1121 0.069 - 0.104: 357 0.104 - 0.139: 207 0.139 - 0.174: 17 Chirality restraints: 4956 Sorted by residual: chirality pdb=" CB ILE A 108 " pdb=" CA ILE A 108 " pdb=" CG1 ILE A 108 " pdb=" CG2 ILE A 108 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CB ILE H 108 " pdb=" CA ILE H 108 " pdb=" CG1 ILE H 108 " pdb=" CG2 ILE H 108 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CB ILE E 108 " pdb=" CA ILE E 108 " pdb=" CG1 ILE E 108 " pdb=" CG2 ILE E 108 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 4953 not shown) Planarity restraints: 6021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 575 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO B 576 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 576 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 576 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 575 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO C 576 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 576 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 576 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 575 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO F 576 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 576 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 576 " -0.028 5.00e-02 4.00e+02 ... (remaining 6018 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 883 2.69 - 3.24: 31788 3.24 - 3.80: 49971 3.80 - 4.35: 63908 4.35 - 4.90: 107129 Nonbonded interactions: 253679 Sorted by model distance: nonbonded pdb=" OG SER C 548 " pdb=" O ASN C 550 " model vdw 2.141 3.040 nonbonded pdb=" OG SER F 548 " pdb=" O ASN F 550 " model vdw 2.142 3.040 nonbonded pdb=" OG SER B 548 " pdb=" O ASN B 550 " model vdw 2.142 3.040 nonbonded pdb=" OH TYR G 186 " pdb=" OE2 GLU H 258 " model vdw 2.148 3.040 nonbonded pdb=" OH TYR S 186 " pdb=" OE2 GLU A 258 " model vdw 2.148 3.040 ... (remaining 253674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'S' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'S' selection = chain 'D' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.280 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.580 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34206 Z= 0.138 Angle : 0.586 8.642 46530 Z= 0.322 Chirality : 0.044 0.174 4956 Planarity : 0.004 0.051 6021 Dihedral : 13.904 89.837 12354 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.12 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -1.30 (0.13), residues: 4098 helix: -1.72 (0.26), residues: 330 sheet: -0.33 (0.14), residues: 1464 loop : -1.05 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 736 TYR 0.018 0.001 TYR H 31 PHE 0.022 0.001 PHE F 323 TRP 0.012 0.001 TRP F 267 HIS 0.002 0.001 HIS D 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (34206) covalent geometry : angle 0.58647 / 0.32 (46530) hydrogen bonds : bond 0.28985 / 19.28 ( 981) hydrogen bonds : angle 10.32331 / 7.07 ( 2844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.200 Fit side-chains REVERT: B 197 ASP cc_start: 0.8122 (m-30) cc_final: 0.7841 (t0) REVERT: B 365 MET cc_start: 0.8627 (mmp) cc_final: 0.8004 (mmm) REVERT: B 745 PHE cc_start: 0.7585 (m-80) cc_final: 0.7200 (m-80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0714 time to fit residues: 6.5222 Evaluate side-chains 50 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.261 Evaluate side-chains 30 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.054 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0556 time to fit residues: 2.0300 Evaluate side-chains 19 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.091 Evaluate side-chains 32 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.052 Fit side-chains REVERT: A 63 ASP cc_start: 0.8243 (p0) cc_final: 0.7911 (p0) REVERT: A 87 MET cc_start: 0.8386 (mpp) cc_final: 0.8121 (mpp) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0334 time to fit residues: 1.4225 Evaluate side-chains 19 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0270 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 0.0670 overall best weight: 1.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.077002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.064356 restraints weight = 28339.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.065688 restraints weight = 17546.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.066654 restraints weight = 12342.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.067367 restraints weight = 9355.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.067804 restraints weight = 7584.374| |-----------------------------------------------------------------------------| r_work (final): 0.3081 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.078782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.071120 restraints weight = 6413.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.073250 restraints weight = 3357.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.074616 restraints weight = 1996.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.075537 restraints weight = 1287.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.076194 restraints weight = 880.520| |-----------------------------------------------------------------------------| r_work (final): 0.2855 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.075819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.068822 restraints weight = 6112.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.070829 restraints weight = 3098.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.072130 restraints weight = 1810.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.073045 restraints weight = 1153.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.073685 restraints weight = 782.068| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34206 Z= 0.112 Angle : 0.544 6.708 46530 Z= 0.292 Chirality : 0.046 0.168 4956 Planarity : 0.004 0.045 6021 Dihedral : 4.404 16.319 4575 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: -1.01 (0.13), residues: 4098 helix: -1.48 (0.26), residues: 324 sheet: -0.07 (0.14), residues: 1452 loop : -0.91 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 22 TYR 0.014 0.001 TYR H 31 PHE 0.023 0.001 PHE B 323 TRP 0.007 0.001 TRP C 761 HIS 0.002 0.001 HIS B 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (34206) covalent geometry : angle 0.54443 / 0.29 (46530) hydrogen bonds : bond 0.04312 / 2.85 ( 981) hydrogen bonds : angle 6.69645 / 4.57 ( 2844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.253 Fit side-chains REVERT: B 66 ASN cc_start: 0.8515 (t0) cc_final: 0.8305 (t0) REVERT: B 134 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 176 GLU cc_start: 0.7561 (mp0) cc_final: 0.7317 (mp0) REVERT: B 704 MET cc_start: 0.8860 (ptp) cc_final: 0.8262 (ptt) REVERT: B 745 PHE cc_start: 0.7374 (m-80) cc_final: 0.7097 (m-80) REVERT: B 816 LEU cc_start: 0.7746 (mt) cc_final: 0.7389 (mt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0603 time to fit residues: 6.8908 Evaluate side-chains 57 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.247 Evaluate side-chains 31 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.086 Fit side-chains REVERT: D 247 ASP cc_start: 0.7263 (p0) cc_final: 0.6854 (p0) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0393 time to fit residues: 1.5734 Evaluate side-chains 24 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.085 Evaluate side-chains 35 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.083 Fit side-chains REVERT: E 182 ASN cc_start: 0.7662 (m-40) cc_final: 0.6941 (p0) REVERT: E 210 ASP cc_start: 0.7681 (t0) cc_final: 0.7338 (t0) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0429 time to fit residues: 1.9131 Evaluate side-chains 19 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 235 optimal weight: 0.0010 chunk 405 optimal weight: 5.9990 chunk 353 optimal weight: 9.9990 chunk 371 optimal weight: 0.0470 chunk 236 optimal weight: 5.9990 chunk 6 optimal weight: 0.0020 chunk 201 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 299 optimal weight: 0.0970 overall best weight: 1.0292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.078373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.065416 restraints weight = 27930.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.066923 restraints weight = 16749.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.067906 restraints weight = 11447.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.068667 restraints weight = 8636.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.069126 restraints weight = 6936.950| |-----------------------------------------------------------------------------| r_work (final): 0.3111 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.080159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.072807 restraints weight = 6151.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.074762 restraints weight = 3291.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.076207 restraints weight = 1988.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.077153 restraints weight = 1278.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.077723 restraints weight = 868.824| |-----------------------------------------------------------------------------| r_work (final): 0.2876 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.080853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.073705 restraints weight = 6319.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.075706 restraints weight = 3201.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.077089 restraints weight = 1894.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.078001 restraints weight = 1214.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.078686 restraints weight = 824.049| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34206 Z= 0.094 Angle : 0.513 6.986 46530 Z= 0.271 Chirality : 0.045 0.191 4956 Planarity : 0.004 0.047 6021 Dihedral : 4.146 16.471 4575 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.13), residues: 4098 helix: -1.29 (0.27), residues: 327 sheet: 0.08 (0.14), residues: 1452 loop : -0.91 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 58 TYR 0.009 0.001 TYR B 310 PHE 0.018 0.001 PHE C 323 TRP 0.006 0.001 TRP G 139 HIS 0.003 0.000 HIS S 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (34206) covalent geometry : angle 0.51292 / 0.27 (46530) hydrogen bonds : bond 0.03578 / 2.35 ( 981) hydrogen bonds : angle 5.99091 / 4.10 ( 2844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.255 Fit side-chains REVERT: B 134 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7859 (mm-30) REVERT: B 176 GLU cc_start: 0.7157 (mp0) cc_final: 0.6939 (mp0) REVERT: B 365 MET cc_start: 0.8212 (mmm) cc_final: 0.7490 (mmm) REVERT: B 745 PHE cc_start: 0.7561 (m-80) cc_final: 0.7111 (m-80) REVERT: B 816 LEU cc_start: 0.7840 (mt) cc_final: 0.7406 (mt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0627 time to fit residues: 7.3917 Evaluate side-chains 61 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.245 Evaluate side-chains 33 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.081 Fit side-chains REVERT: S 38 ASN cc_start: 0.8799 (m110) cc_final: 0.8482 (m110) REVERT: S 217 MET cc_start: 0.8027 (mtm) cc_final: 0.7826 (mtp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0716 time to fit residues: 2.7808 Evaluate side-chains 20 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.089 Evaluate side-chains 31 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.084 Fit side-chains REVERT: E 182 ASN cc_start: 0.7902 (m-40) cc_final: 0.6943 (p0) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0460 time to fit residues: 1.8360 Evaluate side-chains 21 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 383 optimal weight: 7.9990 chunk 343 optimal weight: 10.0000 chunk 165 optimal weight: 0.3980 chunk 203 optimal weight: 2.9990 chunk 255 optimal weight: 0.4980 chunk 145 optimal weight: 5.9990 chunk 398 optimal weight: 8.9990 chunk 370 optimal weight: 2.9990 chunk 280 optimal weight: 20.0000 chunk 307 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.078213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.065149 restraints weight = 28171.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.066567 restraints weight = 17375.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.067596 restraints weight = 12179.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.068319 restraints weight = 9206.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.068778 restraints weight = 7475.432| |-----------------------------------------------------------------------------| r_work (final): 0.3101 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.081582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.074327 restraints weight = 6072.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.076317 restraints weight = 3125.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.077675 restraints weight = 1849.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.078593 restraints weight = 1193.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.079214 restraints weight = 811.049| |-----------------------------------------------------------------------------| r_work (final): 0.2887 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.078947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.071211 restraints weight = 6187.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.073353 restraints weight = 3146.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.074758 restraints weight = 1862.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.075764 restraints weight = 1215.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.076489 restraints weight = 838.966| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 34206 Z= 0.100 Angle : 0.514 6.087 46530 Z= 0.271 Chirality : 0.045 0.169 4956 Planarity : 0.004 0.060 6021 Dihedral : 4.115 16.063 4575 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 4098 helix: -1.38 (0.26), residues: 327 sheet: 0.05 (0.14), residues: 1458 loop : -0.96 (0.13), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 216 TYR 0.021 0.001 TYR C 780 PHE 0.019 0.001 PHE E 176 TRP 0.006 0.001 TRP B 267 HIS 0.003 0.001 HIS F 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (34206) covalent geometry : angle 0.51388 / 0.27 (46530) hydrogen bonds : bond 0.03361 / 2.19 ( 981) hydrogen bonds : angle 5.71215 / 3.91 ( 2844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.220 Fit side-chains REVERT: F 50 MET cc_start: 0.7139 (ppp) cc_final: 0.5960 (ppp) REVERT: F 134 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7553 (mm-30) REVERT: F 174 LEU cc_start: 0.9068 (tp) cc_final: 0.8817 (tp) REVERT: F 365 MET cc_start: 0.8592 (mmm) cc_final: 0.8170 (mmm) REVERT: F 399 MET cc_start: 0.6608 (tmm) cc_final: 0.6194 (tmm) REVERT: F 691 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7379 (mm-30) REVERT: F 816 LEU cc_start: 0.8019 (mt) cc_final: 0.7610 (mt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0584 time to fit residues: 6.6854 Evaluate side-chains 60 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.253 Evaluate side-chains 35 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: S 30 ILE cc_start: 0.8040 (mp) cc_final: 0.7777 (mt) REVERT: S 38 ASN cc_start: 0.8780 (m110) cc_final: 0.8478 (m110) REVERT: S 45 ILE cc_start: 0.8839 (mp) cc_final: 0.8637 (tt) REVERT: S 177 GLU cc_start: 0.8671 (pp20) cc_final: 0.8436 (pp20) REVERT: S 217 MET cc_start: 0.8140 (mtm) cc_final: 0.7939 (mtp) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0554 time to fit residues: 2.4026 Evaluate side-chains 22 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.079 Evaluate side-chains 36 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.083 Fit side-chains REVERT: A 87 MET cc_start: 0.8749 (mpp) cc_final: 0.8539 (mpp) REVERT: A 182 ASN cc_start: 0.7703 (m-40) cc_final: 0.6905 (p0) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0366 time to fit residues: 1.7411 Evaluate side-chains 21 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 3 optimal weight: 6.9990 chunk 384 optimal weight: 9.9990 chunk 368 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 188 optimal weight: 7.9990 chunk 325 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 311 optimal weight: 0.0070 chunk 252 optimal weight: 10.0000 chunk 322 optimal weight: 8.9990 chunk 354 optimal weight: 6.9990 overall best weight: 3.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 38 ASN A 155 GLN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.076999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.064173 restraints weight = 28261.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.065561 restraints weight = 17250.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.066567 restraints weight = 11949.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.067268 restraints weight = 9035.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.067704 restraints weight = 7312.860| |-----------------------------------------------------------------------------| r_work (final): 0.3078 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.078452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.071009 restraints weight = 6426.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.073091 restraints weight = 3312.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.074513 restraints weight = 1944.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.075420 restraints weight = 1244.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.076069 restraints weight = 839.517| |-----------------------------------------------------------------------------| r_work (final): 0.2851 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.077120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.070306 restraints weight = 6223.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.072236 restraints weight = 3258.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.073523 restraints weight = 1944.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.074401 restraints weight = 1253.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.075060 restraints weight = 862.031| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34206 Z= 0.132 Angle : 0.523 5.736 46530 Z= 0.278 Chirality : 0.044 0.167 4956 Planarity : 0.004 0.071 6021 Dihedral : 4.217 15.883 4575 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.00 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.13), residues: 4098 helix: -1.17 (0.26), residues: 342 sheet: 0.01 (0.14), residues: 1428 loop : -0.93 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 736 TYR 0.015 0.001 TYR C 310 PHE 0.032 0.001 PHE C 323 TRP 0.006 0.001 TRP B 761 HIS 0.003 0.001 HIS B 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (34206) covalent geometry : angle 0.52273 / 0.28 (46530) hydrogen bonds : bond 0.03381 / 2.22 ( 981) hydrogen bonds : angle 5.47575 / 3.75 ( 2844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.156 Fit side-chains REVERT: F 50 MET cc_start: 0.6856 (ppp) cc_final: 0.5425 (ppp) REVERT: F 134 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7682 (mm-30) REVERT: F 174 LEU cc_start: 0.9139 (tp) cc_final: 0.8586 (tp) REVERT: F 365 MET cc_start: 0.8423 (mmm) cc_final: 0.7916 (mmm) REVERT: F 399 MET cc_start: 0.6734 (tmm) cc_final: 0.6140 (tmm) REVERT: F 594 CYS cc_start: 0.7557 (t) cc_final: 0.7315 (t) REVERT: F 597 CYS cc_start: 0.7956 (m) cc_final: 0.7461 (m) REVERT: F 816 LEU cc_start: 0.8081 (mt) cc_final: 0.7619 (mt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0616 time to fit residues: 7.3263 Evaluate side-chains 58 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.263 Evaluate side-chains 29 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.089 Fit side-chains REVERT: D 30 ILE cc_start: 0.8045 (mp) cc_final: 0.7659 (mt) REVERT: D 31 TYR cc_start: 0.8318 (t80) cc_final: 0.7906 (t80) REVERT: D 247 ASP cc_start: 0.7297 (p0) cc_final: 0.6805 (p0) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0587 time to fit residues: 2.0692 Evaluate side-chains 23 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.084 Evaluate side-chains 32 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.084 Fit side-chains REVERT: E 100 MET cc_start: 0.8746 (mtm) cc_final: 0.8355 (mtm) REVERT: E 210 ASP cc_start: 0.7782 (t0) cc_final: 0.7574 (t0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0398 time to fit residues: 1.6742 Evaluate side-chains 23 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 347 optimal weight: 0.3980 chunk 168 optimal weight: 9.9990 chunk 296 optimal weight: 0.9980 chunk 328 optimal weight: 9.9990 chunk 361 optimal weight: 0.0770 chunk 283 optimal weight: 0.6980 chunk 403 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 373 optimal weight: 2.9990 chunk 277 optimal weight: 0.0030 chunk 98 optimal weight: 5.9990 overall best weight: 0.4348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 ASN E 155 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.078743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.065765 restraints weight = 28288.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.067215 restraints weight = 17524.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.068262 restraints weight = 12170.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.068986 restraints weight = 9195.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.069482 restraints weight = 7441.730| |-----------------------------------------------------------------------------| r_work (final): 0.3115 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.080949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.073456 restraints weight = 6390.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.075512 restraints weight = 3311.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.076879 restraints weight = 1951.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.077826 restraints weight = 1247.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.078412 restraints weight = 850.252| |-----------------------------------------------------------------------------| r_work (final): 0.2902 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.078969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.071833 restraints weight = 6131.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.073873 restraints weight = 3161.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.075280 restraints weight = 1864.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.076175 restraints weight = 1189.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.076840 restraints weight = 813.813| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 34206 Z= 0.091 Angle : 0.509 6.634 46530 Z= 0.268 Chirality : 0.045 0.155 4956 Planarity : 0.004 0.045 6021 Dihedral : 4.037 16.817 4575 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.27 % Favored : 94.66 % Rotamer: Outliers : 0.08 % Allowed : 1.16 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 4098 helix: -1.14 (0.25), residues: 363 sheet: 0.01 (0.14), residues: 1464 loop : -0.87 (0.13), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 216 TYR 0.013 0.001 TYR C 310 PHE 0.027 0.001 PHE B 323 TRP 0.011 0.001 TRP D 120 HIS 0.003 0.000 HIS F 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (34206) covalent geometry : angle 0.50905 / 0.27 (46530) hydrogen bonds : bond 0.03012 / 1.97 ( 981) hydrogen bonds : angle 5.26617 / 3.61 ( 2844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: F 50 MET cc_start: 0.7150 (ppp) cc_final: 0.5829 (ppp) REVERT: F 134 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7772 (mm-30) REVERT: F 176 GLU cc_start: 0.7535 (mp0) cc_final: 0.6999 (mp0) REVERT: F 183 LYS cc_start: 0.8902 (mppt) cc_final: 0.8683 (mtmt) REVERT: F 314 MET cc_start: 0.5191 (mmm) cc_final: 0.4125 (tpp) REVERT: F 365 MET cc_start: 0.8509 (mmm) cc_final: 0.8027 (mmm) REVERT: F 594 CYS cc_start: 0.7654 (t) cc_final: 0.7453 (t) REVERT: F 597 CYS cc_start: 0.7824 (m) cc_final: 0.7224 (m) REVERT: F 762 MET cc_start: 0.7224 (ttp) cc_final: 0.6231 (ttp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0641 time to fit residues: 7.2549 Evaluate side-chains 56 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.323 Evaluate side-chains 27 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.095 Fit side-chains REVERT: D 30 ILE cc_start: 0.7954 (mp) cc_final: 0.7540 (mt) REVERT: D 247 ASP cc_start: 0.7335 (p0) cc_final: 0.6922 (p0) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0445 time to fit residues: 1.5640 Evaluate side-chains 22 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.087 Evaluate side-chains 33 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.087 Fit side-chains REVERT: E 100 MET cc_start: 0.8546 (mtm) cc_final: 0.8324 (mtm) REVERT: E 177 GLU cc_start: 0.8244 (tm-30) cc_final: 0.8004 (tm-30) REVERT: E 179 ASP cc_start: 0.8616 (t70) cc_final: 0.8347 (t70) REVERT: E 210 ASP cc_start: 0.7687 (t0) cc_final: 0.7363 (t0) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.0433 time to fit residues: 1.8448 Evaluate side-chains 21 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 277 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 219 optimal weight: 0.0000 chunk 50 optimal weight: 10.0000 chunk 155 optimal weight: 0.0870 chunk 377 optimal weight: 10.0000 chunk 384 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 overall best weight: 3.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 182 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.063636 restraints weight = 28443.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.065043 restraints weight = 17545.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.066040 restraints weight = 12205.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.066664 restraints weight = 9235.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.067177 restraints weight = 7557.578| |-----------------------------------------------------------------------------| r_work (final): 0.3062 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.079674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.072299 restraints weight = 6525.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.074315 restraints weight = 3361.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.075589 restraints weight = 1998.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.076610 restraints weight = 1311.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.077212 restraints weight = 888.049| |-----------------------------------------------------------------------------| r_work (final): 0.2876 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.077121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.070349 restraints weight = 6285.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.072276 restraints weight = 3267.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.073498 restraints weight = 1952.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.074409 restraints weight = 1270.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.075039 restraints weight = 870.694| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34206 Z= 0.141 Angle : 0.527 6.708 46530 Z= 0.280 Chirality : 0.044 0.156 4956 Planarity : 0.004 0.115 6021 Dihedral : 4.196 16.213 4575 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.00 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4098 helix: -1.06 (0.26), residues: 357 sheet: -0.11 (0.14), residues: 1464 loop : -0.90 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 216 TYR 0.013 0.001 TYR C 310 PHE 0.021 0.001 PHE B 323 TRP 0.011 0.001 TRP D 242 HIS 0.003 0.001 HIS C 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (34206) covalent geometry : angle 0.52715 / 0.28 (46530) hydrogen bonds : bond 0.03288 / 2.13 ( 981) hydrogen bonds : angle 5.29227 / 3.64 ( 2844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: F 50 MET cc_start: 0.7078 (ppp) cc_final: 0.5382 (ppp) REVERT: F 134 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7831 (mm-30) REVERT: F 183 LYS cc_start: 0.8917 (mppt) cc_final: 0.8641 (mtmm) REVERT: F 365 MET cc_start: 0.8465 (mmm) cc_final: 0.7994 (mmm) REVERT: F 436 ARG cc_start: 0.7977 (mtm110) cc_final: 0.7464 (mmm160) REVERT: F 594 CYS cc_start: 0.7718 (t) cc_final: 0.7489 (t) REVERT: F 597 CYS cc_start: 0.7917 (m) cc_final: 0.7410 (m) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0647 time to fit residues: 6.8952 Evaluate side-chains 57 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.252 Evaluate side-chains 28 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.085 Fit side-chains REVERT: D 30 ILE cc_start: 0.7874 (mp) cc_final: 0.7565 (mt) REVERT: D 62 LYS cc_start: 0.8670 (tttt) cc_final: 0.8437 (tttm) REVERT: D 124 MET cc_start: 0.8538 (mtt) cc_final: 0.8137 (mtt) REVERT: D 177 GLU cc_start: 0.8805 (pp20) cc_final: 0.8592 (pp20) REVERT: D 247 ASP cc_start: 0.7379 (p0) cc_final: 0.6849 (p0) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0600 time to fit residues: 2.0807 Evaluate side-chains 21 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.104 Evaluate side-chains 26 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.104 Fit side-chains REVERT: E 100 MET cc_start: 0.8647 (mtm) cc_final: 0.8432 (mtm) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0424 time to fit residues: 1.4750 Evaluate side-chains 20 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 324 optimal weight: 2.9990 chunk 361 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 370 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 301 optimal weight: 4.9990 chunk 393 optimal weight: 0.5980 chunk 153 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 214 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.064342 restraints weight = 28268.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.065761 restraints weight = 17237.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.066786 restraints weight = 11927.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067496 restraints weight = 8961.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.067976 restraints weight = 7226.561| |-----------------------------------------------------------------------------| r_work (final): 0.3081 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.079732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.072789 restraints weight = 6330.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.074786 restraints weight = 3259.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.076162 restraints weight = 1907.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.077012 restraints weight = 1201.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.077619 restraints weight = 804.057| |-----------------------------------------------------------------------------| r_work (final): 0.2873 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.077800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.070293 restraints weight = 6069.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.072321 restraints weight = 3147.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.073691 restraints weight = 1881.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.074628 restraints weight = 1229.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.075330 restraints weight = 855.531| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34206 Z= 0.116 Angle : 0.530 6.973 46530 Z= 0.280 Chirality : 0.045 0.254 4956 Planarity : 0.004 0.102 6021 Dihedral : 4.170 17.117 4575 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4098 helix: -1.07 (0.26), residues: 357 sheet: -0.10 (0.14), residues: 1464 loop : -0.91 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 216 TYR 0.021 0.001 TYR C 780 PHE 0.028 0.001 PHE C 323 TRP 0.010 0.001 TRP G 242 HIS 0.003 0.001 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (34206) covalent geometry : angle 0.53040 / 0.28 (46530) hydrogen bonds : bond 0.03116 / 2.01 ( 981) hydrogen bonds : angle 5.24803 / 3.60 ( 2844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.252 Fit side-chains REVERT: F 50 MET cc_start: 0.7018 (ppp) cc_final: 0.5367 (ppp) REVERT: F 176 GLU cc_start: 0.7688 (mp0) cc_final: 0.7183 (mp0) REVERT: F 183 LYS cc_start: 0.8902 (mppt) cc_final: 0.8650 (mtmm) REVERT: F 314 MET cc_start: 0.5391 (tpp) cc_final: 0.4077 (mtp) REVERT: F 365 MET cc_start: 0.8435 (mmm) cc_final: 0.7953 (mmm) REVERT: F 436 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7506 (mmm160) REVERT: F 590 MET cc_start: 0.9144 (tmm) cc_final: 0.8925 (tmm) REVERT: F 594 CYS cc_start: 0.7755 (t) cc_final: 0.7536 (t) REVERT: F 597 CYS cc_start: 0.7842 (m) cc_final: 0.7398 (m) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0681 time to fit residues: 7.1373 Evaluate side-chains 53 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.251 Evaluate side-chains 26 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.085 Fit side-chains REVERT: S 30 ILE cc_start: 0.8101 (mp) cc_final: 0.7724 (mt) REVERT: S 38 ASN cc_start: 0.8787 (m110) cc_final: 0.8477 (m110) REVERT: S 177 GLU cc_start: 0.8805 (pp20) cc_final: 0.8484 (pp20) REVERT: S 242 TRP cc_start: 0.7689 (m100) cc_final: 0.7316 (m-10) REVERT: S 247 ASP cc_start: 0.7370 (p0) cc_final: 0.7167 (p0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0441 time to fit residues: 1.4937 Evaluate side-chains 20 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.083 Evaluate side-chains 27 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.083 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0427 time to fit residues: 1.5200 Evaluate side-chains 20 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 198 optimal weight: 7.9990 chunk 81 optimal weight: 0.0070 chunk 22 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 391 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 308 optimal weight: 9.9990 overall best weight: 2.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 38 ASN E 182 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.076672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.063935 restraints weight = 28455.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065345 restraints weight = 17595.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.066377 restraints weight = 12275.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.067048 restraints weight = 9260.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067422 restraints weight = 7517.478| |-----------------------------------------------------------------------------| r_work (final): 0.3069 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.080125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.073315 restraints weight = 6140.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.075322 restraints weight = 3163.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.076649 restraints weight = 1838.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.077512 restraints weight = 1153.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.078123 restraints weight = 773.442| |-----------------------------------------------------------------------------| r_work (final): 0.2888 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.076717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.069941 restraints weight = 6020.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.071725 restraints weight = 3189.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.073022 restraints weight = 1934.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.073791 restraints weight = 1263.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.074466 restraints weight = 905.939| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34206 Z= 0.119 Angle : 0.533 8.028 46530 Z= 0.279 Chirality : 0.045 0.234 4956 Planarity : 0.004 0.080 6021 Dihedral : 4.174 17.293 4575 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.71 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 4098 helix: -1.08 (0.26), residues: 357 sheet: -0.09 (0.14), residues: 1479 loop : -0.90 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 216 TYR 0.015 0.001 TYR F 135 PHE 0.025 0.001 PHE B 323 TRP 0.009 0.001 TRP G 242 HIS 0.003 0.001 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (34206) covalent geometry : angle 0.53260 / 0.28 (46530) hydrogen bonds : bond 0.03099 / 2.00 ( 981) hydrogen bonds : angle 5.19790 / 3.57 ( 2844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.264 Fit side-chains REVERT: F 50 MET cc_start: 0.7092 (ppp) cc_final: 0.5346 (ppp) REVERT: F 183 LYS cc_start: 0.8900 (mppt) cc_final: 0.8651 (mtmm) REVERT: F 314 MET cc_start: 0.5392 (tpp) cc_final: 0.4235 (mtp) REVERT: F 365 MET cc_start: 0.8427 (mmm) cc_final: 0.7937 (mmm) REVERT: F 436 ARG cc_start: 0.7984 (mtm110) cc_final: 0.7673 (mmm160) REVERT: F 590 MET cc_start: 0.9102 (tmm) cc_final: 0.8870 (tmm) REVERT: F 594 CYS cc_start: 0.7794 (t) cc_final: 0.7543 (t) REVERT: F 597 CYS cc_start: 0.7940 (m) cc_final: 0.7495 (m) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0688 time to fit residues: 7.2431 Evaluate side-chains 53 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.308 Evaluate side-chains 26 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.110 Fit side-chains REVERT: S 30 ILE cc_start: 0.7972 (mp) cc_final: 0.7665 (mt) REVERT: S 38 ASN cc_start: 0.8788 (m-40) cc_final: 0.8476 (m110) REVERT: S 177 GLU cc_start: 0.8805 (pp20) cc_final: 0.8470 (pp20) REVERT: S 242 TRP cc_start: 0.7707 (m100) cc_final: 0.7227 (m-10) REVERT: S 247 ASP cc_start: 0.7455 (p0) cc_final: 0.7184 (p0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0414 time to fit residues: 1.4622 Evaluate side-chains 20 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.093 Evaluate side-chains 24 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0350 time to fit residues: 1.1842 Evaluate side-chains 21 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 175 optimal weight: 0.0970 chunk 46 optimal weight: 0.0370 chunk 240 optimal weight: 0.9980 chunk 351 optimal weight: 0.0980 chunk 66 optimal weight: 8.9990 chunk 271 optimal weight: 0.6980 chunk 365 optimal weight: 7.9990 chunk 150 optimal weight: 0.0050 chunk 136 optimal weight: 10.0000 chunk 392 optimal weight: 4.9990 chunk 210 optimal weight: 9.9990 overall best weight: 0.1870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 155 GLN F 747 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.079062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.066120 restraints weight = 28179.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067542 restraints weight = 17197.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.068561 restraints weight = 11917.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.069296 restraints weight = 9054.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.069816 restraints weight = 7298.184| |-----------------------------------------------------------------------------| r_work (final): 0.3123 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.083424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.076175 restraints weight = 6068.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.078261 restraints weight = 3133.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.079667 restraints weight = 1836.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.080574 restraints weight = 1155.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.081218 restraints weight = 776.271| |-----------------------------------------------------------------------------| r_work (final): 0.2943 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.082921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.075301 restraints weight = 6159.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.077367 restraints weight = 3192.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.078686 restraints weight = 1897.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.079613 restraints weight = 1254.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.080383 restraints weight = 881.623| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34206 Z= 0.094 Angle : 0.533 8.309 46530 Z= 0.276 Chirality : 0.045 0.249 4956 Planarity : 0.004 0.045 6021 Dihedral : 3.940 18.012 4575 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 0.08 % Allowed : 0.00 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.13), residues: 4098 helix: -0.98 (0.26), residues: 357 sheet: -0.01 (0.14), residues: 1491 loop : -0.81 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 216 TYR 0.010 0.001 TYR F 475 PHE 0.025 0.001 PHE C 323 TRP 0.009 0.001 TRP F 493 HIS 0.002 0.000 HIS F 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (34206) covalent geometry : angle 0.53318 / 0.28 (46530) hydrogen bonds : bond 0.02685 / 1.74 ( 981) hydrogen bonds : angle 5.02472 / 3.45 ( 2844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8196 Ramachandran restraints generated. 4098 Oldfield, 0 Emsley, 4098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.256 Fit side-chains REVERT: F 31 TYR cc_start: 0.6223 (m-10) cc_final: 0.5936 (m-10) REVERT: F 50 MET cc_start: 0.7188 (ppp) cc_final: 0.5594 (ppp) REVERT: F 176 GLU cc_start: 0.7508 (mp0) cc_final: 0.7165 (mp0) REVERT: F 314 MET cc_start: 0.5259 (tpp) cc_final: 0.4142 (mtp) REVERT: F 365 MET cc_start: 0.8422 (mmm) cc_final: 0.7914 (mmm) REVERT: F 436 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7529 (mmm160) REVERT: F 590 MET cc_start: 0.9156 (tmm) cc_final: 0.8930 (tmm) REVERT: F 594 CYS cc_start: 0.7736 (t) cc_final: 0.7495 (t) REVERT: F 597 CYS cc_start: 0.7848 (m) cc_final: 0.7303 (m) REVERT: F 621 SER cc_start: 0.8944 (m) cc_final: 0.8366 (t) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0753 time to fit residues: 8.1865 Evaluate side-chains 56 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.251 Evaluate side-chains 29 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: S 30 ILE cc_start: 0.7859 (mp) cc_final: 0.7506 (mt) REVERT: S 38 ASN cc_start: 0.8680 (m-40) cc_final: 0.8402 (m110) REVERT: S 177 GLU cc_start: 0.8752 (pp20) cc_final: 0.8398 (pp20) REVERT: S 242 TRP cc_start: 0.7741 (m100) cc_final: 0.7241 (m-10) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0406 time to fit residues: 1.5728 Evaluate side-chains 19 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.085 Evaluate side-chains 34 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.085 Fit side-chains REVERT: E 212 MET cc_start: 0.8230 (mmm) cc_final: 0.7616 (tpp) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.0342 time to fit residues: 1.5991 Evaluate side-chains 22 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 174 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 0.0370 chunk 335 optimal weight: 0.9980 chunk 243 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 85 optimal weight: 0.0020 chunk 177 optimal weight: 0.2980 chunk 193 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 359 optimal weight: 10.0000 overall best weight: 0.4266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 747 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.066614 restraints weight = 28169.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.068042 restraints weight = 17468.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.069072 restraints weight = 12204.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.069746 restraints weight = 9220.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.070251 restraints weight = 7512.663| |-----------------------------------------------------------------------------| r_work (final): 0.3129 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.084325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.076989 restraints weight = 6048.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.079043 restraints weight = 3108.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.080471 restraints weight = 1829.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.081392 restraints weight = 1158.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.082062 restraints weight = 782.107| |-----------------------------------------------------------------------------| r_work (final): 0.2966 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.081585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.073732 restraints weight = 6092.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.076040 restraints weight = 3000.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.077468 restraints weight = 1734.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.078497 restraints weight = 1110.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.079205 restraints weight = 755.080| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 34206 Z= 0.092 Angle : 0.525 8.389 46530 Z= 0.271 Chirality : 0.045 0.226 4956 Planarity : 0.004 0.043 6021 Dihedral : 3.881 16.728 4575 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 4098 helix: -1.00 (0.26), residues: 363 sheet: 0.08 (0.14), residues: 1464 loop : -0.75 (0.13), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 216 TYR 0.013 0.001 TYR B 780 PHE 0.025 0.001 PHE B 323 TRP 0.019 0.001 TRP D 12 HIS 0.002 0.000 HIS B 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (34206) covalent geometry : angle 0.52474 / 0.27 (46530) hydrogen bonds : bond 0.02641 / 1.70 ( 981) hydrogen bonds : angle 4.94817 / 3.39 ( 2844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.12 seconds wall clock time: 46 minutes 27.83 seconds (2787.83 seconds total)