Starting phenix.real_space_refine on Mon Aug 25 07:36:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgk_44516/08_2025/9bgk_44516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgk_44516/08_2025/9bgk_44516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bgk_44516/08_2025/9bgk_44516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgk_44516/08_2025/9bgk_44516.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgk_44516/08_2025/9bgk_44516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgk_44516/08_2025/9bgk_44516.cif" } resolution = 3.28 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= 0.002 sd= 0.034 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: 6 Type Number sf(0) Gaussians P 75 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 16461 2.51 5 N 4587 2.21 5 O 5144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26331 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 254 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "B" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 506 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "C" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 541 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "E" Number of atoms: 5589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5589 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 650} Chain: "F" Number of atoms: 9591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1189, 9591 Classifications: {'peptide': 1189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 1154} Chain breaks: 1 Chain: "G" Number of atoms: 9600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 9600 Classifications: {'peptide': 1190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 1155} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.91, per 1000 atoms: 0.19 Number of scatterers: 26331 At special positions: 0 Unit cell: (155.4, 148.74, 174.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 75 15.00 Mg 1 11.99 O 5144 8.00 N 4587 7.00 C 16461 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 76 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 932.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5828 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 26 sheets defined 46.1% alpha, 12.1% beta 5 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'E' and resid 24 through 30 Processing helix chain 'E' and resid 46 through 61 removed outlier: 3.978A pdb=" N ARG E 50 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 120 removed outlier: 3.822A pdb=" N ALA E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ILE E 117 " --> pdb=" O LEU E 113 " (cutoff:3.500A) Proline residue: E 118 - end of helix Processing helix chain 'E' and resid 184 through 187 Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.486A pdb=" N PHE E 199 " --> pdb=" O LYS E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 242 Processing helix chain 'E' and resid 245 through 249 removed outlier: 3.602A pdb=" N LEU E 248 " --> pdb=" O GLY E 245 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER E 249 " --> pdb=" O PHE E 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 245 through 249' Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.524A pdb=" N MET E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 266 Processing helix chain 'E' and resid 286 through 302 removed outlier: 3.516A pdb=" N GLY E 295 " --> pdb=" O ASN E 291 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA E 299 " --> pdb=" O GLY E 295 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 328 Processing helix chain 'E' and resid 361 through 369 Processing helix chain 'E' and resid 379 through 384 removed outlier: 3.647A pdb=" N ARG E 382 " --> pdb=" O TYR E 379 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU E 383 " --> pdb=" O PRO E 380 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP E 384 " --> pdb=" O GLU E 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 379 through 384' Processing helix chain 'E' and resid 391 through 411 removed outlier: 4.072A pdb=" N VAL E 395 " --> pdb=" O ASN E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 474 removed outlier: 3.523A pdb=" N GLU E 470 " --> pdb=" O LEU E 466 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU E 471 " --> pdb=" O GLU E 467 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP E 472 " --> pdb=" O ASP E 468 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY E 474 " --> pdb=" O GLU E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 482 Processing helix chain 'E' and resid 512 through 526 removed outlier: 3.555A pdb=" N ARG E 518 " --> pdb=" O ALA E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 542 removed outlier: 3.909A pdb=" N LEU E 535 " --> pdb=" O PRO E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 558 removed outlier: 3.554A pdb=" N ALA E 553 " --> pdb=" O ASN E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 removed outlier: 3.535A pdb=" N GLU E 568 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER E 570 " --> pdb=" O ASP E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 590 removed outlier: 3.869A pdb=" N GLN E 581 " --> pdb=" O SER E 577 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE E 582 " --> pdb=" O ASP E 578 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR E 583 " --> pdb=" O GLU E 579 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN E 589 " --> pdb=" O TRP E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 651 through 657 removed outlier: 3.873A pdb=" N PHE E 656 " --> pdb=" O GLU E 653 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP E 657 " --> pdb=" O ASN E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 676 removed outlier: 3.829A pdb=" N HIS E 675 " --> pdb=" O TYR E 671 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU E 676 " --> pdb=" O PRO E 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 671 through 676' Processing helix chain 'E' and resid 677 through 679 No H-bonds generated for 'chain 'E' and resid 677 through 679' Processing helix chain 'F' and resid 4 through 9 removed outlier: 3.989A pdb=" N THR F 9 " --> pdb=" O GLU F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 37 removed outlier: 3.890A pdb=" N LEU F 24 " --> pdb=" O SER F 20 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL F 25 " --> pdb=" O PRO F 21 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 3.752A pdb=" N ASN F 32 " --> pdb=" O GLU F 28 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS F 33 " --> pdb=" O PRO F 29 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE F 34 " --> pdb=" O LEU F 30 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 77 removed outlier: 3.521A pdb=" N GLN F 66 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL F 71 " --> pdb=" O MET F 67 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS F 76 " --> pdb=" O ARG F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 111 removed outlier: 3.549A pdb=" N VAL F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 130 removed outlier: 3.715A pdb=" N GLU F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 128 " --> pdb=" O GLN F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 143 removed outlier: 3.513A pdb=" N LEU F 143 " --> pdb=" O SER F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 157 removed outlier: 3.545A pdb=" N LEU F 150 " --> pdb=" O SER F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 178 removed outlier: 4.054A pdb=" N GLN F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS F 178 " --> pdb=" O GLY F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 207 removed outlier: 3.928A pdb=" N SER F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR F 194 " --> pdb=" O ARG F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 227 Processing helix chain 'F' and resid 229 through 234 removed outlier: 3.786A pdb=" N ARG F 233 " --> pdb=" O GLY F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 259 through 263 removed outlier: 3.806A pdb=" N ASP F 263 " --> pdb=" O PRO F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 286 removed outlier: 3.900A pdb=" N VAL F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU F 282 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 303 removed outlier: 3.768A pdb=" N ILE F 297 " --> pdb=" O LEU F 293 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA F 302 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN F 303 " --> pdb=" O THR F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 337 removed outlier: 3.726A pdb=" N GLU F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU F 331 " --> pdb=" O GLU F 327 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP F 336 " --> pdb=" O PHE F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 434 removed outlier: 3.610A pdb=" N PHE F 405 " --> pdb=" O LEU F 401 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 411 " --> pdb=" O ASN F 407 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE F 412 " --> pdb=" O GLU F 408 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU F 417 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR F 419 " --> pdb=" O TRP F 415 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET F 420 " --> pdb=" O PHE F 416 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG F 421 " --> pdb=" O LEU F 417 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS F 422 " --> pdb=" O GLY F 418 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY F 433 " --> pdb=" O GLU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.727A pdb=" N VAL F 452 " --> pdb=" O PHE F 448 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU F 455 " --> pdb=" O ALA F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 471 removed outlier: 3.934A pdb=" N SER F 471 " --> pdb=" O ALA F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 497 removed outlier: 3.706A pdb=" N HIS F 496 " --> pdb=" O SER F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 536 removed outlier: 3.622A pdb=" N VAL F 533 " --> pdb=" O LEU F 529 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY F 536 " --> pdb=" O MET F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 564 removed outlier: 3.564A pdb=" N LEU F 564 " --> pdb=" O LEU F 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 587 Processing helix chain 'F' and resid 604 through 616 removed outlier: 4.065A pdb=" N LEU F 608 " --> pdb=" O ARG F 604 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU F 611 " --> pdb=" O PHE F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 629 removed outlier: 3.866A pdb=" N ILE F 625 " --> pdb=" O SER F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 657 removed outlier: 3.846A pdb=" N LYS F 646 " --> pdb=" O SER F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 674 No H-bonds generated for 'chain 'F' and resid 672 through 674' Processing helix chain 'F' and resid 675 through 693 removed outlier: 3.723A pdb=" N PHE F 681 " --> pdb=" O ASN F 677 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE F 693 " --> pdb=" O TRP F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 704 through 709 Processing helix chain 'F' and resid 714 through 723 removed outlier: 3.540A pdb=" N LYS F 718 " --> pdb=" O ASP F 714 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU F 723 " --> pdb=" O HIS F 719 " (cutoff:3.500A) Processing helix chain 'F' and resid 734 through 738 removed outlier: 3.634A pdb=" N ALA F 738 " --> pdb=" O SER F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 789 through 808 removed outlier: 3.781A pdb=" N ASN F 793 " --> pdb=" O SER F 789 " (cutoff:3.500A) Processing helix chain 'F' and resid 811 through 824 Processing helix chain 'F' and resid 827 through 836 removed outlier: 3.509A pdb=" N SER F 831 " --> pdb=" O SER F 827 " (cutoff:3.500A) Processing helix chain 'F' and resid 839 through 855 removed outlier: 3.844A pdb=" N SER F 843 " --> pdb=" O SER F 839 " (cutoff:3.500A) Processing helix chain 'F' and resid 874 through 880 Processing helix chain 'F' and resid 889 through 901 removed outlier: 3.940A pdb=" N VAL F 893 " --> pdb=" O SER F 889 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 894 " --> pdb=" O HIS F 890 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER F 901 " --> pdb=" O ASN F 897 " (cutoff:3.500A) Processing helix chain 'F' and resid 909 through 937 removed outlier: 3.829A pdb=" N ARG F 913 " --> pdb=" O ASP F 909 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE F 916 " --> pdb=" O VAL F 912 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET F 927 " --> pdb=" O ASN F 923 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU F 928 " --> pdb=" O LYS F 924 " (cutoff:3.500A) Processing helix chain 'F' and resid 944 through 960 removed outlier: 3.557A pdb=" N ILE F 953 " --> pdb=" O GLU F 949 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG F 954 " --> pdb=" O TRP F 950 " (cutoff:3.500A) Processing helix chain 'F' and resid 1000 through 1002 No H-bonds generated for 'chain 'F' and resid 1000 through 1002' Processing helix chain 'F' and resid 1010 through 1013 removed outlier: 3.712A pdb=" N CYS F1013 " --> pdb=" O GLU F1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1010 through 1013' Processing helix chain 'F' and resid 1014 through 1019 Processing helix chain 'F' and resid 1024 through 1031 Processing helix chain 'F' and resid 1052 through 1069 removed outlier: 3.780A pdb=" N GLN F1060 " --> pdb=" O ALA F1056 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA F1061 " --> pdb=" O LEU F1057 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU F1063 " --> pdb=" O GLU F1059 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F1064 " --> pdb=" O GLN F1060 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL F1065 " --> pdb=" O ALA F1061 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR F1067 " --> pdb=" O GLU F1063 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE F1069 " --> pdb=" O VAL F1065 " (cutoff:3.500A) Processing helix chain 'F' and resid 1112 through 1127 removed outlier: 3.949A pdb=" N SER F1116 " --> pdb=" O SER F1112 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU F1125 " --> pdb=" O LEU F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1176 through 1187 Processing helix chain 'G' and resid 4 through 9 Processing helix chain 'G' and resid 20 through 36 removed outlier: 3.865A pdb=" N LEU G 24 " --> pdb=" O SER G 20 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL G 25 " --> pdb=" O PRO G 21 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Proline residue: G 29 - end of helix removed outlier: 3.596A pdb=" N GLU G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL G 36 " --> pdb=" O ASN G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 76 removed outlier: 3.565A pdb=" N GLN G 66 " --> pdb=" O PHE G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 111 removed outlier: 3.676A pdb=" N VAL G 98 " --> pdb=" O SER G 94 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU G 106 " --> pdb=" O LYS G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 130 removed outlier: 3.530A pdb=" N GLU G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR G 127 " --> pdb=" O GLU G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 142 removed outlier: 3.610A pdb=" N LEU G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 157 Processing helix chain 'G' and resid 162 through 178 removed outlier: 3.878A pdb=" N GLN G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA G 167 " --> pdb=" O ARG G 163 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG G 177 " --> pdb=" O SER G 173 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS G 178 " --> pdb=" O GLY G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 208 removed outlier: 3.896A pdb=" N SER G 187 " --> pdb=" O GLU G 183 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG G 190 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY G 193 " --> pdb=" O ASN G 189 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG G 197 " --> pdb=" O GLY G 193 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN G 198 " --> pdb=" O TYR G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 227 Processing helix chain 'G' and resid 229 through 234 removed outlier: 4.044A pdb=" N ARG G 233 " --> pdb=" O GLY G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 250 removed outlier: 3.536A pdb=" N LYS G 249 " --> pdb=" O SER G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 287 Processing helix chain 'G' and resid 293 through 304 Processing helix chain 'G' and resid 312 through 316 Processing helix chain 'G' and resid 318 through 321 Processing helix chain 'G' and resid 322 through 336 removed outlier: 3.674A pdb=" N ARG G 326 " --> pdb=" O PHE G 322 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU G 327 " --> pdb=" O GLU G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 401 through 433 removed outlier: 3.799A pdb=" N LEU G 417 " --> pdb=" O TYR G 413 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS G 422 " --> pdb=" O GLY G 418 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY G 433 " --> pdb=" O GLU G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 443 through 459 removed outlier: 4.523A pdb=" N GLN G 449 " --> pdb=" O GLU G 445 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU G 450 " --> pdb=" O GLY G 446 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE G 459 " --> pdb=" O LEU G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 472 Processing helix chain 'G' and resid 474 through 478 removed outlier: 3.976A pdb=" N LEU G 477 " --> pdb=" O THR G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 535 removed outlier: 3.528A pdb=" N VAL G 528 " --> pdb=" O SER G 524 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU G 529 " --> pdb=" O PRO G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 558 through 564 removed outlier: 3.943A pdb=" N GLU G 562 " --> pdb=" O LYS G 558 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG G 563 " --> pdb=" O TYR G 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 568 removed outlier: 4.006A pdb=" N LEU G 568 " --> pdb=" O GLY G 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 565 through 568' Processing helix chain 'G' and resid 572 through 587 Processing helix chain 'G' and resid 604 through 616 removed outlier: 4.018A pdb=" N LEU G 608 " --> pdb=" O ARG G 604 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR G 615 " --> pdb=" O LEU G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 621 through 629 removed outlier: 3.593A pdb=" N ILE G 625 " --> pdb=" O SER G 621 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 626 " --> pdb=" O SER G 622 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN G 627 " --> pdb=" O HIS G 623 " (cutoff:3.500A) Processing helix chain 'G' and resid 636 through 656 removed outlier: 3.683A pdb=" N VAL G 640 " --> pdb=" O GLU G 636 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS G 646 " --> pdb=" O SER G 642 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER G 650 " --> pdb=" O LYS G 646 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE G 651 " --> pdb=" O LEU G 647 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER G 656 " --> pdb=" O LYS G 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 672 through 674 No H-bonds generated for 'chain 'G' and resid 672 through 674' Processing helix chain 'G' and resid 675 through 693 removed outlier: 3.683A pdb=" N CYS G 685 " --> pdb=" O PHE G 681 " (cutoff:3.500A) Processing helix chain 'G' and resid 713 through 723 removed outlier: 3.770A pdb=" N SER G 717 " --> pdb=" O TYR G 713 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS G 719 " --> pdb=" O GLU G 715 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU G 720 " --> pdb=" O ILE G 716 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN G 721 " --> pdb=" O SER G 717 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU G 723 " --> pdb=" O HIS G 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 733 through 737 Processing helix chain 'G' and resid 747 through 751 Processing helix chain 'G' and resid 790 through 808 removed outlier: 3.854A pdb=" N GLN G 794 " --> pdb=" O HIS G 790 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN G 807 " --> pdb=" O SER G 803 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY G 808 " --> pdb=" O LEU G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 811 through 825 Processing helix chain 'G' and resid 827 through 836 removed outlier: 4.024A pdb=" N GLN G 833 " --> pdb=" O GLU G 829 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN G 834 " --> pdb=" O ARG G 830 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR G 835 " --> pdb=" O SER G 831 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS G 836 " --> pdb=" O LEU G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 839 through 855 removed outlier: 3.889A pdb=" N SER G 843 " --> pdb=" O SER G 839 " (cutoff:3.500A) Processing helix chain 'G' and resid 873 through 879 removed outlier: 4.384A pdb=" N ILE G 877 " --> pdb=" O GLY G 873 " (cutoff:3.500A) Processing helix chain 'G' and resid 890 through 901 Processing helix chain 'G' and resid 909 through 939 removed outlier: 3.706A pdb=" N ARG G 913 " --> pdb=" O ASP G 909 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN G 920 " --> pdb=" O PHE G 916 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET G 927 " --> pdb=" O ASN G 923 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU G 928 " --> pdb=" O LYS G 924 " (cutoff:3.500A) Processing helix chain 'G' and resid 944 through 960 removed outlier: 3.542A pdb=" N TRP G 950 " --> pdb=" O ASP G 946 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 954 " --> pdb=" O TRP G 950 " (cutoff:3.500A) Processing helix chain 'G' and resid 1000 through 1002 No H-bonds generated for 'chain 'G' and resid 1000 through 1002' Processing helix chain 'G' and resid 1009 through 1013 Processing helix chain 'G' and resid 1014 through 1019 removed outlier: 3.618A pdb=" N LEU G1018 " --> pdb=" O SER G1014 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL G1019 " --> pdb=" O LEU G1015 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1014 through 1019' Processing helix chain 'G' and resid 1024 through 1032 removed outlier: 3.731A pdb=" N PHE G1028 " --> pdb=" O VAL G1024 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU G1029 " --> pdb=" O ARG G1025 " (cutoff:3.500A) Processing helix chain 'G' and resid 1046 through 1051 Processing helix chain 'G' and resid 1052 through 1071 removed outlier: 3.655A pdb=" N VAL G1065 " --> pdb=" O ALA G1061 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE G1069 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP G1070 " --> pdb=" O LEU G1066 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE G1071 " --> pdb=" O THR G1067 " (cutoff:3.500A) Processing helix chain 'G' and resid 1111 through 1126 Processing helix chain 'G' and resid 1176 through 1189 removed outlier: 3.523A pdb=" N HIS G1188 " --> pdb=" O ILE G1184 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS G1189 " --> pdb=" O LYS G1185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 270 through 275 removed outlier: 7.072A pdb=" N SER E 270 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE E 21 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS E 272 " --> pdb=" O GLU E 19 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU E 17 " --> pdb=" O GLN E 274 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E 14 " --> pdb=" O LEU E 509 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR E 16 " --> pdb=" O GLN E 507 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN E 507 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N ILE E 18 " --> pdb=" O GLY E 505 " (cutoff:3.500A) removed outlier: 13.562A pdb=" N GLY E 505 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 20.883A pdb=" N GLN E 20 " --> pdb=" O ASP E 503 " (cutoff:3.500A) removed outlier: 24.587A pdb=" N ASP E 503 " --> pdb=" O GLN E 20 " (cutoff:3.500A) removed outlier: 31.870A pdb=" N SER E 22 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 35.424A pdb=" N PHE E 501 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU E 638 " --> pdb=" O THR E 504 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N HIS E 637 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ALA E 622 " --> pdb=" O HIS E 637 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR E 639 " --> pdb=" O TYR E 620 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR E 620 " --> pdb=" O TYR E 639 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 270 through 275 removed outlier: 7.072A pdb=" N SER E 270 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE E 21 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS E 272 " --> pdb=" O GLU E 19 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU E 17 " --> pdb=" O GLN E 274 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E 14 " --> pdb=" O LEU E 509 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR E 16 " --> pdb=" O GLN E 507 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN E 507 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N ILE E 18 " --> pdb=" O GLY E 505 " (cutoff:3.500A) removed outlier: 13.562A pdb=" N GLY E 505 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 20.883A pdb=" N GLN E 20 " --> pdb=" O ASP E 503 " (cutoff:3.500A) removed outlier: 24.587A pdb=" N ASP E 503 " --> pdb=" O GLN E 20 " (cutoff:3.500A) removed outlier: 31.870A pdb=" N SER E 22 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 35.424A pdb=" N PHE E 501 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP E 497 " --> pdb=" O TRP E 492 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE E 490 " --> pdb=" O ALA E 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 33 through 35 removed outlier: 3.994A pdb=" N TYR E 35 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL E 79 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS E 66 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.622A pdb=" N ALA E 95 " --> pdb=" O SER E 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 136 through 144 removed outlier: 6.670A pdb=" N TYR E 137 " --> pdb=" O ILE E 159 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ILE E 159 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 139 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL E 157 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS E 141 " --> pdb=" O THR E 155 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N TYR E 152 " --> pdb=" O PRO E 182 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP E 160 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS E 170 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR E 220 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 236 through 237 removed outlier: 3.526A pdb=" N ILE E 632 " --> pdb=" O ILE E 236 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 334 through 335 removed outlier: 6.458A pdb=" N VAL E 306 " --> pdb=" O ILE E 346 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE E 348 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N CYS E 308 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 43 through 48 removed outlier: 5.993A pdb=" N ALA F 43 " --> pdb=" O ILE F 539 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLY F 541 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU F 45 " --> pdb=" O GLY F 541 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N SER F 543 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU F 47 " --> pdb=" O SER F 543 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL F 268 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE F 270 " --> pdb=" O TYR F 89 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP F 272 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU F 88 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU F 242 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N TYR F 90 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 251 through 252 Processing sheet with id=AB1, first strand: chain 'F' and resid 291 through 292 removed outlier: 3.546A pdb=" N VAL F 354 " --> pdb=" O VAL F 504 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 342 through 344 removed outlier: 7.159A pdb=" N ASN F 343 " --> pdb=" O ILE F 385 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 595 through 601 removed outlier: 6.388A pdb=" N ILE F 774 " --> pdb=" O PHE F 869 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASP F 871 " --> pdb=" O ILE F 774 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU F 776 " --> pdb=" O ASP F 871 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER F 773 " --> pdb=" O TYR F 662 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET F 663 " --> pdb=" O VAL F 729 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N SER F 731 " --> pdb=" O MET F 663 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER F 665 " --> pdb=" O SER F 731 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 744 through 745 removed outlier: 3.683A pdb=" N TYR F 744 " --> pdb=" O SER F 769 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 974 through 975 Processing sheet with id=AB6, first strand: chain 'F' and resid 997 through 998 removed outlier: 3.701A pdb=" N GLU F 997 " --> pdb=" O GLN F 986 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 1072 through 1073 removed outlier: 3.686A pdb=" N ASN F1086 " --> pdb=" O LEU F1099 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE F1097 " --> pdb=" O VAL F1088 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F1134 " --> pdb=" O ASP F1100 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 43 through 47 removed outlier: 3.767A pdb=" N ILE G 270 " --> pdb=" O TYR G 89 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP G 272 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU G 88 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU G 242 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N TYR G 90 " --> pdb=" O LEU G 242 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 113 through 114 Processing sheet with id=AC1, first strand: chain 'G' and resid 251 through 252 removed outlier: 3.511A pdb=" N PHE G 251 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 291 through 292 removed outlier: 3.654A pdb=" N VAL G 354 " --> pdb=" O VAL G 504 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 341 through 344 removed outlier: 6.374A pdb=" N ALA G 341 " --> pdb=" O ASN G 383 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE G 385 " --> pdb=" O ALA G 341 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASN G 343 " --> pdb=" O ILE G 385 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 595 through 601 removed outlier: 6.457A pdb=" N ILE G 774 " --> pdb=" O PHE G 869 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ASP G 871 " --> pdb=" O ILE G 774 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU G 776 " --> pdb=" O ASP G 871 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER G 773 " --> pdb=" O TYR G 662 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 756 through 757 Processing sheet with id=AC6, first strand: chain 'G' and resid 974 through 976 Processing sheet with id=AC7, first strand: chain 'G' and resid 997 through 998 Processing sheet with id=AC8, first strand: chain 'G' and resid 1072 through 1075 removed outlier: 3.543A pdb=" N THR G1072 " --> pdb=" O ILE G1089 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE G1089 " --> pdb=" O THR G1072 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN G1086 " --> pdb=" O LEU G1099 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU G1099 " --> pdb=" O ASN G1086 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL G1088 " --> pdb=" O ILE G1097 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE G1097 " --> pdb=" O VAL G1088 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN G1135 " --> pdb=" O ILE G1164 " (cutoff:3.500A) 962 hydrogen bonds defined for protein. 2733 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 4.98 Time building geometry restraints manager: 2.48 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: 8502 1.34 - 1.47: 6741 1.47 - 1.59: 11554 1.59 - 1.72: 146 1.72 - 1.84: 99 Bond restraints: 27042 Sorted by residual: bond pdb=" N GLN F 940 " pdb=" CA GLN F 940 " ideal model delta sigma weight residual 1.462 1.489 -0.027 9.50e-03 1.11e+04 8.13e+00 bond pdb=" N ASN F 939 " pdb=" CA ASN F 939 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.27e-02 6.20e+03 5.67e+00 bond pdb=" CA ALA F 942 " pdb=" CB ALA F 942 " ideal model delta sigma weight residual 1.532 1.497 0.034 1.74e-02 3.30e+03 3.85e+00 bond pdb=" P DT C 2 " pdb=" OP2 DT C 2 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" P DC B 25 " pdb=" OP1 DC B 25 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.51e+00 ... (remaining 27037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 35896 1.90 - 3.80: 832 3.80 - 5.69: 119 5.69 - 7.59: 34 7.59 - 9.49: 9 Bond angle restraints: 36890 Sorted by residual: angle pdb=" CA TYR E 363 " pdb=" CB TYR E 363 " pdb=" CG TYR E 363 " ideal model delta sigma weight residual 113.90 122.65 -8.75 1.80e+00 3.09e-01 2.36e+01 angle pdb=" C SER F 642 " pdb=" N TRP F 643 " pdb=" CA TRP F 643 " ideal model delta sigma weight residual 120.58 112.81 7.77 1.71e+00 3.42e-01 2.06e+01 angle pdb=" C LYS F1102 " pdb=" N TYR F1103 " pdb=" CA TYR F1103 " ideal model delta sigma weight residual 121.54 130.18 -8.64 1.91e+00 2.74e-01 2.04e+01 angle pdb=" CA CYS E 36 " pdb=" CB CYS E 36 " pdb=" SG CYS E 36 " ideal model delta sigma weight residual 114.40 123.89 -9.49 2.30e+00 1.89e-01 1.70e+01 angle pdb=" N TRP F1104 " pdb=" CA TRP F1104 " pdb=" CB TRP F1104 " ideal model delta sigma weight residual 109.94 115.24 -5.30 1.44e+00 4.82e-01 1.35e+01 ... (remaining 36885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 15561 35.87 - 71.73: 519 71.73 - 107.60: 18 107.60 - 143.46: 0 143.46 - 179.33: 4 Dihedral angle restraints: 16102 sinusoidal: 7092 harmonic: 9010 Sorted by residual: dihedral pdb=" CA GLU G1094 " pdb=" C GLU G1094 " pdb=" N GLN G1095 " pdb=" CA GLN G1095 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA VAL G 746 " pdb=" C VAL G 746 " pdb=" N ASN G 747 " pdb=" CA ASN G 747 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ALA E 75 " pdb=" C ALA E 75 " pdb=" N CYS E 76 " pdb=" CA CYS E 76 " ideal model delta harmonic sigma weight residual 180.00 157.32 22.68 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 16099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 3990 0.127 - 0.254: 40 0.254 - 0.381: 1 0.381 - 0.508: 2 0.508 - 0.635: 10 Chirality restraints: 4043 Sorted by residual: chirality pdb=" P DG C 1 " pdb=" OP1 DG C 1 " pdb=" OP2 DG C 1 " pdb=" O5' DG C 1 " both_signs ideal model delta sigma weight residual True 2.35 2.98 -0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CB ILE E 117 " pdb=" CA ILE E 117 " pdb=" CG1 ILE E 117 " pdb=" CG2 ILE E 117 " both_signs ideal model delta sigma weight residual False 2.64 2.01 0.63 2.00e-01 2.50e+01 9.95e+00 chirality pdb=" P DA C 5 " pdb=" OP1 DA C 5 " pdb=" OP2 DA C 5 " pdb=" O5' DA C 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.26e+00 ... (remaining 4040 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 639 " 0.030 2.00e-02 2.50e+03 4.09e-02 2.93e+01 pdb=" CG PHE F 639 " -0.094 2.00e-02 2.50e+03 pdb=" CD1 PHE F 639 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE F 639 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE F 639 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 639 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE F 639 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F1104 " 0.029 2.00e-02 2.50e+03 3.11e-02 2.41e+01 pdb=" CG TRP F1104 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP F1104 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP F1104 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F1104 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F1104 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F1104 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP F1104 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F1104 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F1104 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 47 " -0.353 9.50e-02 1.11e+02 1.59e-01 1.58e+01 pdb=" NE ARG E 47 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG E 47 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 47 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG E 47 " -0.009 2.00e-02 2.50e+03 ... (remaining 4515 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 531 2.69 - 3.24: 24363 3.24 - 3.80: 36729 3.80 - 4.35: 49463 4.35 - 4.90: 81747 Nonbonded interactions: 192833 Sorted by model distance: nonbonded pdb=" NH1 ARG G 846 " pdb=" OE1 GLU G 881 " model vdw 2.140 3.120 nonbonded pdb=" OG SER E 9 " pdb=" NE2 GLN E 274 " model vdw 2.204 3.120 nonbonded pdb=" O ASP F 787 " pdb=" NH2 ARG G 163 " model vdw 2.214 3.120 nonbonded pdb=" OE1 GLU F 230 " pdb=" OG1 THR F 254 " model vdw 2.216 3.040 nonbonded pdb=" O ASP F1085 " pdb=" ND2 ASN F1086 " model vdw 2.219 3.120 ... (remaining 192828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 77 or resid 79 through 1190)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.990 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 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 0.056 27043 Z= 0.182 Angle : 0.702 9.489 36892 Z= 0.385 Chirality : 0.054 0.635 4043 Planarity : 0.006 0.159 4518 Dihedral : 16.629 179.325 10271 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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 aren not related in a simple way. whole: -1.33 (0.15), residues: 3058 helix: 0.24 (0.15), residues: 1233 sheet: 0.13 (0.26), residues: 443 loop : -2.34 (0.15), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 47 TYR 0.062 0.002 TYR E 363 PHE 0.094 0.002 PHE F 639 TRP 0.085 0.002 TRP F1104 HIS 0.011 0.001 HIS E 413 Details of bonding type rmsd covalent geometry : bond 0.00333 (27042) covalent geometry : angle 0.70113 (36890) SS BOND : bond 0.00468 ( 1) SS BOND : angle 4.29890 ( 2) hydrogen bonds : bond 0.19200 ( 970) hydrogen bonds : angle 6.67761 ( 2755) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 58 THR cc_start: 0.7452 (m) cc_final: 0.7002 (p) REVERT: E 240 LYS cc_start: 0.7425 (mmtt) cc_final: 0.7212 (mptt) REVERT: E 241 GLU cc_start: 0.7338 (mp0) cc_final: 0.6977 (mp0) REVERT: E 265 TYR cc_start: 0.6319 (m-10) cc_final: 0.6021 (m-10) REVERT: E 302 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7114 (tm-30) REVERT: E 348 ILE cc_start: 0.7561 (mt) cc_final: 0.7285 (mt) REVERT: E 486 ARG cc_start: 0.6904 (mtt180) cc_final: 0.6703 (mtt90) REVERT: E 545 SER cc_start: 0.7636 (t) cc_final: 0.7224 (p) REVERT: E 558 TRP cc_start: 0.7023 (t-100) cc_final: 0.6726 (t-100) REVERT: E 608 SER cc_start: 0.8134 (m) cc_final: 0.7713 (t) REVERT: E 654 ASN cc_start: 0.7548 (m-40) cc_final: 0.7303 (m110) REVERT: F 93 ASP cc_start: 0.7989 (t0) cc_final: 0.7654 (t0) REVERT: F 162 GLU cc_start: 0.6438 (mt-10) cc_final: 0.6190 (mt-10) REVERT: F 561 ASN cc_start: 0.8232 (m-40) cc_final: 0.7982 (m-40) REVERT: F 951 GLN cc_start: 0.6522 (mm-40) cc_final: 0.6039 (mm-40) REVERT: F 952 ASP cc_start: 0.5954 (m-30) cc_final: 0.5735 (m-30) REVERT: F 989 LEU cc_start: 0.7535 (mt) cc_final: 0.7274 (mt) REVERT: F 1001 ARG cc_start: 0.6110 (mtt90) cc_final: 0.5194 (mtt90) REVERT: F 1025 ARG cc_start: 0.7193 (ttm110) cc_final: 0.6719 (ttm110) REVERT: F 1059 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6795 (mt-10) REVERT: G 24 LEU cc_start: 0.7851 (mt) cc_final: 0.7529 (mt) REVERT: G 72 ARG cc_start: 0.6917 (ttm170) cc_final: 0.6615 (ttm-80) REVERT: G 189 ASN cc_start: 0.6664 (m110) cc_final: 0.6297 (m-40) REVERT: G 306 ASP cc_start: 0.7276 (p0) cc_final: 0.6995 (p0) REVERT: G 558 LYS cc_start: 0.8325 (ttmm) cc_final: 0.8117 (ttmm) REVERT: G 681 PHE cc_start: 0.7891 (t80) cc_final: 0.7675 (t80) REVERT: G 688 LYS cc_start: 0.7162 (ttpp) cc_final: 0.6935 (ttpp) REVERT: G 772 ASP cc_start: 0.6356 (p0) cc_final: 0.5700 (p0) REVERT: G 928 LEU cc_start: 0.8292 (mt) cc_final: 0.7944 (mt) REVERT: G 1030 ARG cc_start: 0.7879 (ttp-170) cc_final: 0.6588 (ttp-170) REVERT: G 1033 PHE cc_start: 0.7156 (m-10) cc_final: 0.6885 (m-10) REVERT: G 1039 LYS cc_start: 0.7609 (mtmt) cc_final: 0.7396 (mtpp) REVERT: G 1059 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7179 (tp30) outliers start: 0 outliers final: 0 residues processed: 473 average time/residue: 0.1799 time to fit residues: 127.5966 Evaluate side-chains 416 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.0770 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0020 chunk 298 optimal weight: 10.0000 overall best weight: 0.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN F 308 GLN F 566 ASN F 842 GLN ** F1060 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1086 ASN G 32 ASN G 70 GLN G 124 GLN G 337 ASN ** G 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1078 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.180776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148540 restraints weight = 36984.896| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.16 r_work: 0.3649 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27043 Z= 0.122 Angle : 0.556 7.708 36892 Z= 0.301 Chirality : 0.041 0.277 4043 Planarity : 0.004 0.056 4518 Dihedral : 15.813 173.352 4169 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.85 % Allowed : 6.69 % Favored : 92.46 % 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 aren not related in a simple way. whole: -0.77 (0.15), residues: 3058 helix: 0.95 (0.15), residues: 1262 sheet: 0.24 (0.25), residues: 458 loop : -2.31 (0.15), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 47 TYR 0.020 0.001 TYR E 363 PHE 0.026 0.001 PHE G 684 TRP 0.042 0.001 TRP F1104 HIS 0.007 0.001 HIS F 938 Details of bonding type rmsd covalent geometry : bond 0.00238 (27042) covalent geometry : angle 0.55567 (36890) SS BOND : bond 0.00140 ( 1) SS BOND : angle 3.72701 ( 2) hydrogen bonds : bond 0.05558 ( 970) hydrogen bonds : angle 4.58969 ( 2755) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 425 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: E 58 THR cc_start: 0.7264 (m) cc_final: 0.6745 (p) REVERT: E 240 LYS cc_start: 0.7095 (mmtt) cc_final: 0.6889 (mmtt) REVERT: E 241 GLU cc_start: 0.7484 (mp0) cc_final: 0.7011 (mp0) REVERT: E 263 GLN cc_start: 0.7773 (pp30) cc_final: 0.7184 (pp30) REVERT: E 301 LYS cc_start: 0.7856 (mtpp) cc_final: 0.7598 (ttmm) REVERT: E 302 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6947 (tm-30) REVERT: E 348 ILE cc_start: 0.7382 (mt) cc_final: 0.7102 (mt) REVERT: E 412 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7557 (mmmt) REVERT: E 486 ARG cc_start: 0.6792 (mtt180) cc_final: 0.6498 (mtt90) REVERT: E 566 PHE cc_start: 0.7884 (t80) cc_final: 0.7626 (t80) REVERT: E 654 ASN cc_start: 0.7602 (m-40) cc_final: 0.7310 (m110) REVERT: F 31 LYS cc_start: 0.7267 (tppt) cc_final: 0.6999 (tppt) REVERT: F 93 ASP cc_start: 0.7933 (t0) cc_final: 0.7605 (t0) REVERT: F 162 GLU cc_start: 0.6484 (mt-10) cc_final: 0.6157 (mt-10) REVERT: F 199 LEU cc_start: 0.7707 (tt) cc_final: 0.7293 (tp) REVERT: F 203 LEU cc_start: 0.7884 (tt) cc_final: 0.7442 (mp) REVERT: F 420 MET cc_start: 0.7255 (mmt) cc_final: 0.7015 (mmm) REVERT: F 951 GLN cc_start: 0.6568 (mm-40) cc_final: 0.6086 (mm-40) REVERT: F 984 ARG cc_start: 0.7793 (mtt180) cc_final: 0.7588 (mtt-85) REVERT: F 1001 ARG cc_start: 0.6200 (mtt90) cc_final: 0.5625 (mtt90) REVERT: F 1059 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6681 (mt-10) REVERT: G 65 GLN cc_start: 0.7418 (tp-100) cc_final: 0.7140 (tp40) REVERT: G 72 ARG cc_start: 0.6860 (ttm170) cc_final: 0.6608 (ttm-80) REVERT: G 124 GLN cc_start: 0.6520 (mt0) cc_final: 0.6283 (mt0) REVERT: G 306 ASP cc_start: 0.7269 (p0) cc_final: 0.7056 (p0) REVERT: G 487 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7869 (mtmm) REVERT: G 511 ARG cc_start: 0.7639 (ttt180) cc_final: 0.7410 (ttt180) REVERT: G 532 MET cc_start: 0.8265 (mtt) cc_final: 0.7914 (mtp) REVERT: G 688 LYS cc_start: 0.7326 (ttpp) cc_final: 0.7096 (ttpp) REVERT: G 830 ARG cc_start: 0.7205 (mtp85) cc_final: 0.6929 (mmt-90) REVERT: G 853 VAL cc_start: 0.8449 (t) cc_final: 0.8216 (p) REVERT: G 875 LYS cc_start: 0.7463 (tttt) cc_final: 0.7147 (tttp) REVERT: G 928 LEU cc_start: 0.8307 (mt) cc_final: 0.7923 (mt) REVERT: G 1030 ARG cc_start: 0.7558 (ttp80) cc_final: 0.7288 (ttp-170) REVERT: G 1039 LYS cc_start: 0.7628 (mtmt) cc_final: 0.7411 (mtpp) REVERT: G 1059 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7156 (tp30) outliers start: 23 outliers final: 15 residues processed: 431 average time/residue: 0.1896 time to fit residues: 120.3715 Evaluate side-chains 424 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 409 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 929 SER Chi-restraints excluded: chain F residue 975 LEU Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 1002 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 234 optimal weight: 2.9990 chunk 193 optimal weight: 0.0770 chunk 34 optimal weight: 0.2980 chunk 257 optimal weight: 8.9990 chunk 284 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 GLN F 308 GLN F 865 GLN F1060 GLN G 308 GLN G 660 ASN ** G 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 800 GLN G 966 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.176215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142744 restraints weight = 36736.773| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.26 r_work: 0.3564 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27043 Z= 0.157 Angle : 0.564 7.501 36892 Z= 0.304 Chirality : 0.042 0.301 4043 Planarity : 0.004 0.049 4518 Dihedral : 15.908 177.428 4169 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.25 % Allowed : 8.60 % Favored : 90.15 % 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 aren not related in a simple way. whole: -0.68 (0.15), residues: 3058 helix: 1.10 (0.15), residues: 1269 sheet: 0.13 (0.25), residues: 443 loop : -2.28 (0.15), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 954 TYR 0.024 0.001 TYR E 363 PHE 0.023 0.002 PHE G 684 TRP 0.026 0.001 TRP F1104 HIS 0.005 0.001 HIS G 496 Details of bonding type rmsd covalent geometry : bond 0.00346 (27042) covalent geometry : angle 0.56404 (36890) SS BOND : bond 0.00197 ( 1) SS BOND : angle 2.62152 ( 2) hydrogen bonds : bond 0.06409 ( 970) hydrogen bonds : angle 4.40463 ( 2755) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 434 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: E 237 ASP cc_start: 0.7090 (t0) cc_final: 0.6800 (t0) REVERT: E 240 LYS cc_start: 0.6969 (mmtt) cc_final: 0.6717 (mmtt) REVERT: E 241 GLU cc_start: 0.7325 (mp0) cc_final: 0.6834 (mp0) REVERT: E 263 GLN cc_start: 0.7560 (pp30) cc_final: 0.6952 (pp30) REVERT: E 348 ILE cc_start: 0.7096 (mt) cc_final: 0.6871 (mt) REVERT: E 412 LYS cc_start: 0.7735 (mmmt) cc_final: 0.7535 (tptp) REVERT: E 467 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6577 (mt-10) REVERT: E 470 GLU cc_start: 0.7216 (pp20) cc_final: 0.6900 (pm20) REVERT: E 566 PHE cc_start: 0.7823 (t80) cc_final: 0.7380 (t80) REVERT: E 608 SER cc_start: 0.8267 (m) cc_final: 0.7817 (t) REVERT: F 31 LYS cc_start: 0.7173 (tppt) cc_final: 0.6845 (tppt) REVERT: F 93 ASP cc_start: 0.7684 (t0) cc_final: 0.7351 (t0) REVERT: F 162 GLU cc_start: 0.6336 (mt-10) cc_final: 0.6054 (mt-10) REVERT: F 199 LEU cc_start: 0.7504 (tt) cc_final: 0.7196 (tp) REVERT: F 227 LEU cc_start: 0.7987 (mt) cc_final: 0.7784 (mt) REVERT: F 774 ILE cc_start: 0.8761 (mt) cc_final: 0.8517 (tt) REVERT: F 951 GLN cc_start: 0.6489 (mm-40) cc_final: 0.6005 (mm-40) REVERT: F 1001 ARG cc_start: 0.6099 (mtt90) cc_final: 0.5059 (mtt90) REVERT: G 24 LEU cc_start: 0.7917 (mt) cc_final: 0.7711 (mt) REVERT: G 65 GLN cc_start: 0.7228 (tp-100) cc_final: 0.6965 (tp40) REVERT: G 72 ARG cc_start: 0.6583 (ttm170) cc_final: 0.6359 (ttm-80) REVERT: G 234 ASN cc_start: 0.7154 (p0) cc_final: 0.6920 (p0) REVERT: G 306 ASP cc_start: 0.7145 (p0) cc_final: 0.6915 (p0) REVERT: G 364 HIS cc_start: 0.7702 (m-70) cc_final: 0.7446 (m-70) REVERT: G 487 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7842 (mtmm) REVERT: G 532 MET cc_start: 0.8374 (mtt) cc_final: 0.8119 (mtm) REVERT: G 688 LYS cc_start: 0.7227 (ttpp) cc_final: 0.6949 (ttpp) REVERT: G 830 ARG cc_start: 0.7077 (mtp85) cc_final: 0.6762 (mmt-90) REVERT: G 875 LYS cc_start: 0.7461 (tttt) cc_final: 0.7076 (tttp) REVERT: G 952 ASP cc_start: 0.7250 (m-30) cc_final: 0.6942 (m-30) REVERT: G 1030 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7309 (ttp-170) REVERT: G 1039 LYS cc_start: 0.7666 (mtmt) cc_final: 0.7432 (mtpp) REVERT: G 1059 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7145 (tp30) outliers start: 34 outliers final: 26 residues processed: 447 average time/residue: 0.1849 time to fit residues: 122.7379 Evaluate side-chains 445 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 419 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 557 GLU Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 686 CYS Chi-restraints excluded: chain F residue 887 LEU Chi-restraints excluded: chain F residue 929 SER Chi-restraints excluded: chain F residue 975 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain G residue 520 PHE Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 774 ILE Chi-restraints excluded: chain G residue 863 ARG Chi-restraints excluded: chain G residue 994 ASN Chi-restraints excluded: chain G residue 1002 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 217 optimal weight: 0.9980 chunk 286 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 204 optimal weight: 0.3980 chunk 264 optimal weight: 9.9990 chunk 134 optimal weight: 0.8980 chunk 189 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 HIS E 654 ASN F 144 GLN F 308 GLN G 124 GLN G 592 ASN ** G 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 800 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.172498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139414 restraints weight = 36357.941| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.50 r_work: 0.3494 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27043 Z= 0.232 Angle : 0.632 10.482 36892 Z= 0.338 Chirality : 0.044 0.337 4043 Planarity : 0.005 0.051 4518 Dihedral : 16.025 176.344 4169 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.02 % Allowed : 9.82 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.15), residues: 3058 helix: 0.87 (0.15), residues: 1269 sheet: -0.04 (0.25), residues: 450 loop : -2.37 (0.15), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 684 TYR 0.032 0.002 TYR E 363 PHE 0.028 0.002 PHE E 569 TRP 0.030 0.002 TRP G 643 HIS 0.011 0.001 HIS F 307 Details of bonding type rmsd covalent geometry : bond 0.00546 (27042) covalent geometry : angle 0.63175 (36890) SS BOND : bond 0.00161 ( 1) SS BOND : angle 2.62052 ( 2) hydrogen bonds : bond 0.07577 ( 970) hydrogen bonds : angle 4.55983 ( 2755) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 428 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 263 GLN cc_start: 0.7645 (pp30) cc_final: 0.7042 (pp30) REVERT: E 412 LYS cc_start: 0.7918 (mmmt) cc_final: 0.7713 (tptp) REVERT: E 470 GLU cc_start: 0.7309 (pp20) cc_final: 0.7080 (pm20) REVERT: E 545 SER cc_start: 0.7385 (t) cc_final: 0.7126 (p) REVERT: E 578 ASP cc_start: 0.6943 (m-30) cc_final: 0.6665 (m-30) REVERT: E 608 SER cc_start: 0.8574 (m) cc_final: 0.8141 (t) REVERT: E 684 ARG cc_start: 0.6622 (mmt90) cc_final: 0.6172 (mmt90) REVERT: F 31 LYS cc_start: 0.7184 (tppt) cc_final: 0.6834 (tppt) REVERT: F 93 ASP cc_start: 0.7761 (t0) cc_final: 0.7390 (t0) REVERT: F 162 GLU cc_start: 0.6399 (mt-10) cc_final: 0.6057 (mt-10) REVERT: F 199 LEU cc_start: 0.7554 (tt) cc_final: 0.7253 (tp) REVERT: F 230 GLU cc_start: 0.6444 (tp30) cc_final: 0.6242 (tp30) REVERT: F 589 TYR cc_start: 0.7573 (m-10) cc_final: 0.7178 (m-80) REVERT: F 774 ILE cc_start: 0.8842 (mt) cc_final: 0.8589 (tt) REVERT: F 840 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7419 (t70) REVERT: F 951 GLN cc_start: 0.6524 (mm-40) cc_final: 0.6054 (mm-40) REVERT: F 1001 ARG cc_start: 0.6188 (mtt90) cc_final: 0.5666 (mtt90) REVERT: G 24 LEU cc_start: 0.7891 (mt) cc_final: 0.7676 (mt) REVERT: G 65 GLN cc_start: 0.7194 (tp-100) cc_final: 0.6948 (mm-40) REVERT: G 72 ARG cc_start: 0.6619 (ttm170) cc_final: 0.6341 (ttm-80) REVERT: G 189 ASN cc_start: 0.6655 (m110) cc_final: 0.6086 (m-40) REVERT: G 306 ASP cc_start: 0.7157 (p0) cc_final: 0.6905 (p0) REVERT: G 381 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7651 (mtt180) REVERT: G 487 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7807 (mtmm) REVERT: G 511 ARG cc_start: 0.7259 (ttt180) cc_final: 0.6974 (tpt170) REVERT: G 532 MET cc_start: 0.8377 (mtt) cc_final: 0.8085 (mtm) REVERT: G 592 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7285 (t0) REVERT: G 875 LYS cc_start: 0.7576 (tttt) cc_final: 0.7189 (tttp) REVERT: G 1030 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.7365 (ttp-170) REVERT: G 1039 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7528 (mtpp) REVERT: G 1059 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7113 (tp30) outliers start: 55 outliers final: 37 residues processed: 449 average time/residue: 0.1859 time to fit residues: 124.7050 Evaluate side-chains 454 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 415 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 428 MET Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 520 PHE Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 840 ASP Chi-restraints excluded: chain F residue 887 LEU Chi-restraints excluded: chain F residue 929 SER Chi-restraints excluded: chain F residue 975 LEU Chi-restraints excluded: chain F residue 1097 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 359 ASP Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain G residue 520 PHE Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 592 ASN Chi-restraints excluded: chain G residue 758 VAL Chi-restraints excluded: chain G residue 774 ILE Chi-restraints excluded: chain G residue 863 ARG Chi-restraints excluded: chain G residue 927 MET Chi-restraints excluded: chain G residue 994 ASN Chi-restraints excluded: chain G residue 1002 VAL Chi-restraints excluded: chain G residue 1078 ASN Chi-restraints excluded: chain G residue 1152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 283 optimal weight: 0.8980 chunk 282 optimal weight: 0.0570 chunk 171 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 246 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 chunk 6 optimal weight: 0.0470 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN F 144 GLN F 308 GLN F 407 ASN F 496 HIS F 935 HIS G 178 HIS G 277 GLN G 592 ASN ** G 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 890 HIS G1157 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142766 restraints weight = 36665.662| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.30 r_work: 0.3564 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27043 Z= 0.120 Angle : 0.524 8.637 36892 Z= 0.282 Chirality : 0.040 0.312 4043 Planarity : 0.004 0.042 4518 Dihedral : 15.857 177.942 4169 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.73 % Allowed : 11.43 % Favored : 86.84 % 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 aren not related in a simple way. whole: -0.62 (0.15), residues: 3058 helix: 1.19 (0.15), residues: 1277 sheet: 0.05 (0.25), residues: 458 loop : -2.29 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 423 TYR 0.015 0.001 TYR E 363 PHE 0.025 0.001 PHE G 684 TRP 0.023 0.001 TRP G 643 HIS 0.006 0.001 HIS E 675 Details of bonding type rmsd covalent geometry : bond 0.00252 (27042) covalent geometry : angle 0.52422 (36890) SS BOND : bond 0.00046 ( 1) SS BOND : angle 2.09416 ( 2) hydrogen bonds : bond 0.05043 ( 970) hydrogen bonds : angle 4.11075 ( 2755) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 412 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 ARG cc_start: 0.7016 (tpt170) cc_final: 0.6493 (tpt170) REVERT: E 241 GLU cc_start: 0.7383 (mp0) cc_final: 0.6919 (mp0) REVERT: E 263 GLN cc_start: 0.7527 (pp30) cc_final: 0.7074 (pp30) REVERT: E 470 GLU cc_start: 0.7078 (pp20) cc_final: 0.6843 (pm20) REVERT: E 578 ASP cc_start: 0.6815 (m-30) cc_final: 0.6584 (m-30) REVERT: E 608 SER cc_start: 0.8362 (m) cc_final: 0.7931 (t) REVERT: F 31 LYS cc_start: 0.7067 (tppt) cc_final: 0.6729 (tppt) REVERT: F 93 ASP cc_start: 0.7729 (t0) cc_final: 0.7417 (t0) REVERT: F 162 GLU cc_start: 0.6360 (mt-10) cc_final: 0.6052 (mt-10) REVERT: F 594 VAL cc_start: 0.7637 (OUTLIER) cc_final: 0.7410 (m) REVERT: F 774 ILE cc_start: 0.8747 (mt) cc_final: 0.8537 (tt) REVERT: F 951 GLN cc_start: 0.6477 (mm-40) cc_final: 0.6035 (mm-40) REVERT: F 1001 ARG cc_start: 0.6078 (mtt90) cc_final: 0.5587 (mtt90) REVERT: F 1002 VAL cc_start: 0.7776 (t) cc_final: 0.7453 (m) REVERT: G 306 ASP cc_start: 0.7152 (p0) cc_final: 0.6930 (p0) REVERT: G 364 HIS cc_start: 0.7600 (m-70) cc_final: 0.7359 (m-70) REVERT: G 381 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7667 (mtt180) REVERT: G 487 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7798 (mtmm) REVERT: G 511 ARG cc_start: 0.7169 (ttt180) cc_final: 0.6924 (tpt170) REVERT: G 532 MET cc_start: 0.8297 (mtt) cc_final: 0.8089 (mtm) REVERT: G 592 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.6952 (t0) REVERT: G 853 VAL cc_start: 0.8287 (t) cc_final: 0.8065 (p) REVERT: G 875 LYS cc_start: 0.7484 (tttt) cc_final: 0.7079 (tttp) REVERT: G 934 VAL cc_start: 0.8017 (t) cc_final: 0.7708 (t) REVERT: G 952 ASP cc_start: 0.7269 (m-30) cc_final: 0.6917 (m-30) REVERT: G 1029 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7105 (mp0) REVERT: G 1030 ARG cc_start: 0.7772 (ttp-170) cc_final: 0.7334 (ttp-170) REVERT: G 1039 LYS cc_start: 0.7705 (mtmt) cc_final: 0.7503 (mtpp) REVERT: G 1059 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7208 (tm-30) REVERT: G 1078 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7064 (t0) outliers start: 47 outliers final: 33 residues processed: 429 average time/residue: 0.1826 time to fit residues: 117.0714 Evaluate side-chains 437 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 401 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 557 GLU Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain E residue 653 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 520 PHE Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 686 CYS Chi-restraints excluded: chain F residue 833 GLN Chi-restraints excluded: chain F residue 929 SER Chi-restraints excluded: chain F residue 975 LEU Chi-restraints excluded: chain F residue 1017 THR Chi-restraints excluded: chain F residue 1097 ILE Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 359 ASP Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 503 GLU Chi-restraints excluded: chain G residue 520 PHE Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 592 ASN Chi-restraints excluded: chain G residue 863 ARG Chi-restraints excluded: chain G residue 938 HIS Chi-restraints excluded: chain G residue 1002 VAL Chi-restraints excluded: chain G residue 1078 ASN Chi-restraints excluded: chain G residue 1152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 14 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 294 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 267 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN F 144 GLN F1060 GLN G 592 ASN G 668 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.173248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139874 restraints weight = 36377.387| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.29 r_work: 0.3518 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27043 Z= 0.192 Angle : 0.588 8.835 36892 Z= 0.314 Chirality : 0.042 0.346 4043 Planarity : 0.004 0.047 4518 Dihedral : 15.929 177.949 4169 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.28 % Allowed : 11.84 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.15), residues: 3058 helix: 1.04 (0.15), residues: 1271 sheet: 0.00 (0.25), residues: 447 loop : -2.29 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 72 TYR 0.026 0.002 TYR E 363 PHE 0.024 0.002 PHE G 684 TRP 0.023 0.002 TRP F 643 HIS 0.009 0.001 HIS F 307 Details of bonding type rmsd covalent geometry : bond 0.00445 (27042) covalent geometry : angle 0.58786 (36890) SS BOND : bond 0.00046 ( 1) SS BOND : angle 2.18007 ( 2) hydrogen bonds : bond 0.06636 ( 970) hydrogen bonds : angle 4.28667 ( 2755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 421 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 ARG cc_start: 0.6973 (tpt170) cc_final: 0.6426 (tpt170) REVERT: E 241 GLU cc_start: 0.7375 (mp0) cc_final: 0.6867 (mp0) REVERT: E 263 GLN cc_start: 0.7579 (pp30) cc_final: 0.7066 (pp30) REVERT: E 452 VAL cc_start: 0.7558 (t) cc_final: 0.7191 (m) REVERT: E 470 GLU cc_start: 0.7270 (pp20) cc_final: 0.7052 (pm20) REVERT: E 551 LEU cc_start: 0.7899 (mm) cc_final: 0.7569 (mt) REVERT: E 578 ASP cc_start: 0.6886 (m-30) cc_final: 0.6638 (m-30) REVERT: E 600 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7566 (tp40) REVERT: E 608 SER cc_start: 0.8485 (m) cc_final: 0.8062 (t) REVERT: F 31 LYS cc_start: 0.7178 (tppt) cc_final: 0.6867 (tppt) REVERT: F 93 ASP cc_start: 0.7713 (t0) cc_final: 0.7387 (t0) REVERT: F 162 GLU cc_start: 0.6372 (mt-10) cc_final: 0.6042 (mt-10) REVERT: F 199 LEU cc_start: 0.7569 (tt) cc_final: 0.7269 (tp) REVERT: F 594 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7567 (m) REVERT: F 774 ILE cc_start: 0.8802 (mt) cc_final: 0.8564 (tt) REVERT: F 951 GLN cc_start: 0.6542 (mm-40) cc_final: 0.6097 (mm-40) REVERT: F 1001 ARG cc_start: 0.6216 (mtt90) cc_final: 0.5764 (mtt90) REVERT: G 72 ARG cc_start: 0.6749 (ttm-80) cc_final: 0.6374 (ttm-80) REVERT: G 306 ASP cc_start: 0.7239 (p0) cc_final: 0.7016 (p0) REVERT: G 381 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7686 (mtt180) REVERT: G 487 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7800 (mtmm) REVERT: G 511 ARG cc_start: 0.7126 (tpt170) cc_final: 0.6900 (tpt170) REVERT: G 532 MET cc_start: 0.8379 (mtt) cc_final: 0.8100 (mtm) REVERT: G 592 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7075 (t0) REVERT: G 875 LYS cc_start: 0.7569 (tttt) cc_final: 0.7159 (tttp) REVERT: G 1030 ARG cc_start: 0.7795 (ttp-170) cc_final: 0.7031 (ttp80) REVERT: G 1039 LYS cc_start: 0.7751 (mtmt) cc_final: 0.7548 (mtpp) REVERT: G 1059 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7306 (tp30) REVERT: G 1078 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7150 (t0) outliers start: 62 outliers final: 46 residues processed: 444 average time/residue: 0.1941 time to fit residues: 128.4688 Evaluate side-chains 467 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 418 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain E residue 428 MET Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 520 PHE Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 686 CYS Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 833 GLN Chi-restraints excluded: chain F residue 887 LEU Chi-restraints excluded: chain F residue 929 SER Chi-restraints excluded: chain F residue 975 LEU Chi-restraints excluded: chain F residue 1017 THR Chi-restraints excluded: chain F residue 1097 ILE Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 359 ASP Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 503 GLU Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain G residue 520 PHE Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 592 ASN Chi-restraints excluded: chain G residue 758 VAL Chi-restraints excluded: chain G residue 774 ILE Chi-restraints excluded: chain G residue 863 ARG Chi-restraints excluded: chain G residue 927 MET Chi-restraints excluded: chain G residue 938 HIS Chi-restraints excluded: chain G residue 994 ASN Chi-restraints excluded: chain G residue 1002 VAL Chi-restraints excluded: chain G residue 1078 ASN Chi-restraints excluded: chain G residue 1152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 270 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 654 ASN F 144 GLN F 288 GLN F1060 GLN G 178 HIS G 592 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.173046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.139752 restraints weight = 36332.163| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.30 r_work: 0.3519 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27043 Z= 0.185 Angle : 0.578 8.428 36892 Z= 0.310 Chirality : 0.042 0.343 4043 Planarity : 0.004 0.049 4518 Dihedral : 15.924 177.844 4169 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 2.35 % Allowed : 12.54 % Favored : 85.11 % 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 aren not related in a simple way. whole: -0.79 (0.15), residues: 3058 helix: 1.00 (0.15), residues: 1272 sheet: -0.07 (0.24), residues: 448 loop : -2.30 (0.15), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G1025 TYR 0.026 0.001 TYR E 363 PHE 0.024 0.002 PHE G 684 TRP 0.026 0.002 TRP F 643 HIS 0.009 0.001 HIS F 307 Details of bonding type rmsd covalent geometry : bond 0.00429 (27042) covalent geometry : angle 0.57774 (36890) SS BOND : bond 0.00026 ( 1) SS BOND : angle 2.04807 ( 2) hydrogen bonds : bond 0.06440 ( 970) hydrogen bonds : angle 4.27293 ( 2755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 419 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 ARG cc_start: 0.6995 (tpt170) cc_final: 0.6455 (tpt170) REVERT: E 237 ASP cc_start: 0.7068 (t0) cc_final: 0.6807 (t0) REVERT: E 241 GLU cc_start: 0.7368 (mp0) cc_final: 0.6874 (mp0) REVERT: E 263 GLN cc_start: 0.7573 (pp30) cc_final: 0.7064 (pp30) REVERT: E 452 VAL cc_start: 0.7546 (t) cc_final: 0.7192 (m) REVERT: E 470 GLU cc_start: 0.7345 (pp20) cc_final: 0.7138 (pm20) REVERT: E 551 LEU cc_start: 0.7924 (mm) cc_final: 0.7611 (mt) REVERT: E 578 ASP cc_start: 0.6900 (m-30) cc_final: 0.6665 (m-30) REVERT: E 600 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7622 (tp40) REVERT: E 608 SER cc_start: 0.8518 (m) cc_final: 0.8107 (t) REVERT: F 31 LYS cc_start: 0.7193 (tppt) cc_final: 0.6876 (tppt) REVERT: F 93 ASP cc_start: 0.7726 (t0) cc_final: 0.7371 (t0) REVERT: F 199 LEU cc_start: 0.7597 (tt) cc_final: 0.7299 (tp) REVERT: F 774 ILE cc_start: 0.8798 (mt) cc_final: 0.8578 (tt) REVERT: F 951 GLN cc_start: 0.6570 (mm-40) cc_final: 0.6123 (mm-40) REVERT: F 1001 ARG cc_start: 0.6217 (mtt90) cc_final: 0.5766 (mtt90) REVERT: G 72 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6364 (ttm-80) REVERT: G 249 LYS cc_start: 0.7811 (mtpp) cc_final: 0.7522 (mtpt) REVERT: G 306 ASP cc_start: 0.7271 (p0) cc_final: 0.7046 (p0) REVERT: G 381 ARG cc_start: 0.8004 (mtt180) cc_final: 0.7710 (mtt180) REVERT: G 487 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7788 (mtmm) REVERT: G 511 ARG cc_start: 0.7138 (tpt170) cc_final: 0.6899 (tpt170) REVERT: G 532 MET cc_start: 0.8376 (mtt) cc_final: 0.8107 (mtm) REVERT: G 592 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.7009 (t0) REVERT: G 875 LYS cc_start: 0.7551 (tttt) cc_final: 0.7134 (tttp) REVERT: G 1030 ARG cc_start: 0.7754 (ttp-170) cc_final: 0.7022 (ttp80) REVERT: G 1039 LYS cc_start: 0.7754 (mtmt) cc_final: 0.7530 (mtpp) REVERT: G 1059 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7274 (tm-30) REVERT: G 1078 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7162 (t0) outliers start: 64 outliers final: 50 residues processed: 441 average time/residue: 0.1747 time to fit residues: 115.3116 Evaluate side-chains 469 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 416 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 493 SER Chi-restraints excluded: chain F residue 520 PHE Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 686 CYS Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 833 GLN Chi-restraints excluded: chain F residue 887 LEU Chi-restraints excluded: chain F residue 929 SER Chi-restraints excluded: chain F residue 975 LEU Chi-restraints excluded: chain F residue 1017 THR Chi-restraints excluded: chain F residue 1097 ILE Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 359 ASP Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 503 GLU Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain G residue 520 PHE Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 592 ASN Chi-restraints excluded: chain G residue 758 VAL Chi-restraints excluded: chain G residue 774 ILE Chi-restraints excluded: chain G residue 863 ARG Chi-restraints excluded: chain G residue 927 MET Chi-restraints excluded: chain G residue 938 HIS Chi-restraints excluded: chain G residue 994 ASN Chi-restraints excluded: chain G residue 1002 VAL Chi-restraints excluded: chain G residue 1078 ASN Chi-restraints excluded: chain G residue 1152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 125 optimal weight: 1.9990 chunk 287 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 272 optimal weight: 0.6980 chunk 188 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 135 optimal weight: 0.7980 chunk 293 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 HIS G 592 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.174951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141903 restraints weight = 36489.298| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.28 r_work: 0.3546 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27043 Z= 0.131 Angle : 0.531 7.469 36892 Z= 0.285 Chirality : 0.040 0.332 4043 Planarity : 0.004 0.049 4518 Dihedral : 15.848 178.350 4169 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.00 % Favored : 92.97 % Rotamer: Outliers : 1.95 % Allowed : 13.31 % Favored : 84.74 % 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 aren not related in a simple way. whole: -0.58 (0.15), residues: 3058 helix: 1.25 (0.15), residues: 1269 sheet: -0.04 (0.24), residues: 449 loop : -2.21 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 382 TYR 0.019 0.001 TYR E 363 PHE 0.025 0.001 PHE G 684 TRP 0.024 0.001 TRP F 643 HIS 0.005 0.001 HIS F 307 Details of bonding type rmsd covalent geometry : bond 0.00288 (27042) covalent geometry : angle 0.53057 (36890) SS BOND : bond 0.00024 ( 1) SS BOND : angle 1.93282 ( 2) hydrogen bonds : bond 0.05256 ( 970) hydrogen bonds : angle 4.06348 ( 2755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 426 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 ARG cc_start: 0.6977 (tpt170) cc_final: 0.6412 (tpt170) REVERT: E 202 ARG cc_start: 0.6697 (mtm-85) cc_final: 0.6346 (mtm-85) REVERT: E 237 ASP cc_start: 0.7027 (t0) cc_final: 0.6770 (t0) REVERT: E 241 GLU cc_start: 0.7358 (mp0) cc_final: 0.6876 (mp0) REVERT: E 439 VAL cc_start: 0.0742 (OUTLIER) cc_final: 0.0506 (p) REVERT: E 452 VAL cc_start: 0.7502 (t) cc_final: 0.7134 (m) REVERT: E 470 GLU cc_start: 0.7217 (pp20) cc_final: 0.7006 (pm20) REVERT: E 551 LEU cc_start: 0.7878 (mm) cc_final: 0.7553 (mt) REVERT: E 578 ASP cc_start: 0.6853 (m-30) cc_final: 0.6622 (m-30) REVERT: E 600 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7624 (tp40) REVERT: E 608 SER cc_start: 0.8388 (m) cc_final: 0.7975 (t) REVERT: F 31 LYS cc_start: 0.7166 (tppt) cc_final: 0.6865 (tppt) REVERT: F 93 ASP cc_start: 0.7724 (t0) cc_final: 0.7387 (t0) REVERT: F 162 GLU cc_start: 0.7012 (mp0) cc_final: 0.6609 (mp0) REVERT: F 951 GLN cc_start: 0.6646 (mm-40) cc_final: 0.6167 (mm-40) REVERT: F 1001 ARG cc_start: 0.6138 (mtt90) cc_final: 0.5711 (mtt90) REVERT: F 1002 VAL cc_start: 0.7789 (t) cc_final: 0.7506 (m) REVERT: G 72 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6353 (ttm-80) REVERT: G 249 LYS cc_start: 0.7807 (mtpp) cc_final: 0.7527 (mtpt) REVERT: G 306 ASP cc_start: 0.7298 (p0) cc_final: 0.7074 (p0) REVERT: G 364 HIS cc_start: 0.7634 (m-70) cc_final: 0.7412 (m-70) REVERT: G 381 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7699 (mtt180) REVERT: G 487 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7785 (mtmm) REVERT: G 532 MET cc_start: 0.8341 (mtt) cc_final: 0.8103 (mtm) REVERT: G 592 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.6802 (t0) REVERT: G 860 SER cc_start: 0.7868 (m) cc_final: 0.7583 (t) REVERT: G 875 LYS cc_start: 0.7489 (tttt) cc_final: 0.7128 (tttp) REVERT: G 934 VAL cc_start: 0.8043 (t) cc_final: 0.7710 (t) REVERT: G 952 ASP cc_start: 0.7294 (m-30) cc_final: 0.6956 (m-30) REVERT: G 1030 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.6984 (ttp80) REVERT: G 1059 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7288 (tm-30) REVERT: G 1078 ASN cc_start: 0.7472 (OUTLIER) cc_final: 0.7186 (t0) outliers start: 53 outliers final: 41 residues processed: 446 average time/residue: 0.1798 time to fit residues: 120.2592 Evaluate side-chains 465 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 420 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 493 SER Chi-restraints excluded: chain F residue 520 PHE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 686 CYS Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 833 GLN Chi-restraints excluded: chain F residue 929 SER Chi-restraints excluded: chain F residue 975 LEU Chi-restraints excluded: chain F residue 1017 THR Chi-restraints excluded: chain F residue 1097 ILE Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 359 ASP Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 503 GLU Chi-restraints excluded: chain G residue 520 PHE Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 592 ASN Chi-restraints excluded: chain G residue 758 VAL Chi-restraints excluded: chain G residue 938 HIS Chi-restraints excluded: chain G residue 994 ASN Chi-restraints excluded: chain G residue 1002 VAL Chi-restraints excluded: chain G residue 1078 ASN Chi-restraints excluded: chain G residue 1152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 224 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 143 optimal weight: 0.0170 chunk 158 optimal weight: 0.6980 chunk 260 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 592 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.175294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142168 restraints weight = 36551.020| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.30 r_work: 0.3553 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27043 Z= 0.127 Angle : 0.527 7.640 36892 Z= 0.283 Chirality : 0.040 0.349 4043 Planarity : 0.004 0.048 4518 Dihedral : 15.820 178.710 4169 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.95 % Allowed : 13.79 % Favored : 84.26 % 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 aren not related in a simple way. whole: -0.47 (0.15), residues: 3058 helix: 1.36 (0.15), residues: 1270 sheet: -0.01 (0.24), residues: 449 loop : -2.18 (0.15), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 382 TYR 0.018 0.001 TYR E 363 PHE 0.025 0.001 PHE G 684 TRP 0.022 0.001 TRP F 643 HIS 0.004 0.001 HIS F 307 Details of bonding type rmsd covalent geometry : bond 0.00278 (27042) covalent geometry : angle 0.52710 (36890) SS BOND : bond 0.00014 ( 1) SS BOND : angle 1.85694 ( 2) hydrogen bonds : bond 0.05029 ( 970) hydrogen bonds : angle 4.00088 ( 2755) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 416 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 ARG cc_start: 0.6969 (tpt170) cc_final: 0.6394 (tpt170) REVERT: E 202 ARG cc_start: 0.6662 (mtm-85) cc_final: 0.6325 (mtm-85) REVERT: E 237 ASP cc_start: 0.7016 (t0) cc_final: 0.6755 (t0) REVERT: E 241 GLU cc_start: 0.7353 (mp0) cc_final: 0.6898 (mp0) REVERT: E 452 VAL cc_start: 0.7498 (t) cc_final: 0.7118 (m) REVERT: E 470 GLU cc_start: 0.7206 (pp20) cc_final: 0.6995 (pm20) REVERT: E 551 LEU cc_start: 0.7879 (mm) cc_final: 0.7538 (mt) REVERT: E 578 ASP cc_start: 0.6838 (m-30) cc_final: 0.6620 (m-30) REVERT: E 600 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7639 (tp40) REVERT: E 608 SER cc_start: 0.8355 (m) cc_final: 0.7958 (t) REVERT: F 31 LYS cc_start: 0.7157 (tppt) cc_final: 0.6880 (tppt) REVERT: F 93 ASP cc_start: 0.7739 (t0) cc_final: 0.7400 (t0) REVERT: F 951 GLN cc_start: 0.6629 (mm-40) cc_final: 0.6155 (mm-40) REVERT: F 1001 ARG cc_start: 0.6094 (mtt90) cc_final: 0.5701 (mtt90) REVERT: F 1002 VAL cc_start: 0.7777 (t) cc_final: 0.7514 (m) REVERT: G 72 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6340 (ttm-80) REVERT: G 249 LYS cc_start: 0.7810 (mtpp) cc_final: 0.7532 (mtpt) REVERT: G 306 ASP cc_start: 0.7302 (p0) cc_final: 0.7073 (p0) REVERT: G 364 HIS cc_start: 0.7607 (m-70) cc_final: 0.7388 (m-70) REVERT: G 381 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7712 (mtt180) REVERT: G 487 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7768 (mtmm) REVERT: G 532 MET cc_start: 0.8313 (mtt) cc_final: 0.8082 (mtm) REVERT: G 592 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.6737 (t0) REVERT: G 875 LYS cc_start: 0.7491 (tttt) cc_final: 0.7143 (tttp) REVERT: G 934 VAL cc_start: 0.8017 (t) cc_final: 0.7686 (t) REVERT: G 952 ASP cc_start: 0.7291 (m-30) cc_final: 0.6941 (m-30) REVERT: G 1030 ARG cc_start: 0.7730 (ttp-170) cc_final: 0.6977 (ttp80) REVERT: G 1059 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7290 (tm-30) REVERT: G 1078 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.7196 (t0) outliers start: 53 outliers final: 46 residues processed: 435 average time/residue: 0.1860 time to fit residues: 121.3512 Evaluate side-chains 463 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 414 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 428 MET Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 520 PHE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 686 CYS Chi-restraints excluded: chain F residue 691 LYS Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 833 GLN Chi-restraints excluded: chain F residue 929 SER Chi-restraints excluded: chain F residue 975 LEU Chi-restraints excluded: chain F residue 1017 THR Chi-restraints excluded: chain F residue 1097 ILE Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 359 ASP Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 371 LYS Chi-restraints excluded: chain G residue 503 GLU Chi-restraints excluded: chain G residue 520 PHE Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 592 ASN Chi-restraints excluded: chain G residue 758 VAL Chi-restraints excluded: chain G residue 938 HIS Chi-restraints excluded: chain G residue 994 ASN Chi-restraints excluded: chain G residue 1002 VAL Chi-restraints excluded: chain G residue 1078 ASN Chi-restraints excluded: chain G residue 1152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 306 optimal weight: 0.0170 chunk 160 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 0.2980 chunk 56 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 592 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.176479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143484 restraints weight = 36439.797| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.30 r_work: 0.3570 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27043 Z= 0.111 Angle : 0.510 7.816 36892 Z= 0.273 Chirality : 0.040 0.320 4043 Planarity : 0.004 0.049 4518 Dihedral : 15.781 179.720 4169 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.73 % Allowed : 14.12 % Favored : 84.15 % 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 aren not related in a simple way. whole: -0.31 (0.15), residues: 3058 helix: 1.50 (0.15), residues: 1277 sheet: 0.06 (0.25), residues: 437 loop : -2.09 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 382 TYR 0.013 0.001 TYR E 363 PHE 0.025 0.001 PHE G 684 TRP 0.020 0.001 TRP G 643 HIS 0.003 0.001 HIS F 496 Details of bonding type rmsd covalent geometry : bond 0.00237 (27042) covalent geometry : angle 0.50943 (36890) SS BOND : bond 0.00004 ( 1) SS BOND : angle 1.72533 ( 2) hydrogen bonds : bond 0.04321 ( 970) hydrogen bonds : angle 3.86555 ( 2755) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6116 Ramachandran restraints generated. 3058 Oldfield, 0 Emsley, 3058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 415 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 ARG cc_start: 0.6954 (tpt170) cc_final: 0.6370 (tpt170) REVERT: E 202 ARG cc_start: 0.6556 (mtm-85) cc_final: 0.6225 (mtm-85) REVERT: E 241 GLU cc_start: 0.7347 (mp0) cc_final: 0.6921 (mp0) REVERT: E 470 GLU cc_start: 0.7184 (pp20) cc_final: 0.6961 (pm20) REVERT: E 551 LEU cc_start: 0.7874 (mm) cc_final: 0.7528 (mt) REVERT: E 600 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7635 (tp40) REVERT: E 608 SER cc_start: 0.8311 (m) cc_final: 0.7900 (t) REVERT: F 31 LYS cc_start: 0.7140 (tppt) cc_final: 0.6853 (tppt) REVERT: F 93 ASP cc_start: 0.7755 (t0) cc_final: 0.7416 (t0) REVERT: F 406 VAL cc_start: 0.7609 (t) cc_final: 0.7357 (m) REVERT: F 420 MET cc_start: 0.7280 (mmt) cc_final: 0.7034 (mmt) REVERT: F 951 GLN cc_start: 0.6608 (mm-40) cc_final: 0.6140 (mm-40) REVERT: F 1001 ARG cc_start: 0.5997 (mtt90) cc_final: 0.5636 (mtt90) REVERT: F 1002 VAL cc_start: 0.7742 (t) cc_final: 0.7525 (m) REVERT: G 72 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6287 (ttm-80) REVERT: G 306 ASP cc_start: 0.7330 (p0) cc_final: 0.7081 (p0) REVERT: G 381 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7730 (mtt180) REVERT: G 487 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7760 (mtmm) REVERT: G 592 ASN cc_start: 0.7164 (OUTLIER) cc_final: 0.6442 (t0) REVERT: G 875 LYS cc_start: 0.7475 (tttt) cc_final: 0.7115 (tttp) REVERT: G 934 VAL cc_start: 0.8047 (t) cc_final: 0.7690 (t) REVERT: G 952 ASP cc_start: 0.7262 (m-30) cc_final: 0.6921 (m-30) REVERT: G 1030 ARG cc_start: 0.7696 (ttp-170) cc_final: 0.6942 (ttp80) REVERT: G 1059 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7567 (tm-30) REVERT: G 1078 ASN cc_start: 0.7481 (OUTLIER) cc_final: 0.7159 (t0) outliers start: 47 outliers final: 40 residues processed: 432 average time/residue: 0.1877 time to fit residues: 120.8634 Evaluate side-chains 452 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 409 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 520 PHE Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 620 ARG Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 691 LYS Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 833 GLN Chi-restraints excluded: chain F residue 929 SER Chi-restraints excluded: chain F residue 975 LEU Chi-restraints excluded: chain F residue 1017 THR Chi-restraints excluded: chain F residue 1097 ILE Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 359 ASP Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 503 GLU Chi-restraints excluded: chain G residue 520 PHE Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 592 ASN Chi-restraints excluded: chain G residue 758 VAL Chi-restraints excluded: chain G residue 938 HIS Chi-restraints excluded: chain G residue 994 ASN Chi-restraints excluded: chain G residue 1002 VAL Chi-restraints excluded: chain G residue 1078 ASN Chi-restraints excluded: chain G residue 1152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 5 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 217 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 297 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 683 GLN G 592 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.174165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140926 restraints weight = 36332.712| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.28 r_work: 0.3537 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27043 Z= 0.161 Angle : 0.556 7.531 36892 Z= 0.296 Chirality : 0.041 0.357 4043 Planarity : 0.004 0.053 4518 Dihedral : 15.828 179.767 4169 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.19 % Favored : 92.74 % Rotamer: Outliers : 1.91 % Allowed : 13.86 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.15), residues: 3058 helix: 1.37 (0.15), residues: 1272 sheet: -0.04 (0.25), residues: 440 loop : -2.11 (0.15), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 355 TYR 0.023 0.001 TYR E 363 PHE 0.025 0.001 PHE G 684 TRP 0.023 0.001 TRP F 643 HIS 0.007 0.001 HIS F 307 Details of bonding type rmsd covalent geometry : bond 0.00373 (27042) covalent geometry : angle 0.55572 (36890) SS BOND : bond 0.00046 ( 1) SS BOND : angle 1.84682 ( 2) hydrogen bonds : bond 0.05610 ( 970) hydrogen bonds : angle 4.02783 ( 2755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5573.53 seconds wall clock time: 96 minutes 3.23 seconds (5763.23 seconds total)