Starting phenix.real_space_refine on Sun Jun 22 18:18:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgk_44516/06_2025/9bgk_44516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgk_44516/06_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_44516/06_2025/9bgk_44516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgk_44516/06_2025/9bgk_44516.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgk_44516/06_2025/9bgk_44516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgk_44516/06_2025/9bgk_44516.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.45, per 1000 atoms: 0.59 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: 6.12 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 8.67 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: 10.74 Time building geometry restraints manager: 7.36 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: 1.440 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: 0.040 Extract box with map and model: 1.180 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 64.360 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.530 ------------------------------------------------------------------------------- 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 : 7.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.085 0.002 TRP F1104 HIS 0.011 0.001 HIS E 413 PHE 0.094 0.002 PHE F 639 TYR 0.062 0.002 TYR E 363 ARG 0.011 0.001 ARG E 47 Details of bonding type rmsd hydrogen bonds : bond 0.19200 ( 970) hydrogen bonds : angle 6.67761 ( 2755) SS BOND : bond 0.00468 ( 1) SS BOND : angle 4.29890 ( 2) covalent geometry : bond 0.00333 (27042) covalent geometry : angle 0.70113 (36890) *********************** 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 : 3.021 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: 0.4538 time to fit residues: 318.4900 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 : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 282 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN E 376 GLN F 207 GLN 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 308 GLN G 337 ASN G 800 GLN G1078 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.174760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143162 restraints weight = 36212.726| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.26 r_work: 0.3512 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 27043 Z= 0.252 Angle : 0.694 12.038 36892 Z= 0.372 Chirality : 0.046 0.358 4043 Planarity : 0.005 0.063 4518 Dihedral : 16.094 172.677 4169 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.18 % Allowed : 7.13 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.15), residues: 3058 helix: 0.48 (0.15), residues: 1258 sheet: -0.12 (0.25), residues: 448 loop : -2.45 (0.15), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F1104 HIS 0.009 0.002 HIS F 134 PHE 0.033 0.002 PHE E 569 TYR 0.033 0.002 TYR E 363 ARG 0.008 0.001 ARG F 954 Details of bonding type rmsd hydrogen bonds : bond 0.08546 ( 970) hydrogen bonds : angle 5.06633 ( 2755) SS BOND : bond 0.00214 ( 1) SS BOND : angle 3.78321 ( 2) covalent geometry : bond 0.00589 (27042) covalent geometry : angle 0.69383 (36890) *********************** 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 476 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 444 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 58 THR cc_start: 0.7228 (m) cc_final: 0.6709 (p) REVERT: E 237 ASP cc_start: 0.7038 (t0) cc_final: 0.6772 (t0) REVERT: E 240 LYS cc_start: 0.7004 (mmtt) cc_final: 0.6718 (mmtt) REVERT: E 241 GLU cc_start: 0.7398 (mp0) cc_final: 0.6867 (mp0) REVERT: E 277 PRO cc_start: 0.7833 (Cg_endo) cc_final: 0.7633 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6869 (tm-30) REVERT: E 348 ILE cc_start: 0.7284 (mt) cc_final: 0.7019 (mt) REVERT: E 545 SER cc_start: 0.7380 (t) cc_final: 0.7109 (p) REVERT: E 566 PHE cc_start: 0.7847 (t80) cc_final: 0.7421 (t80) REVERT: E 578 ASP cc_start: 0.6952 (m-30) cc_final: 0.6661 (m-30) REVERT: E 588 GLU cc_start: 0.7906 (tp30) cc_final: 0.7681 (tp30) REVERT: E 608 SER cc_start: 0.8485 (m) cc_final: 0.8071 (t) REVERT: F 31 LYS cc_start: 0.7262 (tppt) cc_final: 0.6943 (tppt) REVERT: F 93 ASP cc_start: 0.7666 (t0) cc_final: 0.7376 (t0) REVERT: F 162 GLU cc_start: 0.6384 (mt-10) cc_final: 0.6119 (mt-10) REVERT: F 199 LEU cc_start: 0.7598 (tt) cc_final: 0.7274 (tp) REVERT: F 589 TYR cc_start: 0.7600 (m-10) cc_final: 0.7336 (m-80) REVERT: F 774 ILE cc_start: 0.8891 (mt) cc_final: 0.8621 (tt) REVERT: F 951 GLN cc_start: 0.6447 (mm-40) cc_final: 0.5970 (mm-40) REVERT: F 989 LEU cc_start: 0.7587 (mt) cc_final: 0.7169 (mt) REVERT: F 1001 ARG cc_start: 0.6248 (mtt90) cc_final: 0.5395 (mtt90) REVERT: F 1059 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6348 (mt-10) REVERT: G 189 ASN cc_start: 0.6698 (m110) cc_final: 0.6225 (m-40) REVERT: G 306 ASP cc_start: 0.7106 (p0) cc_final: 0.6883 (p0) REVERT: G 381 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7573 (mtt180) REVERT: G 487 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7863 (mtmm) REVERT: G 558 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7797 (ttmm) REVERT: G 562 GLU cc_start: 0.6455 (mp0) cc_final: 0.6243 (mp0) REVERT: G 688 LYS cc_start: 0.7285 (ttpp) cc_final: 0.7045 (ttpp) REVERT: G 772 ASP cc_start: 0.6572 (p0) cc_final: 0.5857 (p0) REVERT: G 830 ARG cc_start: 0.7142 (mtp85) cc_final: 0.6776 (mmt-90) REVERT: G 875 LYS cc_start: 0.7536 (tttt) cc_final: 0.7236 (tttp) REVERT: G 928 LEU cc_start: 0.8332 (mt) cc_final: 0.8014 (mt) REVERT: G 1030 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7446 (ttp-170) REVERT: G 1039 LYS cc_start: 0.7808 (mtmt) cc_final: 0.7517 (mtpp) REVERT: G 1059 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7065 (tp30) outliers start: 32 outliers final: 22 residues processed: 453 average time/residue: 0.4647 time to fit residues: 312.7675 Evaluate side-chains 450 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 428 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 428 MET 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 540 LEU Chi-restraints excluded: chain F residue 598 VAL 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 32 ASN Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 272 ASP Chi-restraints excluded: chain G residue 359 ASP Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain G residue 927 MET Chi-restraints excluded: chain G residue 994 ASN 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 111 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 232 optimal weight: 0.8980 chunk 262 optimal weight: 0.8980 chunk 229 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 307 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 308 GLN F 407 ASN F 676 GLN F1060 GLN G 178 HIS G 277 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 = 0.4119 r_free = 0.4119 target = 0.178128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.145917 restraints weight = 36354.350| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.22 r_work: 0.3565 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27043 Z= 0.129 Angle : 0.544 8.043 36892 Z= 0.295 Chirality : 0.041 0.284 4043 Planarity : 0.004 0.046 4518 Dihedral : 15.956 176.700 4169 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.43 % Allowed : 8.49 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3058 helix: 0.99 (0.15), residues: 1256 sheet: 0.04 (0.26), residues: 443 loop : -2.38 (0.15), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F1104 HIS 0.003 0.001 HIS F 938 PHE 0.024 0.001 PHE G 684 TYR 0.019 0.001 TYR E 363 ARG 0.004 0.000 ARG G1001 Details of bonding type rmsd hydrogen bonds : bond 0.05748 ( 970) hydrogen bonds : angle 4.43051 ( 2755) SS BOND : bond 0.00131 ( 1) SS BOND : angle 2.60063 ( 2) covalent geometry : bond 0.00270 (27042) covalent geometry : angle 0.54353 (36890) *********************** 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 477 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 438 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 237 ASP cc_start: 0.7072 (t0) cc_final: 0.6799 (t0) REVERT: E 240 LYS cc_start: 0.6949 (mmtt) cc_final: 0.6711 (mmtt) REVERT: E 241 GLU cc_start: 0.7349 (mp0) cc_final: 0.6855 (mp0) REVERT: E 263 GLN cc_start: 0.7549 (pp30) cc_final: 0.6922 (pp30) REVERT: E 348 ILE cc_start: 0.7133 (mt) cc_final: 0.6901 (mt) REVERT: E 566 PHE cc_start: 0.7880 (t80) cc_final: 0.7495 (t80) REVERT: E 578 ASP cc_start: 0.6810 (m-30) cc_final: 0.6547 (m-30) REVERT: E 608 SER cc_start: 0.8343 (m) cc_final: 0.7886 (t) REVERT: E 619 MET cc_start: 0.7870 (mtt) cc_final: 0.7624 (mtt) REVERT: E 631 LYS cc_start: 0.8525 (mttm) cc_final: 0.8141 (mttm) REVERT: F 31 LYS cc_start: 0.7105 (tppt) cc_final: 0.6756 (tppt) REVERT: F 93 ASP cc_start: 0.7657 (t0) cc_final: 0.7396 (t0) REVERT: F 162 GLU cc_start: 0.6320 (mt-10) cc_final: 0.6012 (mt-10) REVERT: F 199 LEU cc_start: 0.7532 (tt) cc_final: 0.7207 (tp) REVERT: F 594 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7535 (m) REVERT: F 774 ILE cc_start: 0.8789 (mt) cc_final: 0.8528 (tt) REVERT: F 951 GLN cc_start: 0.6545 (mm-40) cc_final: 0.6068 (mm-40) REVERT: F 989 LEU cc_start: 0.7537 (mt) cc_final: 0.7135 (mt) REVERT: F 1001 ARG cc_start: 0.6150 (mtt90) cc_final: 0.5383 (mtt90) REVERT: F 1002 VAL cc_start: 0.7799 (t) cc_final: 0.7462 (m) REVERT: G 72 ARG cc_start: 0.6581 (ttm170) cc_final: 0.6284 (ttm-80) REVERT: G 273 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7158 (mm-30) REVERT: G 306 ASP cc_start: 0.7141 (p0) cc_final: 0.6912 (p0) REVERT: G 487 LYS cc_start: 0.8152 (mtpt) cc_final: 0.7807 (mtmm) REVERT: G 511 ARG cc_start: 0.7444 (ttt180) cc_final: 0.7169 (tpt170) REVERT: G 532 MET cc_start: 0.8312 (mtt) cc_final: 0.8111 (mtm) REVERT: G 688 LYS cc_start: 0.7180 (ttpp) cc_final: 0.6976 (ttpp) REVERT: G 830 ARG cc_start: 0.7075 (mtp85) cc_final: 0.6761 (mmt-90) REVERT: G 875 LYS cc_start: 0.7471 (tttt) cc_final: 0.7090 (tttp) REVERT: G 928 LEU cc_start: 0.8131 (mt) cc_final: 0.7757 (mt) REVERT: G 952 ASP cc_start: 0.7237 (m-30) cc_final: 0.6902 (m-30) REVERT: G 1030 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7365 (ttp-170) REVERT: G 1039 LYS cc_start: 0.7713 (mtmt) cc_final: 0.7486 (mtpp) REVERT: G 1059 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7145 (tp30) outliers start: 39 outliers final: 27 residues processed: 449 average time/residue: 0.4684 time to fit residues: 310.6553 Evaluate side-chains 451 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 423 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 487 SER 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 63 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 254 THR 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 594 VAL Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 655 ILE Chi-restraints excluded: chain F residue 686 CYS Chi-restraints excluded: chain F residue 853 VAL 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 G residue 186 ILE Chi-restraints excluded: chain G residue 520 PHE Chi-restraints excluded: chain G residue 774 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 280 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 111 optimal weight: 0.0570 chunk 97 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 409 HIS E 654 ASN F 308 GLN F 496 HIS ** G 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.175656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142432 restraints weight = 36634.026| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.28 r_work: 0.3558 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2244 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= 0.130 Angle : 0.529 7.361 36892 Z= 0.286 Chirality : 0.040 0.293 4043 Planarity : 0.004 0.046 4518 Dihedral : 15.894 177.596 4169 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 1.91 % Allowed : 10.00 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3058 helix: 1.12 (0.15), residues: 1276 sheet: 0.00 (0.25), residues: 453 loop : -2.33 (0.15), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F1104 HIS 0.004 0.001 HIS F 307 PHE 0.025 0.001 PHE G 684 TYR 0.018 0.001 TYR E 363 ARG 0.006 0.000 ARG E 684 Details of bonding type rmsd hydrogen bonds : bond 0.05371 ( 970) hydrogen bonds : angle 4.16737 ( 2755) SS BOND : bond 0.00064 ( 1) SS BOND : angle 2.33499 ( 2) covalent geometry : bond 0.00280 (27042) covalent geometry : angle 0.52923 (36890) *********************** 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 468 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 416 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 ARG cc_start: 0.6960 (tpt170) cc_final: 0.6439 (tpt170) REVERT: E 263 GLN cc_start: 0.7560 (pp30) cc_final: 0.7037 (pp30) REVERT: E 470 GLU cc_start: 0.7090 (pp20) cc_final: 0.6789 (pm20) REVERT: E 578 ASP cc_start: 0.6784 (m-30) cc_final: 0.6537 (m-30) REVERT: E 588 GLU cc_start: 0.7819 (tp30) cc_final: 0.7596 (tp30) REVERT: E 608 SER cc_start: 0.8355 (m) cc_final: 0.7932 (t) REVERT: E 619 MET cc_start: 0.7844 (mtt) cc_final: 0.7625 (mtt) REVERT: E 631 LYS cc_start: 0.8553 (mttm) cc_final: 0.8349 (mttp) REVERT: F 31 LYS cc_start: 0.7048 (tppt) cc_final: 0.6732 (tppt) REVERT: F 93 ASP cc_start: 0.7741 (t0) cc_final: 0.7399 (t0) REVERT: F 162 GLU cc_start: 0.6337 (mt-10) cc_final: 0.6025 (mt-10) REVERT: F 199 LEU cc_start: 0.7545 (tt) cc_final: 0.7241 (tp) REVERT: F 594 VAL cc_start: 0.7697 (OUTLIER) cc_final: 0.7437 (m) REVERT: F 840 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.7049 (t0) REVERT: F 951 GLN cc_start: 0.6607 (mm-40) cc_final: 0.6094 (mm-40) REVERT: F 989 LEU cc_start: 0.7539 (mt) cc_final: 0.7115 (mt) REVERT: F 1001 ARG cc_start: 0.6137 (mtt90) cc_final: 0.5595 (mtt90) REVERT: G 72 ARG cc_start: 0.6604 (ttm170) cc_final: 0.6380 (ttm-80) REVERT: G 306 ASP cc_start: 0.7158 (p0) cc_final: 0.6911 (p0) REVERT: G 381 ARG cc_start: 0.7987 (mtt180) cc_final: 0.7669 (mtt180) REVERT: G 487 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7811 (mtmm) REVERT: G 511 ARG cc_start: 0.7352 (ttt180) cc_final: 0.7104 (tpt170) REVERT: G 532 MET cc_start: 0.8317 (mtt) cc_final: 0.8094 (mtm) REVERT: G 830 ARG cc_start: 0.7080 (mtp85) cc_final: 0.6802 (mmt-90) REVERT: G 875 LYS cc_start: 0.7505 (tttt) cc_final: 0.7119 (tttp) REVERT: G 934 VAL cc_start: 0.8032 (t) cc_final: 0.7720 (t) REVERT: G 952 ASP cc_start: 0.7306 (m-30) cc_final: 0.6977 (m-30) REVERT: G 1030 ARG cc_start: 0.7742 (ttp80) cc_final: 0.7345 (ttp-170) REVERT: G 1059 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7171 (tm-30) REVERT: G 1078 ASN cc_start: 0.7420 (OUTLIER) cc_final: 0.7094 (t0) outliers start: 52 outliers final: 35 residues processed: 436 average time/residue: 0.5179 time to fit residues: 340.9277 Evaluate side-chains 443 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 405 time to evaluate : 2.853 ------------------------------------------------------------------------------- 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 487 SER 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 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 226 LEU Chi-restraints excluded: chain F residue 275 ASP 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 632 ILE Chi-restraints excluded: chain F residue 686 CYS Chi-restraints excluded: chain F residue 833 GLN Chi-restraints excluded: chain F residue 840 ASP Chi-restraints excluded: chain F residue 853 VAL 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 503 GLU Chi-restraints excluded: chain G residue 520 PHE Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 758 VAL Chi-restraints excluded: chain G residue 774 ILE 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 1048 MET 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 289 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 239 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 E 683 GLN G 178 HIS G 668 ASN G 800 GLN G1157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139815 restraints weight = 36351.815| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.49 r_work: 0.3490 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27043 Z= 0.201 Angle : 0.596 9.641 36892 Z= 0.319 Chirality : 0.043 0.380 4043 Planarity : 0.004 0.044 4518 Dihedral : 15.968 177.589 4169 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.13 % Allowed : 11.54 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3058 helix: 0.97 (0.15), residues: 1269 sheet: -0.14 (0.24), residues: 460 loop : -2.38 (0.15), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 643 HIS 0.010 0.001 HIS F 307 PHE 0.024 0.002 PHE G 684 TYR 0.030 0.002 TYR E 363 ARG 0.008 0.000 ARG E 382 Details of bonding type rmsd hydrogen bonds : bond 0.06885 ( 970) hydrogen bonds : angle 4.37373 ( 2755) SS BOND : bond 0.00122 ( 1) SS BOND : angle 2.18536 ( 2) covalent geometry : bond 0.00469 (27042) covalent geometry : angle 0.59539 (36890) *********************** 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 486 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 428 time to evaluate : 3.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 237 ASP cc_start: 0.7092 (t0) cc_final: 0.6836 (t0) REVERT: E 263 GLN cc_start: 0.7593 (pp30) cc_final: 0.7032 (pp30) REVERT: E 277 PRO cc_start: 0.7986 (Cg_endo) cc_final: 0.7747 (Cg_exo) REVERT: E 452 VAL cc_start: 0.7740 (t) cc_final: 0.7362 (m) REVERT: E 467 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6549 (mt-10) REVERT: E 470 GLU cc_start: 0.7201 (pp20) cc_final: 0.6977 (pm20) REVERT: E 578 ASP cc_start: 0.6955 (m-30) cc_final: 0.6701 (m-30) REVERT: E 600 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7632 (tp40) REVERT: E 608 SER cc_start: 0.8538 (m) cc_final: 0.8123 (t) REVERT: F 5 ILE cc_start: 0.7493 (tp) cc_final: 0.7240 (tt) REVERT: F 31 LYS cc_start: 0.7160 (tppt) cc_final: 0.6814 (tppt) REVERT: F 93 ASP cc_start: 0.7747 (t0) cc_final: 0.7402 (t0) REVERT: F 162 GLU cc_start: 0.6397 (mt-10) cc_final: 0.6062 (mt-10) REVERT: F 199 LEU cc_start: 0.7579 (tt) cc_final: 0.7284 (tp) REVERT: F 774 ILE cc_start: 0.8807 (mt) cc_final: 0.8572 (tt) REVERT: F 951 GLN cc_start: 0.6586 (mm-40) cc_final: 0.6116 (mm-40) REVERT: F 989 LEU cc_start: 0.7573 (mt) cc_final: 0.7129 (mt) REVERT: F 1001 ARG cc_start: 0.6285 (mtt90) cc_final: 0.5760 (mtt90) REVERT: G 306 ASP cc_start: 0.7195 (p0) cc_final: 0.6962 (p0) REVERT: G 381 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7731 (mtt180) REVERT: G 487 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7785 (mtmm) REVERT: G 511 ARG cc_start: 0.7330 (ttt180) cc_final: 0.7088 (tpt170) REVERT: G 532 MET cc_start: 0.8365 (mtt) cc_final: 0.8103 (mtm) REVERT: G 875 LYS cc_start: 0.7596 (tttt) cc_final: 0.7205 (tttp) REVERT: G 883 ARG cc_start: 0.7728 (mtm180) cc_final: 0.7358 (mtm110) REVERT: G 952 ASP cc_start: 0.7322 (m-30) cc_final: 0.6885 (m-30) REVERT: G 1025 ARG cc_start: 0.6017 (tpp80) cc_final: 0.5611 (tpt90) REVERT: G 1030 ARG cc_start: 0.7814 (ttp-170) cc_final: 0.7089 (ttp80) REVERT: G 1059 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7226 (tm-30) REVERT: G 1078 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.7112 (t0) outliers start: 58 outliers final: 46 residues processed: 450 average time/residue: 0.5642 time to fit residues: 381.6392 Evaluate side-chains 471 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 424 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 175 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 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 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 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 686 CYS Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 833 GLN Chi-restraints excluded: chain F residue 853 VAL 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 562 GLU Chi-restraints excluded: chain G residue 758 VAL Chi-restraints excluded: chain G residue 774 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 63 optimal weight: 0.0670 chunk 173 optimal weight: 0.9980 chunk 160 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 254 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 285 optimal weight: 2.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- 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 144 GLN F 890 HIS F 935 HIS G 178 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.176301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143133 restraints weight = 36448.916| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.30 r_work: 0.3564 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27043 Z= 0.115 Angle : 0.510 7.688 36892 Z= 0.274 Chirality : 0.040 0.304 4043 Planarity : 0.004 0.047 4518 Dihedral : 15.843 178.480 4169 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.10 % Allowed : 12.32 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 3058 helix: 1.29 (0.15), residues: 1271 sheet: 0.08 (0.25), residues: 450 loop : -2.29 (0.15), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 643 HIS 0.003 0.001 HIS F 890 PHE 0.025 0.001 PHE G 684 TYR 0.015 0.001 TYR E 363 ARG 0.008 0.000 ARG G 72 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 970) hydrogen bonds : angle 3.96860 ( 2755) SS BOND : bond 0.00001 ( 1) SS BOND : angle 1.98558 ( 2) covalent geometry : bond 0.00244 (27042) covalent geometry : angle 0.51029 (36890) *********************** 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 477 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 420 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 ARG cc_start: 0.6938 (tpt170) cc_final: 0.6385 (tpt170) REVERT: E 237 ASP cc_start: 0.7032 (t0) cc_final: 0.6792 (t0) REVERT: E 241 GLU cc_start: 0.7397 (mp0) cc_final: 0.6938 (mp0) REVERT: E 263 GLN cc_start: 0.7513 (pp30) cc_final: 0.7067 (pp30) REVERT: E 470 GLU cc_start: 0.7050 (pp20) cc_final: 0.6810 (pm20) REVERT: E 551 LEU cc_start: 0.7877 (mm) cc_final: 0.7521 (mt) REVERT: E 578 ASP cc_start: 0.6791 (m-30) cc_final: 0.6545 (m-30) REVERT: E 600 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7577 (tp40) REVERT: E 608 SER cc_start: 0.8312 (m) cc_final: 0.7908 (t) REVERT: E 619 MET cc_start: 0.7889 (mtt) cc_final: 0.7642 (mtt) REVERT: F 31 LYS cc_start: 0.7071 (tppt) cc_final: 0.6763 (tppt) REVERT: F 93 ASP cc_start: 0.7737 (t0) cc_final: 0.7404 (t0) REVERT: F 234 ASN cc_start: 0.7592 (p0) cc_final: 0.7351 (p0) REVERT: F 406 VAL cc_start: 0.7652 (t) cc_final: 0.7358 (m) REVERT: F 951 GLN cc_start: 0.6621 (mm-40) cc_final: 0.6138 (mm-40) REVERT: F 989 LEU cc_start: 0.7520 (mt) cc_final: 0.7093 (mt) REVERT: F 1001 ARG cc_start: 0.6084 (mtt90) cc_final: 0.5638 (mtt90) REVERT: F 1002 VAL cc_start: 0.7767 (t) cc_final: 0.7499 (m) REVERT: G 72 ARG cc_start: 0.6665 (ttm-80) cc_final: 0.6330 (ttm-80) REVERT: G 91 VAL cc_start: 0.6665 (OUTLIER) cc_final: 0.5844 (p) REVERT: G 306 ASP cc_start: 0.7281 (p0) cc_final: 0.7064 (p0) REVERT: G 381 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7732 (mtt180) REVERT: G 487 LYS cc_start: 0.8111 (mtpt) cc_final: 0.7765 (mtmm) REVERT: G 875 LYS cc_start: 0.7505 (tttt) cc_final: 0.7152 (tttp) REVERT: G 934 VAL cc_start: 0.8016 (t) cc_final: 0.7700 (t) REVERT: G 952 ASP cc_start: 0.7268 (m-30) cc_final: 0.6926 (m-30) REVERT: G 1030 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.6952 (ttp80) REVERT: G 1059 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7313 (tp30) outliers start: 57 outliers final: 45 residues processed: 443 average time/residue: 0.4507 time to fit residues: 297.9547 Evaluate side-chains 460 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 414 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 306 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 557 GLU 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 354 VAL 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 632 ILE Chi-restraints excluded: chain F residue 644 LEU 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 853 VAL 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 91 VAL 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 562 GLU Chi-restraints excluded: chain G residue 758 VAL Chi-restraints excluded: chain G residue 938 HIS Chi-restraints excluded: chain G residue 1002 VAL Chi-restraints excluded: chain G residue 1048 MET 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 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 307 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 chunk 102 optimal weight: 0.0000 chunk 246 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 G 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.173268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139999 restraints weight = 36482.947| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.50 r_work: 0.3505 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2741 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= 0.183 Angle : 0.576 8.735 36892 Z= 0.308 Chirality : 0.042 0.343 4043 Planarity : 0.004 0.050 4518 Dihedral : 15.916 178.114 4169 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.39 % Allowed : 12.79 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3058 helix: 1.16 (0.15), residues: 1263 sheet: -0.07 (0.24), residues: 450 loop : -2.31 (0.15), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 643 HIS 0.009 0.001 HIS F 307 PHE 0.024 0.002 PHE G 684 TYR 0.027 0.002 TYR E 363 ARG 0.007 0.000 ARG G 72 Details of bonding type rmsd hydrogen bonds : bond 0.06396 ( 970) hydrogen bonds : angle 4.18674 ( 2755) SS BOND : bond 0.00087 ( 1) SS BOND : angle 1.98786 ( 2) covalent geometry : bond 0.00424 (27042) covalent geometry : angle 0.57590 (36890) *********************** 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 485 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 420 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 175 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7316 (ptp) REVERT: E 198 ARG cc_start: 0.6993 (tpt170) cc_final: 0.6420 (tpt170) REVERT: E 237 ASP cc_start: 0.7085 (t0) cc_final: 0.6852 (t0) REVERT: E 263 GLN cc_start: 0.7582 (pp30) cc_final: 0.7081 (pp30) REVERT: E 265 TYR cc_start: 0.6078 (m-10) cc_final: 0.5811 (m-10) REVERT: E 277 PRO cc_start: 0.8015 (Cg_endo) cc_final: 0.7759 (Cg_exo) REVERT: E 452 VAL cc_start: 0.7737 (t) cc_final: 0.7362 (m) REVERT: E 551 LEU cc_start: 0.7921 (mm) cc_final: 0.7596 (mt) REVERT: E 578 ASP cc_start: 0.6921 (m-30) cc_final: 0.6676 (m-30) REVERT: E 588 GLU cc_start: 0.7890 (tp30) cc_final: 0.7669 (tp30) REVERT: E 600 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7665 (tp40) REVERT: E 608 SER cc_start: 0.8523 (m) cc_final: 0.8133 (t) REVERT: F 5 ILE cc_start: 0.7448 (tp) cc_final: 0.7161 (tt) REVERT: F 31 LYS cc_start: 0.7184 (tppt) cc_final: 0.6879 (tppt) REVERT: F 93 ASP cc_start: 0.7749 (t0) cc_final: 0.7378 (t0) REVERT: F 199 LEU cc_start: 0.7580 (tt) cc_final: 0.7277 (tp) REVERT: F 774 ILE cc_start: 0.8775 (mt) cc_final: 0.8567 (tt) REVERT: F 951 GLN cc_start: 0.6698 (mm-40) cc_final: 0.6209 (mm-40) REVERT: F 989 LEU cc_start: 0.7561 (mt) cc_final: 0.7115 (mt) REVERT: F 1001 ARG cc_start: 0.6285 (mtt90) cc_final: 0.5850 (mtt90) REVERT: G 72 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6320 (ttm-80) REVERT: G 91 VAL cc_start: 0.6834 (OUTLIER) cc_final: 0.5961 (p) REVERT: G 140 GLU cc_start: 0.7564 (tp30) cc_final: 0.7356 (tp30) REVERT: G 306 ASP cc_start: 0.7325 (p0) cc_final: 0.7104 (p0) REVERT: G 381 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7758 (mtt180) REVERT: G 487 LYS cc_start: 0.8110 (mtpt) cc_final: 0.7759 (mtmm) REVERT: G 511 ARG cc_start: 0.7287 (ttt180) cc_final: 0.7041 (tpt170) REVERT: G 875 LYS cc_start: 0.7590 (tttt) cc_final: 0.7179 (tttp) REVERT: G 952 ASP cc_start: 0.7341 (m-30) cc_final: 0.6902 (m-30) REVERT: G 1030 ARG cc_start: 0.7761 (ttp-170) cc_final: 0.6991 (ttp80) REVERT: G 1059 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7338 (tp30) outliers start: 65 outliers final: 52 residues processed: 446 average time/residue: 0.4340 time to fit residues: 289.7132 Evaluate side-chains 471 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 416 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 428 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 E residue 648 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 35 GLU 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 354 VAL Chi-restraints excluded: chain F residue 540 LEU 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 644 LEU 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 853 VAL 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 91 VAL 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 510 THR Chi-restraints excluded: chain G residue 520 PHE Chi-restraints excluded: chain G residue 758 VAL Chi-restraints excluded: chain G residue 774 ILE 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 1007 MET Chi-restraints excluded: chain G residue 1039 LYS Chi-restraints excluded: chain G residue 1048 MET 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 47 optimal weight: 0.9990 chunk 260 optimal weight: 4.9990 chunk 26 optimal weight: 0.0060 chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 0.0980 chunk 154 optimal weight: 0.0070 chunk 142 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 307 optimal weight: 0.0040 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.1426 ------------------------------------------------------------------------------- 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 144 GLN G 50 GLN G 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.178529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.145571 restraints weight = 36563.983| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.32 r_work: 0.3598 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27043 Z= 0.101 Angle : 0.490 6.528 36892 Z= 0.263 Chirality : 0.039 0.292 4043 Planarity : 0.004 0.043 4518 Dihedral : 15.799 179.609 4169 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.73 % Allowed : 13.64 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3058 helix: 1.50 (0.15), residues: 1273 sheet: 0.09 (0.25), residues: 443 loop : -2.16 (0.15), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 643 HIS 0.003 0.001 HIS F 307 PHE 0.025 0.001 PHE G 684 TYR 0.009 0.001 TYR E 458 ARG 0.007 0.000 ARG G 72 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 970) hydrogen bonds : angle 3.72293 ( 2755) SS BOND : bond 0.00096 ( 1) SS BOND : angle 1.75130 ( 2) covalent geometry : bond 0.00205 (27042) covalent geometry : angle 0.49000 (36890) *********************** 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 457 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 410 time to evaluate : 2.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 ARG cc_start: 0.6932 (tpt170) cc_final: 0.6341 (tpt170) REVERT: E 237 ASP cc_start: 0.7067 (t0) cc_final: 0.6827 (t0) REVERT: E 241 GLU cc_start: 0.7401 (mp0) cc_final: 0.6970 (mp0) REVERT: E 263 GLN cc_start: 0.7502 (pp30) cc_final: 0.7076 (pp30) REVERT: E 551 LEU cc_start: 0.7837 (mm) cc_final: 0.7512 (mt) REVERT: E 600 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7581 (tp40) REVERT: E 608 SER cc_start: 0.8234 (m) cc_final: 0.7831 (t) REVERT: F 5 ILE cc_start: 0.7488 (tp) cc_final: 0.7158 (tt) REVERT: F 31 LYS cc_start: 0.7096 (tppt) cc_final: 0.6835 (tppt) REVERT: F 93 ASP cc_start: 0.7714 (t0) cc_final: 0.7414 (t0) REVERT: F 234 ASN cc_start: 0.7384 (p0) cc_final: 0.7158 (p0) REVERT: F 406 VAL cc_start: 0.7547 (t) cc_final: 0.7329 (m) REVERT: F 774 ILE cc_start: 0.8659 (mt) cc_final: 0.8456 (tt) REVERT: F 951 GLN cc_start: 0.6598 (mm-40) cc_final: 0.6128 (mm-40) REVERT: F 989 LEU cc_start: 0.7511 (mt) cc_final: 0.7079 (mt) REVERT: F 1001 ARG cc_start: 0.6036 (mtt90) cc_final: 0.5662 (mtt90) REVERT: F 1163 GLU cc_start: 0.6729 (tt0) cc_final: 0.6282 (tm-30) REVERT: G 72 ARG cc_start: 0.6627 (ttm-80) cc_final: 0.6262 (ttm-80) REVERT: G 91 VAL cc_start: 0.6603 (OUTLIER) cc_final: 0.5859 (p) REVERT: G 140 GLU cc_start: 0.7473 (tp30) cc_final: 0.7202 (tp30) REVERT: G 381 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7723 (mtt180) REVERT: G 487 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7756 (mtmm) REVERT: G 875 LYS cc_start: 0.7446 (tttt) cc_final: 0.7102 (tttp) REVERT: G 928 LEU cc_start: 0.8042 (mt) cc_final: 0.7662 (mt) REVERT: G 934 VAL cc_start: 0.8032 (t) cc_final: 0.7671 (t) REVERT: G 952 ASP cc_start: 0.7233 (m-30) cc_final: 0.6894 (m-30) REVERT: G 1030 ARG cc_start: 0.7683 (ttp-170) cc_final: 0.6936 (ttp80) REVERT: G 1059 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7300 (tp30) REVERT: G 1078 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.7156 (t0) outliers start: 47 outliers final: 35 residues processed: 424 average time/residue: 0.4507 time to fit residues: 285.3461 Evaluate side-chains 438 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 401 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 495 THR 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 648 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 354 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 686 CYS Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 975 LEU Chi-restraints excluded: chain F residue 1097 ILE Chi-restraints excluded: chain G residue 91 VAL 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 503 GLU Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain G residue 520 PHE 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 1007 MET Chi-restraints excluded: chain G residue 1039 LYS Chi-restraints excluded: chain G residue 1048 MET 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 164 optimal weight: 9.9990 chunk 137 optimal weight: 0.7980 chunk 300 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 233 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 54 optimal weight: 0.0470 chunk 52 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- 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 144 GLN G 50 GLN G 277 GLN G 890 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.174498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141220 restraints weight = 36529.716| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.28 r_work: 0.3539 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27043 Z= 0.154 Angle : 0.541 7.243 36892 Z= 0.289 Chirality : 0.041 0.320 4043 Planarity : 0.004 0.055 4518 Dihedral : 15.831 179.936 4169 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.00 % Favored : 92.97 % Rotamer: Outliers : 2.02 % Allowed : 13.46 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3058 helix: 1.43 (0.15), residues: 1270 sheet: 0.01 (0.25), residues: 438 loop : -2.17 (0.15), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 643 HIS 0.006 0.001 HIS F 307 PHE 0.024 0.001 PHE G 684 TYR 0.022 0.001 TYR E 363 ARG 0.007 0.000 ARG G 72 Details of bonding type rmsd hydrogen bonds : bond 0.05413 ( 970) hydrogen bonds : angle 3.94238 ( 2755) SS BOND : bond 0.00022 ( 1) SS BOND : angle 1.90515 ( 2) covalent geometry : bond 0.00353 (27042) covalent geometry : angle 0.54088 (36890) *********************** 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 479 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 424 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 ARG cc_start: 0.6968 (tpt170) cc_final: 0.6395 (tpt170) REVERT: E 237 ASP cc_start: 0.7033 (t0) cc_final: 0.6789 (t0) REVERT: E 241 GLU cc_start: 0.7394 (mp0) cc_final: 0.6941 (mp0) REVERT: E 263 GLN cc_start: 0.7521 (pp30) cc_final: 0.7064 (pp30) REVERT: E 277 PRO cc_start: 0.8016 (Cg_endo) cc_final: 0.7732 (Cg_exo) REVERT: E 551 LEU cc_start: 0.7893 (mm) cc_final: 0.7556 (mt) REVERT: E 600 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7642 (tp40) REVERT: E 608 SER cc_start: 0.8414 (m) cc_final: 0.8030 (t) REVERT: F 5 ILE cc_start: 0.7484 (tp) cc_final: 0.7210 (tt) REVERT: F 31 LYS cc_start: 0.7186 (tppt) cc_final: 0.6917 (tppt) REVERT: F 93 ASP cc_start: 0.7732 (t0) cc_final: 0.7368 (t0) REVERT: F 199 LEU cc_start: 0.7573 (tt) cc_final: 0.7295 (tp) REVERT: F 774 ILE cc_start: 0.8735 (mt) cc_final: 0.8530 (tt) REVERT: F 951 GLN cc_start: 0.6627 (mm-40) cc_final: 0.6150 (mm-40) REVERT: F 989 LEU cc_start: 0.7551 (mt) cc_final: 0.7122 (mt) REVERT: F 1001 ARG cc_start: 0.6129 (mtt90) cc_final: 0.5780 (mtt90) REVERT: G 72 ARG cc_start: 0.6680 (ttm-80) cc_final: 0.6319 (ttm-80) REVERT: G 91 VAL cc_start: 0.6813 (OUTLIER) cc_final: 0.5993 (p) REVERT: G 140 GLU cc_start: 0.7451 (tp30) cc_final: 0.7186 (tp30) REVERT: G 381 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7759 (mtt180) REVERT: G 487 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7763 (mtmm) REVERT: G 875 LYS cc_start: 0.7535 (tttt) cc_final: 0.7187 (tttp) REVERT: G 934 VAL cc_start: 0.8026 (t) cc_final: 0.7698 (t) REVERT: G 952 ASP cc_start: 0.7291 (m-30) cc_final: 0.6955 (m-30) REVERT: G 1030 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.6967 (ttp80) REVERT: G 1078 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.7189 (t0) outliers start: 55 outliers final: 44 residues processed: 445 average time/residue: 0.4241 time to fit residues: 281.5599 Evaluate side-chains 464 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 418 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 428 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 541 GLU 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 35 GLU 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 122 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 354 VAL Chi-restraints excluded: chain F residue 520 PHE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 609 ASP Chi-restraints excluded: chain F residue 644 LEU 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 975 LEU Chi-restraints excluded: chain F residue 1097 ILE Chi-restraints excluded: chain G residue 91 VAL 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 503 GLU Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain G residue 758 VAL Chi-restraints excluded: chain G residue 774 ILE 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 1007 MET Chi-restraints excluded: chain G residue 1048 MET 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 244 optimal weight: 1.9990 chunk 282 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 280 optimal weight: 0.0000 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 144 GLN G 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.174620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.141439 restraints weight = 36257.779| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.27 r_work: 0.3542 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27043 Z= 0.144 Angle : 0.537 7.393 36892 Z= 0.288 Chirality : 0.041 0.346 4043 Planarity : 0.004 0.049 4518 Dihedral : 15.818 179.192 4169 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.77 % Favored : 93.20 % Rotamer: Outliers : 1.80 % Allowed : 13.60 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3058 helix: 1.40 (0.15), residues: 1269 sheet: -0.03 (0.25), residues: 441 loop : -2.16 (0.15), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 643 HIS 0.006 0.001 HIS F 307 PHE 0.025 0.001 PHE G 684 TYR 0.022 0.001 TYR E 363 ARG 0.007 0.000 ARG G 72 Details of bonding type rmsd hydrogen bonds : bond 0.05257 ( 970) hydrogen bonds : angle 3.94549 ( 2755) SS BOND : bond 0.00015 ( 1) SS BOND : angle 1.86128 ( 2) covalent geometry : bond 0.00326 (27042) covalent geometry : angle 0.53692 (36890) ********************** 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 465 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 416 time to evaluate : 3.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 175 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7262 (ptp) REVERT: E 198 ARG cc_start: 0.7002 (tpt170) cc_final: 0.6430 (tpt170) REVERT: E 237 ASP cc_start: 0.7033 (t0) cc_final: 0.6789 (t0) REVERT: E 241 GLU cc_start: 0.7385 (mp0) cc_final: 0.6923 (mp0) REVERT: E 551 LEU cc_start: 0.7885 (mm) cc_final: 0.7553 (mt) REVERT: E 600 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7647 (tp40) REVERT: E 608 SER cc_start: 0.8413 (m) cc_final: 0.8038 (t) REVERT: F 5 ILE cc_start: 0.7474 (tp) cc_final: 0.7218 (tt) REVERT: F 31 LYS cc_start: 0.7197 (tppt) cc_final: 0.6917 (tppt) REVERT: F 93 ASP cc_start: 0.7756 (t0) cc_final: 0.7394 (t0) REVERT: F 503 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6647 (tp30) REVERT: F 774 ILE cc_start: 0.8745 (mt) cc_final: 0.8544 (tt) REVERT: F 951 GLN cc_start: 0.6623 (mm-40) cc_final: 0.6136 (mm-40) REVERT: F 989 LEU cc_start: 0.7550 (mt) cc_final: 0.7125 (mt) REVERT: F 1001 ARG cc_start: 0.6092 (mtt90) cc_final: 0.5797 (mtt90) REVERT: G 72 ARG cc_start: 0.6667 (ttm-80) cc_final: 0.6301 (ttm-80) REVERT: G 91 VAL cc_start: 0.6749 (OUTLIER) cc_final: 0.5914 (p) REVERT: G 140 GLU cc_start: 0.7554 (tp30) cc_final: 0.7282 (tp30) REVERT: G 381 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7730 (mtt180) REVERT: G 487 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7759 (mtmm) REVERT: G 875 LYS cc_start: 0.7520 (tttt) cc_final: 0.7175 (tttp) REVERT: G 952 ASP cc_start: 0.7305 (m-30) cc_final: 0.6966 (m-30) REVERT: G 1030 ARG cc_start: 0.7713 (ttp-170) cc_final: 0.7458 (ttp80) REVERT: G 1078 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.7190 (t0) outliers start: 49 outliers final: 42 residues processed: 432 average time/residue: 0.4847 time to fit residues: 314.1383 Evaluate side-chains 454 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 409 time to evaluate : 4.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 428 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain E residue 506 ILE Chi-restraints excluded: chain E residue 541 GLU 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 35 GLU 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 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 275 ASP 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 609 ASP Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 686 CYS Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 975 LEU Chi-restraints excluded: chain F residue 1097 ILE Chi-restraints excluded: chain G residue 91 VAL 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 503 GLU Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain G residue 520 PHE 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 1007 MET Chi-restraints excluded: chain G residue 1048 MET 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 83 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 288 optimal weight: 0.0770 chunk 18 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 683 GLN F 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.173443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140217 restraints weight = 36376.048| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.27 r_work: 0.3525 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3124 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= 0.166 Angle : 0.563 7.394 36892 Z= 0.301 Chirality : 0.042 0.382 4043 Planarity : 0.004 0.057 4518 Dihedral : 15.853 179.267 4169 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.39 % Favored : 92.58 % Rotamer: Outliers : 2.10 % Allowed : 13.46 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3058 helix: 1.33 (0.15), residues: 1265 sheet: -0.11 (0.25), residues: 439 loop : -2.17 (0.15), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 643 HIS 0.008 0.001 HIS F 307 PHE 0.024 0.001 PHE G 684 TYR 0.027 0.001 TYR E 363 ARG 0.007 0.000 ARG G 72 Details of bonding type rmsd hydrogen bonds : bond 0.05957 ( 970) hydrogen bonds : angle 4.06651 ( 2755) SS BOND : bond 0.00044 ( 1) SS BOND : angle 1.87469 ( 2) covalent geometry : bond 0.00383 (27042) covalent geometry : angle 0.56306 (36890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14432.04 seconds wall clock time: 253 minutes 7.71 seconds (15187.71 seconds total)