Starting phenix.real_space_refine on Fri Feb 6 03:32:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9li9_63114/02_2026/9li9_63114_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9li9_63114/02_2026/9li9_63114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9li9_63114/02_2026/9li9_63114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9li9_63114/02_2026/9li9_63114.map" model { file = "/net/cci-nas-00/data/ceres_data/9li9_63114/02_2026/9li9_63114_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9li9_63114/02_2026/9li9_63114_neut.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.097 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 6 5.49 5 Mg 2 5.21 5 S 102 5.16 5 C 14092 2.51 5 N 3700 2.21 5 O 3948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21850 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1380, 10893 Classifications: {'peptide': 1380} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1325} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 12.84, per 1000 atoms: 0.59 Number of scatterers: 21850 At special positions: 0 Unit cell: (126.5, 152.9, 145.2, 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 102 16.00 P 6 15.00 Mg 2 11.99 O 3948 8.00 N 3700 7.00 C 14092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 857.1 milliseconds 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 8 sheets defined 59.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 26 through 28 No H-bonds generated for 'chain 'A' and resid 26 through 28' Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.521A pdb=" N THR A 34 " --> pdb=" O THR A 30 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 36 " --> pdb=" O CYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 56 removed outlier: 4.214A pdb=" N GLN A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.818A pdb=" N PHE A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS A 67 " --> pdb=" O GLU A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 67' Processing helix chain 'A' and resid 76 through 83 removed outlier: 3.508A pdb=" N LEU A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 130 removed outlier: 4.124A pdb=" N GLY A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 162 removed outlier: 3.595A pdb=" N VAL A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 189 removed outlier: 3.686A pdb=" N SER A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.876A pdb=" N ILE A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.513A pdb=" N MET A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 267 through 285 removed outlier: 3.743A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 281 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.826A pdb=" N ALA A 293 " --> pdb=" O TRP A 289 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.666A pdb=" N TRP A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 318 through 330 removed outlier: 4.133A pdb=" N ASN A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 373 removed outlier: 4.131A pdb=" N ILE A 341 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 342 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR A 360 " --> pdb=" O CYS A 356 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 removed outlier: 3.738A pdb=" N ARG A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.555A pdb=" N ARG A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 392' Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 418 through 436 Proline residue: A 424 - end of helix removed outlier: 3.568A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.525A pdb=" N ILE A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 445' Processing helix chain 'A' and resid 446 through 451 removed outlier: 3.588A pdb=" N LEU A 449 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 450 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 474 through 485 removed outlier: 4.407A pdb=" N GLU A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.512A pdb=" N VAL A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 531 removed outlier: 3.616A pdb=" N SER A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL A 504 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.678A pdb=" N VAL A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 568 removed outlier: 3.523A pdb=" N PHE A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 559 " --> pdb=" O ARG A 555 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 563 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.686A pdb=" N VAL A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 663 removed outlier: 3.537A pdb=" N LEU A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.691A pdb=" N ARG A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 712 " --> pdb=" O LYS A 708 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 713 " --> pdb=" O TYR A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 removed outlier: 3.533A pdb=" N GLU A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 724 " --> pdb=" O HIS A 720 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.519A pdb=" N GLN A 746 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 749 " --> pdb=" O LYS A 745 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 782 removed outlier: 3.667A pdb=" N PHE A 779 " --> pdb=" O GLY A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 831 through 836 Processing helix chain 'A' and resid 837 through 839 No H-bonds generated for 'chain 'A' and resid 837 through 839' Processing helix chain 'A' and resid 904 through 916 removed outlier: 3.532A pdb=" N LEU A 908 " --> pdb=" O SER A 904 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 937 removed outlier: 3.923A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 926 " --> pdb=" O MET A 922 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N CYS A 927 " --> pdb=" O MET A 923 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR A 928 " --> pdb=" O LEU A 924 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 930 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR A 931 " --> pdb=" O CYS A 927 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 932 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 947 removed outlier: 3.697A pdb=" N LEU A 942 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 944 " --> pdb=" O THR A 940 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 947 " --> pdb=" O SER A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 1001 removed outlier: 3.948A pdb=" N TYR A 959 " --> pdb=" O GLY A 955 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 962 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 976 " --> pdb=" O LEU A 972 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 978 " --> pdb=" O THR A 974 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 981 " --> pdb=" O ASN A 977 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 982 " --> pdb=" O SER A 978 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 984 " --> pdb=" O TRP A 980 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 988 " --> pdb=" O SER A 984 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1010 removed outlier: 4.161A pdb=" N PHE A1008 " --> pdb=" O PRO A1004 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS A1009 " --> pdb=" O MET A1005 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A1010 " --> pdb=" O SER A1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1004 through 1010' Processing helix chain 'A' and resid 1012 through 1022 removed outlier: 3.802A pdb=" N ILE A1016 " --> pdb=" O PRO A1012 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1030 removed outlier: 3.740A pdb=" N ASP A1028 " --> pdb=" O LEU A1024 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A1029 " --> pdb=" O GLY A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1056 removed outlier: 3.875A pdb=" N ASN A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET A1037 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A1038 " --> pdb=" O PHE A1034 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A1044 " --> pdb=" O GLY A1040 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A1053 " --> pdb=" O VAL A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1062 removed outlier: 3.524A pdb=" N LEU A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1075 Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1092 through 1105 removed outlier: 3.758A pdb=" N TYR A1096 " --> pdb=" O ARG A1092 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN A1098 " --> pdb=" O PRO A1094 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A1105 " --> pdb=" O GLU A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1110 removed outlier: 3.545A pdb=" N ARG A1110 " --> pdb=" O LEU A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1121 Processing helix chain 'A' and resid 1121 through 1126 Processing helix chain 'A' and resid 1130 through 1149 removed outlier: 3.903A pdb=" N ASN A1136 " --> pdb=" O PHE A1132 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A1140 " --> pdb=" O ASN A1136 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A1144 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A1145 " --> pdb=" O ARG A1141 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A1146 " --> pdb=" O TRP A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1166 removed outlier: 3.739A pdb=" N ILE A1155 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A1160 " --> pdb=" O TRP A1156 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL A1163 " --> pdb=" O ALA A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1178 No H-bonds generated for 'chain 'A' and resid 1176 through 1178' Processing helix chain 'A' and resid 1179 through 1185 Processing helix chain 'A' and resid 1188 through 1200 removed outlier: 4.545A pdb=" N THR A1194 " --> pdb=" O THR A1190 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY A1195 " --> pdb=" O SER A1191 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A1199 " --> pdb=" O GLY A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1205 removed outlier: 3.715A pdb=" N GLU A1204 " --> pdb=" O ALA A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1212 Processing helix chain 'A' and resid 1283 through 1288 removed outlier: 3.660A pdb=" N ASN A1287 " --> pdb=" O SER A1283 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A1288 " --> pdb=" O SER A1284 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1283 through 1288' Processing helix chain 'A' and resid 1311 through 1316 Processing helix chain 'A' and resid 1332 through 1338 Processing helix chain 'A' and resid 1344 through 1355 removed outlier: 3.765A pdb=" N LEU A1348 " --> pdb=" O ASN A1344 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP A1349 " --> pdb=" O ASP A1345 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A1350 " --> pdb=" O ALA A1346 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A1353 " --> pdb=" O TRP A1349 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A1354 " --> pdb=" O GLU A1350 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A1355 " --> pdb=" O SER A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1363 Processing helix chain 'A' and resid 1380 through 1387 Processing helix chain 'A' and resid 1388 through 1396 removed outlier: 3.766A pdb=" N ALA A1392 " --> pdb=" O SER A1388 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A1394 " --> pdb=" O SER A1390 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A1395 " --> pdb=" O ARG A1391 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG A1396 " --> pdb=" O ALA A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1425 removed outlier: 3.650A pdb=" N LEU A1416 " --> pdb=" O ARG A1412 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS A1419 " --> pdb=" O ALA A1415 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A1422 " --> pdb=" O GLN A1418 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A1425 " --> pdb=" O ILE A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1440 removed outlier: 3.837A pdb=" N THR A1439 " --> pdb=" O ARG A1436 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A1440 " --> pdb=" O LEU A1437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1436 through 1440' Processing helix chain 'A' and resid 1459 through 1464 Processing helix chain 'A' and resid 1469 through 1477 removed outlier: 3.934A pdb=" N SER A1477 " --> pdb=" O LYS A1473 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.520A pdb=" N THR B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER B 36 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 56 removed outlier: 4.213A pdb=" N GLN B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 removed outlier: 3.818A pdb=" N PHE B 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS B 67 " --> pdb=" O GLU B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 67' Processing helix chain 'B' and resid 76 through 83 removed outlier: 3.509A pdb=" N LEU B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 130 removed outlier: 4.123A pdb=" N GLY B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET B 130 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 162 removed outlier: 3.595A pdb=" N VAL B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 189 removed outlier: 3.686A pdb=" N SER B 178 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 238 removed outlier: 3.877A pdb=" N ILE B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.514A pdb=" N MET B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 248 " --> pdb=" O PRO B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 267 through 285 removed outlier: 3.743A pdb=" N PHE B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS B 281 " --> pdb=" O HIS B 277 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B 284 " --> pdb=" O ASP B 280 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.826A pdb=" N ALA B 293 " --> pdb=" O TRP B 289 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.666A pdb=" N TRP B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 318 through 330 removed outlier: 4.133A pdb=" N ASN B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 373 removed outlier: 4.131A pdb=" N ILE B 341 " --> pdb=" O TRP B 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 351 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 356 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR B 360 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN B 363 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 384 removed outlier: 3.738A pdb=" N ARG B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 392 removed outlier: 3.555A pdb=" N ARG B 391 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 392 " --> pdb=" O ASN B 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 392' Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 418 through 436 Proline residue: B 424 - end of helix removed outlier: 3.569A pdb=" N ILE B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 436 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 445 removed outlier: 3.526A pdb=" N ILE B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 440 through 445' Processing helix chain 'B' and resid 446 through 451 removed outlier: 3.588A pdb=" N LEU B 449 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 450 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 474 through 485 removed outlier: 4.408A pdb=" N GLU B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 494 removed outlier: 3.512A pdb=" N VAL B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 531 removed outlier: 3.617A pdb=" N SER B 502 " --> pdb=" O ASN B 498 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 503 " --> pdb=" O SER B 499 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL B 504 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 507 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP B 514 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 521 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 527 " --> pdb=" O ALA B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 547 removed outlier: 3.678A pdb=" N VAL B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 568 removed outlier: 3.523A pdb=" N PHE B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER B 559 " --> pdb=" O ARG B 555 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 563 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 589 removed outlier: 3.686A pdb=" N VAL B 585 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 589 " --> pdb=" O VAL B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 663 removed outlier: 3.538A pdb=" N LEU B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 removed outlier: 3.690A pdb=" N ARG B 711 " --> pdb=" O GLU B 707 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 713 " --> pdb=" O TYR B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 725 removed outlier: 3.534A pdb=" N GLU B 723 " --> pdb=" O LYS B 719 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 724 " --> pdb=" O HIS B 720 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 725 " --> pdb=" O ASP B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.519A pdb=" N GLN B 746 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 749 " --> pdb=" O LYS B 745 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA B 753 " --> pdb=" O SER B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 782 removed outlier: 3.667A pdb=" N PHE B 779 " --> pdb=" O GLY B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 831 through 836 Processing helix chain 'B' and resid 837 through 839 No H-bonds generated for 'chain 'B' and resid 837 through 839' Processing helix chain 'B' and resid 904 through 916 removed outlier: 3.531A pdb=" N LEU B 908 " --> pdb=" O SER B 904 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 916 " --> pdb=" O GLN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 937 removed outlier: 3.923A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 924 " --> pdb=" O VAL B 920 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 926 " --> pdb=" O MET B 922 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N CYS B 927 " --> pdb=" O MET B 923 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B 928 " --> pdb=" O LEU B 924 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 930 " --> pdb=" O LEU B 926 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B 931 " --> pdb=" O CYS B 927 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B 932 " --> pdb=" O TYR B 928 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 935 " --> pdb=" O THR B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 947 removed outlier: 3.698A pdb=" N LEU B 942 " --> pdb=" O SER B 938 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 944 " --> pdb=" O THR B 940 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 947 " --> pdb=" O SER B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 1001 removed outlier: 3.948A pdb=" N TYR B 959 " --> pdb=" O GLY B 955 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 960 " --> pdb=" O PRO B 956 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 962 " --> pdb=" O PHE B 958 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN B 970 " --> pdb=" O LEU B 966 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 974 " --> pdb=" O GLN B 970 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B 976 " --> pdb=" O LEU B 972 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 978 " --> pdb=" O THR B 974 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 981 " --> pdb=" O ASN B 977 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 982 " --> pdb=" O SER B 978 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 984 " --> pdb=" O TRP B 980 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B 987 " --> pdb=" O MET B 983 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 988 " --> pdb=" O SER B 984 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 996 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B1001 " --> pdb=" O LEU B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1010 removed outlier: 4.161A pdb=" N PHE B1008 " --> pdb=" O PRO B1004 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS B1009 " --> pdb=" O MET B1005 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B1010 " --> pdb=" O SER B1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1004 through 1010' Processing helix chain 'B' and resid 1012 through 1022 removed outlier: 3.802A pdb=" N ILE B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B1019 " --> pdb=" O ARG B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1030 removed outlier: 3.739A pdb=" N ASP B1028 " --> pdb=" O LEU B1024 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG B1029 " --> pdb=" O GLY B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1056 removed outlier: 3.875A pdb=" N ASN B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET B1037 " --> pdb=" O VAL B1033 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B1038 " --> pdb=" O PHE B1034 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN B1044 " --> pdb=" O GLY B1040 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B1047 " --> pdb=" O SER B1043 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B1050 " --> pdb=" O LEU B1046 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B1051 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B1053 " --> pdb=" O VAL B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1062 removed outlier: 3.523A pdb=" N LEU B1060 " --> pdb=" O SER B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1075 Processing helix chain 'B' and resid 1082 through 1087 Processing helix chain 'B' and resid 1092 through 1105 removed outlier: 3.758A pdb=" N TYR B1096 " --> pdb=" O ARG B1092 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B1097 " --> pdb=" O SER B1093 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN B1098 " --> pdb=" O PRO B1094 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B1101 " --> pdb=" O ALA B1097 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B1105 " --> pdb=" O GLU B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1110 removed outlier: 3.545A pdb=" N ARG B1110 " --> pdb=" O LEU B1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1121 Processing helix chain 'B' and resid 1121 through 1126 Processing helix chain 'B' and resid 1130 through 1149 removed outlier: 3.903A pdb=" N ASN B1136 " --> pdb=" O PHE B1132 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B1140 " --> pdb=" O ASN B1136 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B1141 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP B1142 " --> pdb=" O GLY B1138 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B1144 " --> pdb=" O ASN B1140 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B1145 " --> pdb=" O ARG B1141 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B1146 " --> pdb=" O TRP B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1166 removed outlier: 3.738A pdb=" N ILE B1155 " --> pdb=" O GLY B1151 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B1160 " --> pdb=" O TRP B1156 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL B1163 " --> pdb=" O ALA B1159 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1178 No H-bonds generated for 'chain 'B' and resid 1176 through 1178' Processing helix chain 'B' and resid 1179 through 1185 Processing helix chain 'B' and resid 1188 through 1200 removed outlier: 4.544A pdb=" N THR B1194 " --> pdb=" O THR B1190 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY B1195 " --> pdb=" O SER B1191 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B1197 " --> pdb=" O LEU B1193 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B1199 " --> pdb=" O GLY B1195 " (cutoff:3.500A) Processing helix chain 'B' and resid 1200 through 1205 removed outlier: 3.714A pdb=" N GLU B1204 " --> pdb=" O ALA B1200 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1212 Processing helix chain 'B' and resid 1283 through 1288 removed outlier: 3.661A pdb=" N ASN B1287 " --> pdb=" O SER B1283 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B1288 " --> pdb=" O SER B1284 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1283 through 1288' Processing helix chain 'B' and resid 1311 through 1316 Processing helix chain 'B' and resid 1332 through 1338 Processing helix chain 'B' and resid 1344 through 1355 removed outlier: 3.765A pdb=" N LEU B1348 " --> pdb=" O ASN B1344 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP B1349 " --> pdb=" O ASP B1345 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU B1350 " --> pdb=" O ALA B1346 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU B1353 " --> pdb=" O TRP B1349 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B1354 " --> pdb=" O GLU B1350 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B1355 " --> pdb=" O SER B1351 " (cutoff:3.500A) Processing helix chain 'B' and resid 1358 through 1363 Processing helix chain 'B' and resid 1380 through 1387 Processing helix chain 'B' and resid 1388 through 1396 removed outlier: 3.766A pdb=" N ALA B1392 " --> pdb=" O SER B1388 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B1394 " --> pdb=" O SER B1390 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B1395 " --> pdb=" O ARG B1391 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG B1396 " --> pdb=" O ALA B1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1425 removed outlier: 3.651A pdb=" N LEU B1416 " --> pdb=" O ARG B1412 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS B1419 " --> pdb=" O ALA B1415 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B1422 " --> pdb=" O GLN B1418 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B1425 " --> pdb=" O ILE B1421 " (cutoff:3.500A) Processing helix chain 'B' and resid 1436 through 1440 removed outlier: 3.836A pdb=" N THR B1439 " --> pdb=" O ARG B1436 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B1440 " --> pdb=" O LEU B1437 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1436 through 1440' Processing helix chain 'B' and resid 1459 through 1464 Processing helix chain 'B' and resid 1469 through 1477 removed outlier: 3.934A pdb=" N SER B1477 " --> pdb=" O LYS B1473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 632 through 639 removed outlier: 6.173A pdb=" N GLY A 619 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN A 636 " --> pdb=" O ARG A 617 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG A 617 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP A 638 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N SER A 615 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 680 through 683 removed outlier: 6.514A pdb=" N ALA A 681 " --> pdb=" O ILE A 762 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASP A 764 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 683 " --> pdb=" O ASP A 764 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 645 " --> pdb=" O LEU A 794 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 644 " --> pdb=" O ARG A 807 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL A 809 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA A 646 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 811 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 648 " --> pdb=" O VAL A 811 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 810 " --> pdb=" O GLU A 818 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A 818 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1259 through 1266 removed outlier: 7.259A pdb=" N HIS A1260 " --> pdb=" O VAL A1248 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL A1248 " --> pdb=" O HIS A1260 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A1262 " --> pdb=" O ASP A1246 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A1264 " --> pdb=" O PHE A1244 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1242 " --> pdb=" O ILE A1266 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A1247 " --> pdb=" O LYS A1297 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS A1297 " --> pdb=" O VAL A1247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1319 through 1322 removed outlier: 7.061A pdb=" N LEU A1400 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ILE A1433 " --> pdb=" O LEU A1400 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A1402 " --> pdb=" O ILE A1433 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS A1271 " --> pdb=" O LYS A1445 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU A1447 " --> pdb=" O LYS A1271 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY A1273 " --> pdb=" O LEU A1447 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU A1449 " --> pdb=" O GLY A1273 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A1275 " --> pdb=" O LEU A1449 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A1458 " --> pdb=" O ILE A1446 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A1456 " --> pdb=" O VAL A1448 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP A1450 " --> pdb=" O VAL A1454 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL A1454 " --> pdb=" O ASP A1450 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 632 through 639 removed outlier: 6.173A pdb=" N GLY B 619 " --> pdb=" O ASN B 634 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN B 636 " --> pdb=" O ARG B 617 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG B 617 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP B 638 " --> pdb=" O SER B 615 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N SER B 615 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 680 through 683 removed outlier: 6.515A pdb=" N ALA B 681 " --> pdb=" O ILE B 762 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASP B 764 " --> pdb=" O ALA B 681 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 683 " --> pdb=" O ASP B 764 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 645 " --> pdb=" O LEU B 794 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 644 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL B 809 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA B 646 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL B 811 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 648 " --> pdb=" O VAL B 811 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 810 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU B 818 " --> pdb=" O LEU B 810 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1259 through 1266 removed outlier: 7.259A pdb=" N HIS B1260 " --> pdb=" O VAL B1248 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B1248 " --> pdb=" O HIS B1260 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL B1262 " --> pdb=" O ASP B1246 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B1264 " --> pdb=" O PHE B1244 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B1242 " --> pdb=" O ILE B1266 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL B1247 " --> pdb=" O LYS B1297 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS B1297 " --> pdb=" O VAL B1247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1319 through 1322 removed outlier: 7.060A pdb=" N LEU B1400 " --> pdb=" O LEU B1431 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ILE B1433 " --> pdb=" O LEU B1400 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B1402 " --> pdb=" O ILE B1433 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS B1271 " --> pdb=" O LYS B1445 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU B1447 " --> pdb=" O LYS B1271 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY B1273 " --> pdb=" O LEU B1447 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU B1449 " --> pdb=" O GLY B1273 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B1275 " --> pdb=" O LEU B1449 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B1458 " --> pdb=" O ILE B1446 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B1456 " --> pdb=" O VAL B1448 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP B1450 " --> pdb=" O VAL B1454 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL B1454 " --> pdb=" O ASP B1450 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6583 1.33 - 1.45: 3517 1.45 - 1.57: 12030 1.57 - 1.69: 10 1.69 - 1.81: 178 Bond restraints: 22318 Sorted by residual: bond pdb=" C4 ATP B1701 " pdb=" C5 ATP B1701 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C4 ATP A1701 " pdb=" C5 ATP A1701 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C5 ATP B1701 " pdb=" C6 ATP B1701 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.03e+01 bond pdb=" C5 ATP A1701 " pdb=" C6 ATP A1701 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.99e+01 bond pdb=" C4 ATP B1701 " pdb=" N9 ATP B1701 " ideal model delta sigma weight residual 1.374 1.325 0.049 1.00e-02 1.00e+04 2.41e+01 ... (remaining 22313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.01: 30154 5.01 - 10.03: 138 10.03 - 15.04: 4 15.04 - 20.05: 0 20.05 - 25.06: 4 Bond angle restraints: 30300 Sorted by residual: angle pdb=" PB ATP A1701 " pdb=" O3B ATP A1701 " pdb=" PG ATP A1701 " ideal model delta sigma weight residual 139.87 114.81 25.06 1.00e+00 1.00e+00 6.28e+02 angle pdb=" PB ATP B1701 " pdb=" O3B ATP B1701 " pdb=" PG ATP B1701 " ideal model delta sigma weight residual 139.87 114.88 24.99 1.00e+00 1.00e+00 6.24e+02 angle pdb=" PA ATP A1701 " pdb=" O3A ATP A1701 " pdb=" PB ATP A1701 " ideal model delta sigma weight residual 136.83 123.11 13.72 1.00e+00 1.00e+00 1.88e+02 angle pdb=" PA ATP B1701 " pdb=" O3A ATP B1701 " pdb=" PB ATP B1701 " ideal model delta sigma weight residual 136.83 123.15 13.68 1.00e+00 1.00e+00 1.87e+02 angle pdb=" C5 ATP B1701 " pdb=" C4 ATP B1701 " pdb=" N3 ATP B1701 " ideal model delta sigma weight residual 126.80 118.76 8.04 1.00e+00 1.00e+00 6.46e+01 ... (remaining 30295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.56: 12483 14.56 - 29.12: 634 29.12 - 43.68: 189 43.68 - 58.24: 12 58.24 - 72.80: 12 Dihedral angle restraints: 13330 sinusoidal: 5356 harmonic: 7974 Sorted by residual: dihedral pdb=" CA LEU A1357 " pdb=" C LEU A1357 " pdb=" N LYS A1358 " pdb=" CA LYS A1358 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LEU B1357 " pdb=" C LEU B1357 " pdb=" N LYS B1358 " pdb=" CA LYS B1358 " ideal model delta harmonic sigma weight residual 180.00 152.01 27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA LEU B 590 " pdb=" C LEU B 590 " pdb=" N GLU B 591 " pdb=" CA GLU B 591 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 13327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2000 0.045 - 0.091: 1115 0.091 - 0.136: 303 0.136 - 0.181: 58 0.181 - 0.227: 10 Chirality restraints: 3486 Sorted by residual: chirality pdb=" CB ILE A 413 " pdb=" CA ILE A 413 " pdb=" CG1 ILE A 413 " pdb=" CG2 ILE A 413 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE B 413 " pdb=" CA ILE B 413 " pdb=" CG1 ILE B 413 " pdb=" CG2 ILE B 413 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA PHE A 568 " pdb=" N PHE A 568 " pdb=" C PHE A 568 " pdb=" CB PHE A 568 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 3483 not shown) Planarity restraints: 3810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 945 " -0.021 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP A 945 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A 945 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 945 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 945 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 945 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 945 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 945 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 945 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 945 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 945 " 0.021 2.00e-02 2.50e+03 2.03e-02 1.03e+01 pdb=" CG TRP B 945 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B 945 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 945 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 945 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 945 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 945 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 945 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 945 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 945 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 289 " 0.021 2.00e-02 2.50e+03 1.72e-02 7.37e+00 pdb=" CG TRP B 289 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 289 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 289 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 289 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 289 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 289 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 289 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 289 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 289 " 0.002 2.00e-02 2.50e+03 ... (remaining 3807 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 160 2.63 - 3.20: 18946 3.20 - 3.77: 30484 3.77 - 4.33: 43984 4.33 - 4.90: 71268 Nonbonded interactions: 164842 Sorted by model distance: nonbonded pdb=" O2B ATP A1701 " pdb="MG MG A1702 " model vdw 2.067 2.170 nonbonded pdb=" O2B ATP B1701 " pdb="MG MG B1702 " model vdw 2.067 2.170 nonbonded pdb=" O3G ATP A1701 " pdb="MG MG A1702 " model vdw 2.078 2.170 nonbonded pdb=" O3G ATP B1701 " pdb="MG MG B1702 " model vdw 2.078 2.170 nonbonded pdb=" OD2 ASP B 406 " pdb=" NH1 ARG B 589 " model vdw 2.147 3.120 ... (remaining 164837 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 27.010 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 : 0.009 0.078 22318 Z= 0.384 Angle : 1.037 25.063 30300 Z= 0.590 Chirality : 0.057 0.227 3486 Planarity : 0.007 0.066 3810 Dihedral : 10.199 72.802 8194 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.92 (0.10), residues: 2748 helix: -4.70 (0.04), residues: 1530 sheet: -0.89 (0.37), residues: 174 loop : -2.90 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1082 TYR 0.032 0.003 TYR B 142 PHE 0.031 0.003 PHE B1099 TRP 0.055 0.003 TRP A 945 HIS 0.010 0.002 HIS A1009 Details of bonding type rmsd covalent geometry : bond 0.00856 (22318) covalent geometry : angle 1.03654 (30300) hydrogen bonds : bond 0.35173 ( 732) hydrogen bonds : angle 9.78630 ( 2172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 VAL cc_start: 0.8975 (m) cc_final: 0.8755 (m) REVERT: A 109 PHE cc_start: 0.7998 (p90) cc_final: 0.6701 (m-80) REVERT: A 144 ARG cc_start: 0.8080 (mtp-110) cc_final: 0.6635 (tmt170) REVERT: A 488 MET cc_start: 0.9229 (tpp) cc_final: 0.8983 (tpt) REVERT: A 572 MET cc_start: 0.7600 (mpt) cc_final: 0.7309 (mmm) REVERT: A 577 ILE cc_start: 0.8229 (tp) cc_final: 0.7928 (mm) REVERT: A 923 MET cc_start: 0.8576 (mmt) cc_final: 0.8286 (mmt) REVERT: A 987 TYR cc_start: 0.8499 (t80) cc_final: 0.8228 (t80) REVERT: A 1087 MET cc_start: 0.8274 (mtp) cc_final: 0.7996 (mtp) REVERT: A 1137 MET cc_start: 0.8864 (ttp) cc_final: 0.8581 (ttm) REVERT: A 1164 MET cc_start: 0.8672 (ttm) cc_final: 0.8218 (ttm) REVERT: B 92 LEU cc_start: 0.8171 (mm) cc_final: 0.7907 (mp) REVERT: B 109 PHE cc_start: 0.7884 (p90) cc_final: 0.6272 (m-80) REVERT: B 112 PHE cc_start: 0.8303 (m-80) cc_final: 0.7977 (t80) REVERT: B 175 LEU cc_start: 0.9279 (tt) cc_final: 0.9042 (tt) REVERT: B 180 VAL cc_start: 0.9197 (t) cc_final: 0.8889 (t) REVERT: B 488 MET cc_start: 0.9323 (tpp) cc_final: 0.8876 (tpt) REVERT: B 572 MET cc_start: 0.7095 (mpt) cc_final: 0.6863 (mmm) REVERT: B 577 ILE cc_start: 0.8241 (tp) cc_final: 0.7937 (mm) REVERT: B 977 ASN cc_start: 0.8894 (t0) cc_final: 0.8258 (t0) REVERT: B 1126 MET cc_start: 0.9041 (tpt) cc_final: 0.8757 (tpt) REVERT: B 1156 TRP cc_start: 0.8770 (t60) cc_final: 0.8295 (t60) REVERT: B 1185 TYR cc_start: 0.8933 (m-10) cc_final: 0.8565 (m-80) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1756 time to fit residues: 85.3097 Evaluate side-chains 188 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN A 525 ASN A 838 ASN B 456 GLN B 525 ASN ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.091619 restraints weight = 37203.185| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.03 r_work: 0.3013 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22318 Z= 0.146 Angle : 0.648 15.167 30300 Z= 0.335 Chirality : 0.044 0.136 3486 Planarity : 0.005 0.048 3810 Dihedral : 6.679 75.204 3064 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.71 % Allowed : 5.46 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.37 (0.13), residues: 2748 helix: -3.23 (0.09), residues: 1582 sheet: -0.18 (0.40), residues: 164 loop : -2.47 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 91 TYR 0.032 0.002 TYR A 171 PHE 0.022 0.002 PHE B 234 TRP 0.021 0.002 TRP A 241 HIS 0.003 0.001 HIS A1009 Details of bonding type rmsd covalent geometry : bond 0.00307 (22318) covalent geometry : angle 0.64775 (30300) hydrogen bonds : bond 0.07454 ( 732) hydrogen bonds : angle 5.21779 ( 2172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8417 (mt) cc_final: 0.7927 (tt) REVERT: A 109 PHE cc_start: 0.8380 (p90) cc_final: 0.6720 (m-80) REVERT: A 144 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.6687 (tmt170) REVERT: A 452 MET cc_start: 0.8261 (ttp) cc_final: 0.7728 (tmm) REVERT: A 475 ASP cc_start: 0.8546 (m-30) cc_final: 0.8346 (m-30) REVERT: A 577 ILE cc_start: 0.8217 (tp) cc_final: 0.7881 (mm) REVERT: A 977 ASN cc_start: 0.9168 (t0) cc_final: 0.8675 (t0) REVERT: A 1156 TRP cc_start: 0.8720 (t60) cc_final: 0.8323 (t60) REVERT: A 1352 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8400 (pp) REVERT: A 1391 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7627 (mtm-85) REVERT: B 49 LEU cc_start: 0.8842 (mt) cc_final: 0.8199 (tt) REVERT: B 92 LEU cc_start: 0.8388 (mm) cc_final: 0.7729 (mp) REVERT: B 109 PHE cc_start: 0.8240 (p90) cc_final: 0.6152 (m-80) REVERT: B 112 PHE cc_start: 0.8186 (m-80) cc_final: 0.7946 (t80) REVERT: B 137 ARG cc_start: 0.7210 (tpm170) cc_final: 0.6748 (tpm170) REVERT: B 142 TYR cc_start: 0.6814 (m-10) cc_final: 0.6271 (m-10) REVERT: B 265 TRP cc_start: 0.8328 (p-90) cc_final: 0.8000 (p-90) REVERT: B 577 ILE cc_start: 0.8153 (tp) cc_final: 0.7795 (mm) REVERT: B 977 ASN cc_start: 0.9100 (t0) cc_final: 0.8587 (t0) REVERT: B 1156 TRP cc_start: 0.9037 (t60) cc_final: 0.8536 (t60) REVERT: B 1185 TYR cc_start: 0.9161 (m-10) cc_final: 0.8943 (m-80) REVERT: B 1352 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8479 (pp) outliers start: 17 outliers final: 10 residues processed: 236 average time/residue: 0.1438 time to fit residues: 54.5973 Evaluate side-chains 198 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 260 TRP Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 1352 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 118 optimal weight: 0.0770 chunk 204 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN B 411 GLN B 746 GLN B 838 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.115033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.090411 restraints weight = 37418.756| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.08 r_work: 0.2987 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22318 Z= 0.165 Angle : 0.615 16.108 30300 Z= 0.313 Chirality : 0.044 0.171 3486 Planarity : 0.004 0.049 3810 Dihedral : 6.295 79.244 3064 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 1.13 % Allowed : 7.60 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.14), residues: 2748 helix: -2.31 (0.11), residues: 1590 sheet: 0.22 (0.41), residues: 164 loop : -2.24 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1354 TYR 0.037 0.002 TYR A 171 PHE 0.017 0.002 PHE A 234 TRP 0.017 0.001 TRP B 945 HIS 0.005 0.001 HIS A1009 Details of bonding type rmsd covalent geometry : bond 0.00376 (22318) covalent geometry : angle 0.61506 (30300) hydrogen bonds : bond 0.05849 ( 732) hydrogen bonds : angle 4.65756 ( 2172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8519 (mt) cc_final: 0.8044 (tt) REVERT: A 109 PHE cc_start: 0.8498 (p90) cc_final: 0.6520 (m-80) REVERT: A 114 LEU cc_start: 0.9175 (mt) cc_final: 0.8906 (tp) REVERT: A 125 MET cc_start: 0.7764 (mmm) cc_final: 0.7462 (mmm) REVERT: A 144 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.6741 (tmt170) REVERT: A 577 ILE cc_start: 0.8221 (tp) cc_final: 0.7849 (mm) REVERT: A 977 ASN cc_start: 0.9181 (t0) cc_final: 0.8765 (t0) REVERT: A 1126 MET cc_start: 0.9095 (tpt) cc_final: 0.8783 (tpt) REVERT: A 1156 TRP cc_start: 0.8734 (t60) cc_final: 0.8443 (t60) REVERT: A 1352 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8560 (pp) REVERT: A 1391 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7558 (mtm-85) REVERT: B 49 LEU cc_start: 0.8877 (mt) cc_final: 0.8530 (tt) REVERT: B 109 PHE cc_start: 0.8302 (p90) cc_final: 0.6084 (m-80) REVERT: B 112 PHE cc_start: 0.8067 (m-80) cc_final: 0.7861 (t80) REVERT: B 223 GLN cc_start: 0.7269 (mm-40) cc_final: 0.6661 (tm-30) REVERT: B 338 MET cc_start: 0.8675 (tpt) cc_final: 0.8456 (tpp) REVERT: B 577 ILE cc_start: 0.8204 (tp) cc_final: 0.7808 (mm) REVERT: B 746 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8794 (tp40) REVERT: B 977 ASN cc_start: 0.9141 (t0) cc_final: 0.8655 (t0) REVERT: B 1156 TRP cc_start: 0.8957 (t60) cc_final: 0.8507 (t60) REVERT: B 1352 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8454 (pp) outliers start: 27 outliers final: 14 residues processed: 207 average time/residue: 0.1504 time to fit residues: 49.5146 Evaluate side-chains 192 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 260 TRP Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 746 GLN Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1352 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 77 optimal weight: 10.0000 chunk 212 optimal weight: 0.9980 chunk 218 optimal weight: 7.9990 chunk 242 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 109 optimal weight: 0.0050 chunk 114 optimal weight: 8.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.114614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.089937 restraints weight = 37808.178| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.06 r_work: 0.2955 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 22318 Z= 0.194 Angle : 0.618 15.227 30300 Z= 0.315 Chirality : 0.045 0.142 3486 Planarity : 0.004 0.050 3810 Dihedral : 6.204 80.031 3064 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 1.47 % Allowed : 8.48 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.15), residues: 2748 helix: -1.85 (0.12), residues: 1576 sheet: -0.18 (0.39), residues: 174 loop : -2.07 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 589 TYR 0.032 0.002 TYR B 171 PHE 0.018 0.002 PHE B 234 TRP 0.015 0.001 TRP B 289 HIS 0.006 0.001 HIS A1009 Details of bonding type rmsd covalent geometry : bond 0.00457 (22318) covalent geometry : angle 0.61847 (30300) hydrogen bonds : bond 0.05623 ( 732) hydrogen bonds : angle 4.51109 ( 2172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8530 (mt) cc_final: 0.7794 (tt) REVERT: A 68 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5953 (mp) REVERT: A 92 LEU cc_start: 0.8446 (mp) cc_final: 0.8120 (tp) REVERT: A 114 LEU cc_start: 0.9149 (mt) cc_final: 0.8894 (tp) REVERT: A 144 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.6745 (tmt170) REVERT: A 452 MET cc_start: 0.8417 (ttp) cc_final: 0.8198 (tmm) REVERT: A 570 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8057 (tp) REVERT: A 577 ILE cc_start: 0.8340 (tp) cc_final: 0.7939 (mm) REVERT: A 977 ASN cc_start: 0.9188 (t0) cc_final: 0.8778 (t0) REVERT: A 1352 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8717 (pp) REVERT: A 1391 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7733 (mtm-85) REVERT: B 49 LEU cc_start: 0.8886 (mt) cc_final: 0.8223 (tt) REVERT: B 112 PHE cc_start: 0.8043 (m-80) cc_final: 0.7796 (t80) REVERT: B 125 MET cc_start: 0.8074 (mmm) cc_final: 0.7817 (mmm) REVERT: B 155 MET cc_start: 0.9230 (mmp) cc_final: 0.8982 (mmp) REVERT: B 223 GLN cc_start: 0.7484 (mm-40) cc_final: 0.6866 (tm-30) REVERT: B 338 MET cc_start: 0.8813 (tpt) cc_final: 0.8583 (tpp) REVERT: B 577 ILE cc_start: 0.8316 (tp) cc_final: 0.7904 (mm) REVERT: B 977 ASN cc_start: 0.9163 (t0) cc_final: 0.8710 (t0) REVERT: B 1137 MET cc_start: 0.8951 (ttp) cc_final: 0.8395 (ttm) REVERT: B 1352 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8781 (pp) outliers start: 35 outliers final: 18 residues processed: 213 average time/residue: 0.1482 time to fit residues: 50.4160 Evaluate side-chains 197 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 260 TRP Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1352 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 142 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 273 optimal weight: 0.0980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.115097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.090648 restraints weight = 36951.604| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.00 r_work: 0.2984 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22318 Z= 0.125 Angle : 0.557 15.777 30300 Z= 0.282 Chirality : 0.042 0.142 3486 Planarity : 0.003 0.046 3810 Dihedral : 5.964 81.400 3064 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.43 % Allowed : 9.57 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.15), residues: 2748 helix: -1.45 (0.12), residues: 1580 sheet: 0.21 (0.41), residues: 164 loop : -1.95 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1354 TYR 0.043 0.001 TYR B 171 PHE 0.015 0.001 PHE B1175 TRP 0.014 0.001 TRP B 121 HIS 0.003 0.001 HIS A1009 Details of bonding type rmsd covalent geometry : bond 0.00283 (22318) covalent geometry : angle 0.55687 (30300) hydrogen bonds : bond 0.04798 ( 732) hydrogen bonds : angle 4.18450 ( 2172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8494 (mt) cc_final: 0.7731 (tt) REVERT: A 92 LEU cc_start: 0.8418 (mp) cc_final: 0.8189 (tp) REVERT: A 114 LEU cc_start: 0.9140 (mt) cc_final: 0.8912 (tp) REVERT: A 144 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.6641 (tmt170) REVERT: A 223 GLN cc_start: 0.7725 (mm-40) cc_final: 0.6996 (tm-30) REVERT: A 452 MET cc_start: 0.8430 (ttp) cc_final: 0.8183 (tmm) REVERT: A 577 ILE cc_start: 0.8206 (tp) cc_final: 0.7880 (mm) REVERT: A 977 ASN cc_start: 0.9207 (t0) cc_final: 0.8747 (t0) REVERT: A 1156 TRP cc_start: 0.8831 (t60) cc_final: 0.8441 (t60) REVERT: A 1391 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7674 (mtm-85) REVERT: B 49 LEU cc_start: 0.8801 (mt) cc_final: 0.8181 (tt) REVERT: B 68 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6035 (mp) REVERT: B 125 MET cc_start: 0.8192 (mmm) cc_final: 0.7971 (mmm) REVERT: B 223 GLN cc_start: 0.7459 (mm-40) cc_final: 0.6830 (tm-30) REVERT: B 577 ILE cc_start: 0.8209 (tp) cc_final: 0.7884 (mm) REVERT: B 977 ASN cc_start: 0.9191 (t0) cc_final: 0.8789 (t0) REVERT: B 1156 TRP cc_start: 0.8950 (t60) cc_final: 0.8474 (t60) REVERT: B 1185 TYR cc_start: 0.9090 (m-10) cc_final: 0.8764 (m-80) REVERT: B 1352 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8587 (pp) outliers start: 34 outliers final: 22 residues processed: 211 average time/residue: 0.1555 time to fit residues: 52.4646 Evaluate side-chains 199 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1300 ILE Chi-restraints excluded: chain A residue 1357 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 260 TRP Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1070 PHE Chi-restraints excluded: chain B residue 1352 LEU Chi-restraints excluded: chain B residue 1357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 148 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 236 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 217 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 185 optimal weight: 0.4980 chunk 113 optimal weight: 0.0470 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1172 GLN B 456 GLN B 525 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.093175 restraints weight = 36849.476| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.98 r_work: 0.3022 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22318 Z= 0.097 Angle : 0.533 15.939 30300 Z= 0.267 Chirality : 0.041 0.144 3486 Planarity : 0.003 0.043 3810 Dihedral : 5.721 83.038 3064 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.18 % Allowed : 10.16 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.16), residues: 2748 helix: -1.05 (0.13), residues: 1590 sheet: 0.88 (0.42), residues: 152 loop : -1.87 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1422 TYR 0.041 0.001 TYR B 171 PHE 0.018 0.001 PHE B 76 TRP 0.021 0.001 TRP B 121 HIS 0.002 0.000 HIS B1009 Details of bonding type rmsd covalent geometry : bond 0.00203 (22318) covalent geometry : angle 0.53322 (30300) hydrogen bonds : bond 0.04077 ( 732) hydrogen bonds : angle 3.84111 ( 2172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8443 (mt) cc_final: 0.7987 (tt) REVERT: A 58 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6479 (mt) REVERT: A 92 LEU cc_start: 0.8528 (mp) cc_final: 0.8316 (tp) REVERT: A 144 ARG cc_start: 0.8101 (mtp-110) cc_final: 0.6631 (tmt170) REVERT: A 223 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: A 452 MET cc_start: 0.8476 (ttp) cc_final: 0.8237 (tmm) REVERT: A 577 ILE cc_start: 0.8163 (tp) cc_final: 0.7881 (mm) REVERT: A 977 ASN cc_start: 0.9217 (t0) cc_final: 0.8823 (t0) REVERT: A 1425 PHE cc_start: 0.8108 (m-80) cc_final: 0.7741 (m-10) REVERT: B 49 LEU cc_start: 0.8728 (mt) cc_final: 0.8146 (tt) REVERT: B 68 LEU cc_start: 0.6319 (OUTLIER) cc_final: 0.6049 (mp) REVERT: B 125 MET cc_start: 0.8265 (mmm) cc_final: 0.8018 (mmm) REVERT: B 526 MET cc_start: 0.8993 (tpp) cc_final: 0.8729 (tpp) REVERT: B 577 ILE cc_start: 0.8155 (tp) cc_final: 0.7890 (mm) REVERT: B 977 ASN cc_start: 0.9223 (t0) cc_final: 0.8787 (t0) REVERT: B 1156 TRP cc_start: 0.8897 (t60) cc_final: 0.8429 (t60) REVERT: B 1185 TYR cc_start: 0.8994 (m-10) cc_final: 0.8752 (m-80) outliers start: 28 outliers final: 11 residues processed: 208 average time/residue: 0.1310 time to fit residues: 45.2719 Evaluate side-chains 187 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1357 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 260 TRP Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 46 optimal weight: 0.9990 chunk 256 optimal weight: 6.9990 chunk 193 optimal weight: 20.0000 chunk 57 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 chunk 252 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.092591 restraints weight = 36882.614| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.00 r_work: 0.3017 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22318 Z= 0.107 Angle : 0.541 15.774 30300 Z= 0.269 Chirality : 0.042 0.174 3486 Planarity : 0.003 0.040 3810 Dihedral : 5.640 84.100 3064 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.39 % Allowed : 10.54 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.16), residues: 2748 helix: -0.77 (0.13), residues: 1586 sheet: 1.07 (0.43), residues: 152 loop : -1.81 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1422 TYR 0.040 0.001 TYR B 171 PHE 0.009 0.001 PHE A1070 TRP 0.022 0.001 TRP B 121 HIS 0.002 0.000 HIS B1009 Details of bonding type rmsd covalent geometry : bond 0.00239 (22318) covalent geometry : angle 0.54100 (30300) hydrogen bonds : bond 0.04069 ( 732) hydrogen bonds : angle 3.76946 ( 2172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.934 Fit side-chains REVERT: A 49 LEU cc_start: 0.8427 (mt) cc_final: 0.7738 (tt) REVERT: A 58 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6600 (mt) REVERT: A 109 PHE cc_start: 0.8657 (p90) cc_final: 0.6410 (m-10) REVERT: A 144 ARG cc_start: 0.8109 (mtp-110) cc_final: 0.6608 (tmt170) REVERT: A 223 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7113 (tm-30) REVERT: A 526 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8600 (tpp) REVERT: A 577 ILE cc_start: 0.8223 (tp) cc_final: 0.7904 (mm) REVERT: A 977 ASN cc_start: 0.9268 (t0) cc_final: 0.8888 (t0) REVERT: A 1425 PHE cc_start: 0.8135 (m-80) cc_final: 0.7791 (m-10) REVERT: B 49 LEU cc_start: 0.8670 (mt) cc_final: 0.8075 (tt) REVERT: B 68 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6110 (mp) REVERT: B 119 PHE cc_start: 0.7948 (m-10) cc_final: 0.7709 (m-10) REVERT: B 125 MET cc_start: 0.8226 (mmm) cc_final: 0.7997 (mmt) REVERT: B 526 MET cc_start: 0.9024 (tpp) cc_final: 0.8726 (tpp) REVERT: B 577 ILE cc_start: 0.8246 (tp) cc_final: 0.7939 (mm) REVERT: B 977 ASN cc_start: 0.9230 (t0) cc_final: 0.8793 (t0) REVERT: B 1156 TRP cc_start: 0.8924 (t60) cc_final: 0.8443 (t60) REVERT: B 1185 TYR cc_start: 0.9011 (m-10) cc_final: 0.8786 (m-80) outliers start: 33 outliers final: 20 residues processed: 206 average time/residue: 0.1359 time to fit residues: 46.8211 Evaluate side-chains 197 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1357 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 260 TRP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1070 PHE Chi-restraints excluded: chain B residue 1357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 77 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 209 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1172 GLN A1435 HIS B1435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.088062 restraints weight = 37753.065| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.01 r_work: 0.2920 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 22318 Z= 0.253 Angle : 0.667 15.645 30300 Z= 0.336 Chirality : 0.047 0.153 3486 Planarity : 0.004 0.044 3810 Dihedral : 6.058 85.602 3064 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 1.47 % Allowed : 10.62 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.16), residues: 2748 helix: -1.00 (0.13), residues: 1590 sheet: 0.76 (0.42), residues: 154 loop : -1.87 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1354 TYR 0.042 0.002 TYR B 171 PHE 0.019 0.002 PHE A1070 TRP 0.024 0.002 TRP B 265 HIS 0.007 0.001 HIS B1009 Details of bonding type rmsd covalent geometry : bond 0.00605 (22318) covalent geometry : angle 0.66707 (30300) hydrogen bonds : bond 0.05665 ( 732) hydrogen bonds : angle 4.37129 ( 2172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.886 Fit side-chains REVERT: A 58 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6529 (mt) REVERT: A 92 LEU cc_start: 0.8463 (mp) cc_final: 0.7852 (tp) REVERT: A 109 PHE cc_start: 0.8816 (p90) cc_final: 0.6454 (m-10) REVERT: A 125 MET cc_start: 0.8327 (mmm) cc_final: 0.8091 (mmm) REVERT: A 130 MET cc_start: 0.6648 (ptp) cc_final: 0.6269 (mtm) REVERT: A 223 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: A 526 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.9006 (tpp) REVERT: A 577 ILE cc_start: 0.8451 (tp) cc_final: 0.8003 (mm) REVERT: A 932 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8613 (mm-30) REVERT: A 977 ASN cc_start: 0.9199 (t0) cc_final: 0.8785 (t0) REVERT: A 1425 PHE cc_start: 0.8270 (m-80) cc_final: 0.8068 (m-10) REVERT: B 49 LEU cc_start: 0.8926 (mt) cc_final: 0.8252 (tt) REVERT: B 119 PHE cc_start: 0.8031 (m-10) cc_final: 0.7796 (m-10) REVERT: B 127 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7319 (ptp) REVERT: B 223 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7386 (tp40) REVERT: B 577 ILE cc_start: 0.8496 (tp) cc_final: 0.8036 (mm) REVERT: B 977 ASN cc_start: 0.9192 (t0) cc_final: 0.8791 (t0) REVERT: B 1185 TYR cc_start: 0.9009 (m-10) cc_final: 0.8793 (m-80) outliers start: 35 outliers final: 23 residues processed: 203 average time/residue: 0.1416 time to fit residues: 47.6641 Evaluate side-chains 198 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1357 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 260 TRP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1070 PHE Chi-restraints excluded: chain B residue 1357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 181 optimal weight: 0.1980 chunk 248 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 113 optimal weight: 0.0010 chunk 230 optimal weight: 0.7980 chunk 186 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN A 525 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.116572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.092177 restraints weight = 36947.432| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.00 r_work: 0.3010 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22318 Z= 0.102 Angle : 0.549 15.716 30300 Z= 0.275 Chirality : 0.041 0.139 3486 Planarity : 0.003 0.037 3810 Dihedral : 5.715 79.853 3064 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.01 % Allowed : 11.29 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.16), residues: 2748 helix: -0.55 (0.13), residues: 1584 sheet: 1.07 (0.42), residues: 154 loop : -1.75 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1354 TYR 0.050 0.001 TYR B 171 PHE 0.016 0.001 PHE B 234 TRP 0.022 0.001 TRP B 121 HIS 0.002 0.000 HIS B1009 Details of bonding type rmsd covalent geometry : bond 0.00207 (22318) covalent geometry : angle 0.54872 (30300) hydrogen bonds : bond 0.04170 ( 732) hydrogen bonds : angle 3.84716 ( 2172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.897 Fit side-chains REVERT: A 58 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6466 (mt) REVERT: A 92 LEU cc_start: 0.8598 (mp) cc_final: 0.7856 (tp) REVERT: A 94 MET cc_start: 0.5936 (tpp) cc_final: 0.5702 (tpp) REVERT: A 109 PHE cc_start: 0.8781 (p90) cc_final: 0.6357 (m-10) REVERT: A 125 MET cc_start: 0.8271 (mmm) cc_final: 0.7912 (mmm) REVERT: A 154 ASP cc_start: 0.8499 (m-30) cc_final: 0.8218 (t0) REVERT: A 223 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: A 577 ILE cc_start: 0.8233 (tp) cc_final: 0.7984 (mm) REVERT: A 977 ASN cc_start: 0.9225 (t0) cc_final: 0.8814 (t0) REVERT: A 1425 PHE cc_start: 0.8001 (m-80) cc_final: 0.7787 (m-10) REVERT: B 49 LEU cc_start: 0.8729 (mt) cc_final: 0.8154 (tt) REVERT: B 526 MET cc_start: 0.9033 (tpp) cc_final: 0.8592 (tpp) REVERT: B 577 ILE cc_start: 0.8274 (tp) cc_final: 0.7998 (mm) REVERT: B 977 ASN cc_start: 0.9234 (t0) cc_final: 0.8815 (t0) REVERT: B 1156 TRP cc_start: 0.8897 (t60) cc_final: 0.8440 (t60) outliers start: 24 outliers final: 16 residues processed: 194 average time/residue: 0.1440 time to fit residues: 46.0271 Evaluate side-chains 193 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1300 ILE Chi-restraints excluded: chain A residue 1357 LEU Chi-restraints excluded: chain B residue 83 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 260 TRP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1070 PHE Chi-restraints excluded: chain B residue 1357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 96 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 225 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.090673 restraints weight = 37135.709| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.01 r_work: 0.2984 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22318 Z= 0.133 Angle : 0.567 15.808 30300 Z= 0.282 Chirality : 0.043 0.141 3486 Planarity : 0.003 0.037 3810 Dihedral : 5.711 79.763 3064 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.92 % Allowed : 11.54 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.16), residues: 2748 helix: -0.44 (0.13), residues: 1582 sheet: 1.13 (0.42), residues: 154 loop : -1.74 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1354 TYR 0.051 0.001 TYR B 171 PHE 0.011 0.001 PHE B1070 TRP 0.024 0.001 TRP B 121 HIS 0.003 0.001 HIS B1009 Details of bonding type rmsd covalent geometry : bond 0.00308 (22318) covalent geometry : angle 0.56720 (30300) hydrogen bonds : bond 0.04395 ( 732) hydrogen bonds : angle 3.87899 ( 2172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.847 Fit side-chains REVERT: A 58 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6472 (mt) REVERT: A 94 MET cc_start: 0.6353 (tpp) cc_final: 0.5947 (tpp) REVERT: A 109 PHE cc_start: 0.8801 (p90) cc_final: 0.6324 (m-10) REVERT: A 125 MET cc_start: 0.8358 (mmm) cc_final: 0.8003 (mmm) REVERT: A 144 ARG cc_start: 0.8112 (mtp-110) cc_final: 0.6595 (tmt170) REVERT: A 154 ASP cc_start: 0.8521 (m-30) cc_final: 0.8224 (t0) REVERT: A 223 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7389 (tp40) REVERT: A 577 ILE cc_start: 0.8357 (tp) cc_final: 0.8088 (mm) REVERT: A 977 ASN cc_start: 0.9198 (t0) cc_final: 0.8797 (t0) REVERT: A 1425 PHE cc_start: 0.8214 (m-80) cc_final: 0.7794 (m-10) REVERT: B 49 LEU cc_start: 0.8749 (mt) cc_final: 0.8164 (tt) REVERT: B 526 MET cc_start: 0.9079 (tpp) cc_final: 0.8554 (tpp) REVERT: B 577 ILE cc_start: 0.8366 (tp) cc_final: 0.8058 (mm) REVERT: B 977 ASN cc_start: 0.9205 (t0) cc_final: 0.8800 (t0) REVERT: B 1425 PHE cc_start: 0.7846 (m-10) cc_final: 0.7186 (m-10) outliers start: 22 outliers final: 20 residues processed: 188 average time/residue: 0.1428 time to fit residues: 44.2431 Evaluate side-chains 192 residues out of total 2382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1300 ILE Chi-restraints excluded: chain A residue 1357 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 260 TRP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1070 PHE Chi-restraints excluded: chain B residue 1357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 189 optimal weight: 0.0980 chunk 198 optimal weight: 0.8980 chunk 270 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 chunk 174 optimal weight: 0.0770 chunk 120 optimal weight: 0.0050 chunk 58 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 242 optimal weight: 0.6980 overall best weight: 0.3552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN A1172 GLN B 331 GLN B 505 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.094309 restraints weight = 36683.270| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.99 r_work: 0.3039 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22318 Z= 0.093 Angle : 0.540 15.803 30300 Z= 0.266 Chirality : 0.041 0.141 3486 Planarity : 0.003 0.040 3810 Dihedral : 5.541 77.050 3064 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.63 % Allowed : 11.80 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.17), residues: 2748 helix: -0.14 (0.14), residues: 1584 sheet: 1.42 (0.42), residues: 162 loop : -1.64 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1391 TYR 0.052 0.001 TYR B 171 PHE 0.023 0.001 PHE B1425 TRP 0.023 0.001 TRP B 121 HIS 0.002 0.000 HIS B1356 Details of bonding type rmsd covalent geometry : bond 0.00190 (22318) covalent geometry : angle 0.54046 (30300) hydrogen bonds : bond 0.03660 ( 732) hydrogen bonds : angle 3.62529 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4679.85 seconds wall clock time: 80 minutes 53.23 seconds (4853.23 seconds total)